anno_start anno_end anno_text entity_type sentence section 57 79 Pseudomonas aeruginosa species Structural insights into the regulatory mechanism of the Pseudomonas aeruginosa YfiBNR system TITLE 80 86 YfiBNR complex_assembly Structural insights into the regulatory mechanism of the Pseudomonas aeruginosa YfiBNR system TITLE 0 6 YfiBNR complex_assembly YfiBNR is a recently identified bis-(3’-5’)-cyclic dimeric GMP (c-di-GMP) signaling system in opportunistic pathogens. ABSTRACT 32 62 bis-(3’-5’)-cyclic dimeric GMP chemical YfiBNR is a recently identified bis-(3’-5’)-cyclic dimeric GMP (c-di-GMP) signaling system in opportunistic pathogens. ABSTRACT 64 72 c-di-GMP chemical YfiBNR is a recently identified bis-(3’-5’)-cyclic dimeric GMP (c-di-GMP) signaling system in opportunistic pathogens. ABSTRACT 28 32 YfiB protein In response to cell stress, YfiB in the outer membrane can sequester the periplasmic protein YfiR, releasing its inhibition of YfiN on the inner membrane and thus provoking the diguanylate cyclase activity of YfiN to induce c-di-GMP production. ABSTRACT 93 97 YfiR protein In response to cell stress, YfiB in the outer membrane can sequester the periplasmic protein YfiR, releasing its inhibition of YfiN on the inner membrane and thus provoking the diguanylate cyclase activity of YfiN to induce c-di-GMP production. ABSTRACT 127 131 YfiN protein In response to cell stress, YfiB in the outer membrane can sequester the periplasmic protein YfiR, releasing its inhibition of YfiN on the inner membrane and thus provoking the diguanylate cyclase activity of YfiN to induce c-di-GMP production. ABSTRACT 209 213 YfiN protein In response to cell stress, YfiB in the outer membrane can sequester the periplasmic protein YfiR, releasing its inhibition of YfiN on the inner membrane and thus provoking the diguanylate cyclase activity of YfiN to induce c-di-GMP production. ABSTRACT 224 232 c-di-GMP chemical In response to cell stress, YfiB in the outer membrane can sequester the periplasmic protein YfiR, releasing its inhibition of YfiN on the inner membrane and thus provoking the diguanylate cyclase activity of YfiN to induce c-di-GMP production. ABSTRACT 20 38 crystal structures evidence Here, we report the crystal structures of YfiB alone and of an active mutant YfiBL43P complexed with YfiR with 2:2 stoichiometry. ABSTRACT 42 46 YfiB protein Here, we report the crystal structures of YfiB alone and of an active mutant YfiBL43P complexed with YfiR with 2:2 stoichiometry. ABSTRACT 47 52 alone protein_state Here, we report the crystal structures of YfiB alone and of an active mutant YfiBL43P complexed with YfiR with 2:2 stoichiometry. ABSTRACT 63 69 active protein_state Here, we report the crystal structures of YfiB alone and of an active mutant YfiBL43P complexed with YfiR with 2:2 stoichiometry. ABSTRACT 70 76 mutant protein_state Here, we report the crystal structures of YfiB alone and of an active mutant YfiBL43P complexed with YfiR with 2:2 stoichiometry. ABSTRACT 77 85 YfiBL43P mutant Here, we report the crystal structures of YfiB alone and of an active mutant YfiBL43P complexed with YfiR with 2:2 stoichiometry. ABSTRACT 86 100 complexed with protein_state Here, we report the crystal structures of YfiB alone and of an active mutant YfiBL43P complexed with YfiR with 2:2 stoichiometry. ABSTRACT 101 105 YfiR protein Here, we report the crystal structures of YfiB alone and of an active mutant YfiBL43P complexed with YfiR with 2:2 stoichiometry. ABSTRACT 0 19 Structural analyses experimental_method Structural analyses revealed that in contrast to the compact conformation of the dimeric YfiB alone, YfiBL43P adopts a stretched conformation allowing activated YfiB to penetrate the peptidoglycan (PG) layer and access YfiR. YfiBL43P shows a more compact PG-binding pocket and much higher PG binding affinity than wild-type YfiB, suggesting a tight correlation between PG binding and YfiB activation. ABSTRACT 53 73 compact conformation protein_state Structural analyses revealed that in contrast to the compact conformation of the dimeric YfiB alone, YfiBL43P adopts a stretched conformation allowing activated YfiB to penetrate the peptidoglycan (PG) layer and access YfiR. YfiBL43P shows a more compact PG-binding pocket and much higher PG binding affinity than wild-type YfiB, suggesting a tight correlation between PG binding and YfiB activation. ABSTRACT 81 88 dimeric oligomeric_state Structural analyses revealed that in contrast to the compact conformation of the dimeric YfiB alone, YfiBL43P adopts a stretched conformation allowing activated YfiB to penetrate the peptidoglycan (PG) layer and access YfiR. YfiBL43P shows a more compact PG-binding pocket and much higher PG binding affinity than wild-type YfiB, suggesting a tight correlation between PG binding and YfiB activation. ABSTRACT 89 93 YfiB protein Structural analyses revealed that in contrast to the compact conformation of the dimeric YfiB alone, YfiBL43P adopts a stretched conformation allowing activated YfiB to penetrate the peptidoglycan (PG) layer and access YfiR. YfiBL43P shows a more compact PG-binding pocket and much higher PG binding affinity than wild-type YfiB, suggesting a tight correlation between PG binding and YfiB activation. ABSTRACT 94 99 alone protein_state Structural analyses revealed that in contrast to the compact conformation of the dimeric YfiB alone, YfiBL43P adopts a stretched conformation allowing activated YfiB to penetrate the peptidoglycan (PG) layer and access YfiR. YfiBL43P shows a more compact PG-binding pocket and much higher PG binding affinity than wild-type YfiB, suggesting a tight correlation between PG binding and YfiB activation. ABSTRACT 101 109 YfiBL43P mutant Structural analyses revealed that in contrast to the compact conformation of the dimeric YfiB alone, YfiBL43P adopts a stretched conformation allowing activated YfiB to penetrate the peptidoglycan (PG) layer and access YfiR. YfiBL43P shows a more compact PG-binding pocket and much higher PG binding affinity than wild-type YfiB, suggesting a tight correlation between PG binding and YfiB activation. ABSTRACT 119 141 stretched conformation protein_state Structural analyses revealed that in contrast to the compact conformation of the dimeric YfiB alone, YfiBL43P adopts a stretched conformation allowing activated YfiB to penetrate the peptidoglycan (PG) layer and access YfiR. YfiBL43P shows a more compact PG-binding pocket and much higher PG binding affinity than wild-type YfiB, suggesting a tight correlation between PG binding and YfiB activation. ABSTRACT 151 160 activated protein_state Structural analyses revealed that in contrast to the compact conformation of the dimeric YfiB alone, YfiBL43P adopts a stretched conformation allowing activated YfiB to penetrate the peptidoglycan (PG) layer and access YfiR. YfiBL43P shows a more compact PG-binding pocket and much higher PG binding affinity than wild-type YfiB, suggesting a tight correlation between PG binding and YfiB activation. ABSTRACT 161 165 YfiB protein Structural analyses revealed that in contrast to the compact conformation of the dimeric YfiB alone, YfiBL43P adopts a stretched conformation allowing activated YfiB to penetrate the peptidoglycan (PG) layer and access YfiR. YfiBL43P shows a more compact PG-binding pocket and much higher PG binding affinity than wild-type YfiB, suggesting a tight correlation between PG binding and YfiB activation. ABSTRACT 183 196 peptidoglycan chemical Structural analyses revealed that in contrast to the compact conformation of the dimeric YfiB alone, YfiBL43P adopts a stretched conformation allowing activated YfiB to penetrate the peptidoglycan (PG) layer and access YfiR. YfiBL43P shows a more compact PG-binding pocket and much higher PG binding affinity than wild-type YfiB, suggesting a tight correlation between PG binding and YfiB activation. ABSTRACT 198 200 PG chemical Structural analyses revealed that in contrast to the compact conformation of the dimeric YfiB alone, YfiBL43P adopts a stretched conformation allowing activated YfiB to penetrate the peptidoglycan (PG) layer and access YfiR. YfiBL43P shows a more compact PG-binding pocket and much higher PG binding affinity than wild-type YfiB, suggesting a tight correlation between PG binding and YfiB activation. ABSTRACT 219 223 YfiR protein Structural analyses revealed that in contrast to the compact conformation of the dimeric YfiB alone, YfiBL43P adopts a stretched conformation allowing activated YfiB to penetrate the peptidoglycan (PG) layer and access YfiR. YfiBL43P shows a more compact PG-binding pocket and much higher PG binding affinity than wild-type YfiB, suggesting a tight correlation between PG binding and YfiB activation. ABSTRACT 225 233 YfiBL43P mutant Structural analyses revealed that in contrast to the compact conformation of the dimeric YfiB alone, YfiBL43P adopts a stretched conformation allowing activated YfiB to penetrate the peptidoglycan (PG) layer and access YfiR. YfiBL43P shows a more compact PG-binding pocket and much higher PG binding affinity than wild-type YfiB, suggesting a tight correlation between PG binding and YfiB activation. ABSTRACT 255 272 PG-binding pocket site Structural analyses revealed that in contrast to the compact conformation of the dimeric YfiB alone, YfiBL43P adopts a stretched conformation allowing activated YfiB to penetrate the peptidoglycan (PG) layer and access YfiR. YfiBL43P shows a more compact PG-binding pocket and much higher PG binding affinity than wild-type YfiB, suggesting a tight correlation between PG binding and YfiB activation. ABSTRACT 289 308 PG binding affinity evidence Structural analyses revealed that in contrast to the compact conformation of the dimeric YfiB alone, YfiBL43P adopts a stretched conformation allowing activated YfiB to penetrate the peptidoglycan (PG) layer and access YfiR. YfiBL43P shows a more compact PG-binding pocket and much higher PG binding affinity than wild-type YfiB, suggesting a tight correlation between PG binding and YfiB activation. ABSTRACT 314 323 wild-type protein_state Structural analyses revealed that in contrast to the compact conformation of the dimeric YfiB alone, YfiBL43P adopts a stretched conformation allowing activated YfiB to penetrate the peptidoglycan (PG) layer and access YfiR. YfiBL43P shows a more compact PG-binding pocket and much higher PG binding affinity than wild-type YfiB, suggesting a tight correlation between PG binding and YfiB activation. ABSTRACT 324 328 YfiB protein Structural analyses revealed that in contrast to the compact conformation of the dimeric YfiB alone, YfiBL43P adopts a stretched conformation allowing activated YfiB to penetrate the peptidoglycan (PG) layer and access YfiR. YfiBL43P shows a more compact PG-binding pocket and much higher PG binding affinity than wild-type YfiB, suggesting a tight correlation between PG binding and YfiB activation. ABSTRACT 384 388 YfiB protein Structural analyses revealed that in contrast to the compact conformation of the dimeric YfiB alone, YfiBL43P adopts a stretched conformation allowing activated YfiB to penetrate the peptidoglycan (PG) layer and access YfiR. YfiBL43P shows a more compact PG-binding pocket and much higher PG binding affinity than wild-type YfiB, suggesting a tight correlation between PG binding and YfiB activation. ABSTRACT 17 42 crystallographic analyses experimental_method In addition, our crystallographic analyses revealed that YfiR binds Vitamin B6 (VB6) or L-Trp at a YfiB-binding site and that both VB6 and L-Trp are able to reduce YfiBL43P-induced biofilm formation. ABSTRACT 57 61 YfiR protein In addition, our crystallographic analyses revealed that YfiR binds Vitamin B6 (VB6) or L-Trp at a YfiB-binding site and that both VB6 and L-Trp are able to reduce YfiBL43P-induced biofilm formation. ABSTRACT 68 78 Vitamin B6 chemical In addition, our crystallographic analyses revealed that YfiR binds Vitamin B6 (VB6) or L-Trp at a YfiB-binding site and that both VB6 and L-Trp are able to reduce YfiBL43P-induced biofilm formation. ABSTRACT 80 83 VB6 chemical In addition, our crystallographic analyses revealed that YfiR binds Vitamin B6 (VB6) or L-Trp at a YfiB-binding site and that both VB6 and L-Trp are able to reduce YfiBL43P-induced biofilm formation. ABSTRACT 88 93 L-Trp chemical In addition, our crystallographic analyses revealed that YfiR binds Vitamin B6 (VB6) or L-Trp at a YfiB-binding site and that both VB6 and L-Trp are able to reduce YfiBL43P-induced biofilm formation. ABSTRACT 99 116 YfiB-binding site site In addition, our crystallographic analyses revealed that YfiR binds Vitamin B6 (VB6) or L-Trp at a YfiB-binding site and that both VB6 and L-Trp are able to reduce YfiBL43P-induced biofilm formation. ABSTRACT 131 134 VB6 chemical In addition, our crystallographic analyses revealed that YfiR binds Vitamin B6 (VB6) or L-Trp at a YfiB-binding site and that both VB6 and L-Trp are able to reduce YfiBL43P-induced biofilm formation. ABSTRACT 139 144 L-Trp chemical In addition, our crystallographic analyses revealed that YfiR binds Vitamin B6 (VB6) or L-Trp at a YfiB-binding site and that both VB6 and L-Trp are able to reduce YfiBL43P-induced biofilm formation. ABSTRACT 164 172 YfiBL43P mutant In addition, our crystallographic analyses revealed that YfiR binds Vitamin B6 (VB6) or L-Trp at a YfiB-binding site and that both VB6 and L-Trp are able to reduce YfiBL43P-induced biofilm formation. ABSTRACT 13 44 structural and biochemical data evidence Based on the structural and biochemical data, we propose an updated regulatory model of the YfiBNR system. ABSTRACT 92 98 YfiBNR complex_assembly Based on the structural and biochemical data, we propose an updated regulatory model of the YfiBNR system. ABSTRACT 0 30 Bis-(3’-5’)-cyclic dimeric GMP chemical Bis-(3’-5’)-cyclic dimeric GMP (c-di-GMP) is a ubiquitous second messenger that bacteria use to facilitate behavioral adaptations to their ever-changing environment. INTRO 32 40 c-di-GMP chemical Bis-(3’-5’)-cyclic dimeric GMP (c-di-GMP) is a ubiquitous second messenger that bacteria use to facilitate behavioral adaptations to their ever-changing environment. INTRO 80 88 bacteria taxonomy_domain Bis-(3’-5’)-cyclic dimeric GMP (c-di-GMP) is a ubiquitous second messenger that bacteria use to facilitate behavioral adaptations to their ever-changing environment. INTRO 15 23 c-di-GMP chemical An increase in c-di-GMP promotes biofilm formation, and a decrease results in biofilm degradation (Boehm et al.,; Duerig et al.,; Hickman et al.,; Jenal,; Romling et al.,). INTRO 4 12 c-di-GMP chemical The c-di-GMP level is regulated by two reciprocal enzyme systems, namely, diguanylate cyclases (DGCs) that synthesize c-di-GMP and phosphodiesterases (PDEs) that hydrolyze c-di-GMP (Kulasakara et al.,; Ross et al.,; Ross et al.,). Many of these enzymes are multiple-domain proteins containing a variable N-terminal domain that commonly acts as a signal sensor or transduction module, followed by the relatively conserved GGDEF motif in DGCs or EAL/HD-GYP domains in PDEs (Hengge,; Navarro et al.,; Schirmer and Jenal,). INTRO 74 94 diguanylate cyclases protein_type The c-di-GMP level is regulated by two reciprocal enzyme systems, namely, diguanylate cyclases (DGCs) that synthesize c-di-GMP and phosphodiesterases (PDEs) that hydrolyze c-di-GMP (Kulasakara et al.,; Ross et al.,; Ross et al.,). Many of these enzymes are multiple-domain proteins containing a variable N-terminal domain that commonly acts as a signal sensor or transduction module, followed by the relatively conserved GGDEF motif in DGCs or EAL/HD-GYP domains in PDEs (Hengge,; Navarro et al.,; Schirmer and Jenal,). INTRO 96 100 DGCs protein_type The c-di-GMP level is regulated by two reciprocal enzyme systems, namely, diguanylate cyclases (DGCs) that synthesize c-di-GMP and phosphodiesterases (PDEs) that hydrolyze c-di-GMP (Kulasakara et al.,; Ross et al.,; Ross et al.,). Many of these enzymes are multiple-domain proteins containing a variable N-terminal domain that commonly acts as a signal sensor or transduction module, followed by the relatively conserved GGDEF motif in DGCs or EAL/HD-GYP domains in PDEs (Hengge,; Navarro et al.,; Schirmer and Jenal,). INTRO 118 126 c-di-GMP chemical The c-di-GMP level is regulated by two reciprocal enzyme systems, namely, diguanylate cyclases (DGCs) that synthesize c-di-GMP and phosphodiesterases (PDEs) that hydrolyze c-di-GMP (Kulasakara et al.,; Ross et al.,; Ross et al.,). Many of these enzymes are multiple-domain proteins containing a variable N-terminal domain that commonly acts as a signal sensor or transduction module, followed by the relatively conserved GGDEF motif in DGCs or EAL/HD-GYP domains in PDEs (Hengge,; Navarro et al.,; Schirmer and Jenal,). INTRO 131 149 phosphodiesterases protein_type The c-di-GMP level is regulated by two reciprocal enzyme systems, namely, diguanylate cyclases (DGCs) that synthesize c-di-GMP and phosphodiesterases (PDEs) that hydrolyze c-di-GMP (Kulasakara et al.,; Ross et al.,; Ross et al.,). Many of these enzymes are multiple-domain proteins containing a variable N-terminal domain that commonly acts as a signal sensor or transduction module, followed by the relatively conserved GGDEF motif in DGCs or EAL/HD-GYP domains in PDEs (Hengge,; Navarro et al.,; Schirmer and Jenal,). INTRO 151 155 PDEs protein_type The c-di-GMP level is regulated by two reciprocal enzyme systems, namely, diguanylate cyclases (DGCs) that synthesize c-di-GMP and phosphodiesterases (PDEs) that hydrolyze c-di-GMP (Kulasakara et al.,; Ross et al.,; Ross et al.,). Many of these enzymes are multiple-domain proteins containing a variable N-terminal domain that commonly acts as a signal sensor or transduction module, followed by the relatively conserved GGDEF motif in DGCs or EAL/HD-GYP domains in PDEs (Hengge,; Navarro et al.,; Schirmer and Jenal,). INTRO 172 180 c-di-GMP chemical The c-di-GMP level is regulated by two reciprocal enzyme systems, namely, diguanylate cyclases (DGCs) that synthesize c-di-GMP and phosphodiesterases (PDEs) that hydrolyze c-di-GMP (Kulasakara et al.,; Ross et al.,; Ross et al.,). Many of these enzymes are multiple-domain proteins containing a variable N-terminal domain that commonly acts as a signal sensor or transduction module, followed by the relatively conserved GGDEF motif in DGCs or EAL/HD-GYP domains in PDEs (Hengge,; Navarro et al.,; Schirmer and Jenal,). INTRO 304 321 N-terminal domain structure_element The c-di-GMP level is regulated by two reciprocal enzyme systems, namely, diguanylate cyclases (DGCs) that synthesize c-di-GMP and phosphodiesterases (PDEs) that hydrolyze c-di-GMP (Kulasakara et al.,; Ross et al.,; Ross et al.,). Many of these enzymes are multiple-domain proteins containing a variable N-terminal domain that commonly acts as a signal sensor or transduction module, followed by the relatively conserved GGDEF motif in DGCs or EAL/HD-GYP domains in PDEs (Hengge,; Navarro et al.,; Schirmer and Jenal,). INTRO 400 420 relatively conserved protein_state The c-di-GMP level is regulated by two reciprocal enzyme systems, namely, diguanylate cyclases (DGCs) that synthesize c-di-GMP and phosphodiesterases (PDEs) that hydrolyze c-di-GMP (Kulasakara et al.,; Ross et al.,; Ross et al.,). Many of these enzymes are multiple-domain proteins containing a variable N-terminal domain that commonly acts as a signal sensor or transduction module, followed by the relatively conserved GGDEF motif in DGCs or EAL/HD-GYP domains in PDEs (Hengge,; Navarro et al.,; Schirmer and Jenal,). INTRO 421 432 GGDEF motif structure_element The c-di-GMP level is regulated by two reciprocal enzyme systems, namely, diguanylate cyclases (DGCs) that synthesize c-di-GMP and phosphodiesterases (PDEs) that hydrolyze c-di-GMP (Kulasakara et al.,; Ross et al.,; Ross et al.,). Many of these enzymes are multiple-domain proteins containing a variable N-terminal domain that commonly acts as a signal sensor or transduction module, followed by the relatively conserved GGDEF motif in DGCs or EAL/HD-GYP domains in PDEs (Hengge,; Navarro et al.,; Schirmer and Jenal,). INTRO 436 440 DGCs protein_type The c-di-GMP level is regulated by two reciprocal enzyme systems, namely, diguanylate cyclases (DGCs) that synthesize c-di-GMP and phosphodiesterases (PDEs) that hydrolyze c-di-GMP (Kulasakara et al.,; Ross et al.,; Ross et al.,). Many of these enzymes are multiple-domain proteins containing a variable N-terminal domain that commonly acts as a signal sensor or transduction module, followed by the relatively conserved GGDEF motif in DGCs or EAL/HD-GYP domains in PDEs (Hengge,; Navarro et al.,; Schirmer and Jenal,). INTRO 444 462 EAL/HD-GYP domains structure_element The c-di-GMP level is regulated by two reciprocal enzyme systems, namely, diguanylate cyclases (DGCs) that synthesize c-di-GMP and phosphodiesterases (PDEs) that hydrolyze c-di-GMP (Kulasakara et al.,; Ross et al.,; Ross et al.,). Many of these enzymes are multiple-domain proteins containing a variable N-terminal domain that commonly acts as a signal sensor or transduction module, followed by the relatively conserved GGDEF motif in DGCs or EAL/HD-GYP domains in PDEs (Hengge,; Navarro et al.,; Schirmer and Jenal,). INTRO 466 470 PDEs protein_type The c-di-GMP level is regulated by two reciprocal enzyme systems, namely, diguanylate cyclases (DGCs) that synthesize c-di-GMP and phosphodiesterases (PDEs) that hydrolyze c-di-GMP (Kulasakara et al.,; Ross et al.,; Ross et al.,). Many of these enzymes are multiple-domain proteins containing a variable N-terminal domain that commonly acts as a signal sensor or transduction module, followed by the relatively conserved GGDEF motif in DGCs or EAL/HD-GYP domains in PDEs (Hengge,; Navarro et al.,; Schirmer and Jenal,). INTRO 69 78 bacterium taxonomy_domain Intriguingly, studies in diverse species have revealed that a single bacterium can have dozens of DGCs and PDEs (Hickman et al.,; Kirillina et al.,; Kulasakara et al.,; Tamayo et al.,). INTRO 98 102 DGCs protein_type Intriguingly, studies in diverse species have revealed that a single bacterium can have dozens of DGCs and PDEs (Hickman et al.,; Kirillina et al.,; Kulasakara et al.,; Tamayo et al.,). INTRO 107 111 PDEs protein_type Intriguingly, studies in diverse species have revealed that a single bacterium can have dozens of DGCs and PDEs (Hickman et al.,; Kirillina et al.,; Kulasakara et al.,; Tamayo et al.,). INTRO 3 25 Pseudomonas aeruginosa species In Pseudomonas aeruginosa in particular, 42 genes containing putative DGCs and/or PDEs were identified (Kulasakara et al.,). INTRO 70 74 DGCs protein_type In Pseudomonas aeruginosa in particular, 42 genes containing putative DGCs and/or PDEs were identified (Kulasakara et al.,). INTRO 82 86 PDEs protein_type In Pseudomonas aeruginosa in particular, 42 genes containing putative DGCs and/or PDEs were identified (Kulasakara et al.,). INTRO 59 67 c-di-GMP chemical The functional role of a number of downstream effectors of c-di-GMP has been characterized as affecting exopolysaccharide (EPS) production, transcription, motility, and surface attachment (Caly et al.,; Camilli and Bassler,; Ha and O’Toole,; Pesavento and Hengge,). INTRO 104 121 exopolysaccharide chemical The functional role of a number of downstream effectors of c-di-GMP has been characterized as affecting exopolysaccharide (EPS) production, transcription, motility, and surface attachment (Caly et al.,; Camilli and Bassler,; Ha and O’Toole,; Pesavento and Hengge,). INTRO 123 126 EPS chemical The functional role of a number of downstream effectors of c-di-GMP has been characterized as affecting exopolysaccharide (EPS) production, transcription, motility, and surface attachment (Caly et al.,; Camilli and Bassler,; Ha and O’Toole,; Pesavento and Hengge,). INTRO 33 41 c-di-GMP chemical However, due to the intricacy of c-di-GMP signaling networks and the diversity of experimental cues, the detailed mechanisms by which these signaling pathways specifically sense and integrate different inputs remain largely elusive. INTRO 38 46 bacteria taxonomy_domain Biofilm formation protects pathogenic bacteria from antibiotic treatment, and c-di-GMP-regulated biofilm formation has been extensively studied in P. aeruginosa (Evans,; Kirisits et al.,; Malone,; Reinhardt et al.,). INTRO 147 160 P. aeruginosa species Biofilm formation protects pathogenic bacteria from antibiotic treatment, and c-di-GMP-regulated biofilm formation has been extensively studied in P. aeruginosa (Evans,; Kirisits et al.,; Malone,; Reinhardt et al.,). INTRO 139 152 P. aeruginosa species In the lungs of cystic fibrosis (CF) patients, adherent biofilm formation and the appearance of small colony variant (SCV) morphologies of P. aeruginosa correlate with prolonged persistence of infection and poor lung function (Govan and Deretic,; Haussler et al.,; Haussler et al.,; Parsek and Singh,; Smith et al.,). INTRO 46 56 tripartite protein_state Recently, Malone and coworkers identified the tripartite c-di-GMP signaling module system YfiBNR (also known as AwsXRO (Beaumont et al.,; Giddens et al.,) or Tbp (Ueda and Wood,)) by genetic screening for mutants that displayed SCV phenotypes in P. aeruginosa PAO1 (Malone et al.,; Malone et al.,). INTRO 57 65 c-di-GMP chemical Recently, Malone and coworkers identified the tripartite c-di-GMP signaling module system YfiBNR (also known as AwsXRO (Beaumont et al.,; Giddens et al.,) or Tbp (Ueda and Wood,)) by genetic screening for mutants that displayed SCV phenotypes in P. aeruginosa PAO1 (Malone et al.,; Malone et al.,). INTRO 90 96 YfiBNR complex_assembly Recently, Malone and coworkers identified the tripartite c-di-GMP signaling module system YfiBNR (also known as AwsXRO (Beaumont et al.,; Giddens et al.,) or Tbp (Ueda and Wood,)) by genetic screening for mutants that displayed SCV phenotypes in P. aeruginosa PAO1 (Malone et al.,; Malone et al.,). INTRO 112 118 AwsXRO complex_assembly Recently, Malone and coworkers identified the tripartite c-di-GMP signaling module system YfiBNR (also known as AwsXRO (Beaumont et al.,; Giddens et al.,) or Tbp (Ueda and Wood,)) by genetic screening for mutants that displayed SCV phenotypes in P. aeruginosa PAO1 (Malone et al.,; Malone et al.,). INTRO 158 161 Tbp complex_assembly Recently, Malone and coworkers identified the tripartite c-di-GMP signaling module system YfiBNR (also known as AwsXRO (Beaumont et al.,; Giddens et al.,) or Tbp (Ueda and Wood,)) by genetic screening for mutants that displayed SCV phenotypes in P. aeruginosa PAO1 (Malone et al.,; Malone et al.,). INTRO 183 200 genetic screening experimental_method Recently, Malone and coworkers identified the tripartite c-di-GMP signaling module system YfiBNR (also known as AwsXRO (Beaumont et al.,; Giddens et al.,) or Tbp (Ueda and Wood,)) by genetic screening for mutants that displayed SCV phenotypes in P. aeruginosa PAO1 (Malone et al.,; Malone et al.,). INTRO 246 264 P. aeruginosa PAO1 species Recently, Malone and coworkers identified the tripartite c-di-GMP signaling module system YfiBNR (also known as AwsXRO (Beaumont et al.,; Giddens et al.,) or Tbp (Ueda and Wood,)) by genetic screening for mutants that displayed SCV phenotypes in P. aeruginosa PAO1 (Malone et al.,; Malone et al.,). INTRO 4 10 YfiBNR complex_assembly The YfiBNR system contains three protein members and modulates intracellular c-di-GMP levels in response to signals received in the periplasm (Malone et al.,). INTRO 77 85 c-di-GMP chemical The YfiBNR system contains three protein members and modulates intracellular c-di-GMP levels in response to signals received in the periplasm (Malone et al.,). INTRO 54 76 Gram-negative bacteria taxonomy_domain More recently, this system was also reported in other Gram-negative bacteria, such as Escherichia coli (Hufnagel et al.,; Raterman et al.,; Sanchez-Torres et al.,), Klebsiella pneumonia (Huertas et al.,) and Yersinia pestis (Ren et al.,). INTRO 86 102 Escherichia coli species More recently, this system was also reported in other Gram-negative bacteria, such as Escherichia coli (Hufnagel et al.,; Raterman et al.,; Sanchez-Torres et al.,), Klebsiella pneumonia (Huertas et al.,) and Yersinia pestis (Ren et al.,). INTRO 165 185 Klebsiella pneumonia species More recently, this system was also reported in other Gram-negative bacteria, such as Escherichia coli (Hufnagel et al.,; Raterman et al.,; Sanchez-Torres et al.,), Klebsiella pneumonia (Huertas et al.,) and Yersinia pestis (Ren et al.,). INTRO 208 223 Yersinia pestis species More recently, this system was also reported in other Gram-negative bacteria, such as Escherichia coli (Hufnagel et al.,; Raterman et al.,; Sanchez-Torres et al.,), Klebsiella pneumonia (Huertas et al.,) and Yersinia pestis (Ren et al.,). INTRO 0 4 YfiN protein YfiN is an integral inner-membrane protein with two potential transmembrane helices, a periplasmic Per-Arnt-Sim (PAS) domain, and cytosolic domains containing a HAMP domain (mediate input-output signaling in histidine kinases, adenylyl cyclases, methyl-accepting chemotaxis proteins, and phosphatases) and a C-terminal GGDEF domain indicating a DGC’s function (Giardina et al.,; Malone et al.,). INTRO 62 83 transmembrane helices structure_element YfiN is an integral inner-membrane protein with two potential transmembrane helices, a periplasmic Per-Arnt-Sim (PAS) domain, and cytosolic domains containing a HAMP domain (mediate input-output signaling in histidine kinases, adenylyl cyclases, methyl-accepting chemotaxis proteins, and phosphatases) and a C-terminal GGDEF domain indicating a DGC’s function (Giardina et al.,; Malone et al.,). INTRO 99 111 Per-Arnt-Sim structure_element YfiN is an integral inner-membrane protein with two potential transmembrane helices, a periplasmic Per-Arnt-Sim (PAS) domain, and cytosolic domains containing a HAMP domain (mediate input-output signaling in histidine kinases, adenylyl cyclases, methyl-accepting chemotaxis proteins, and phosphatases) and a C-terminal GGDEF domain indicating a DGC’s function (Giardina et al.,; Malone et al.,). INTRO 113 116 PAS structure_element YfiN is an integral inner-membrane protein with two potential transmembrane helices, a periplasmic Per-Arnt-Sim (PAS) domain, and cytosolic domains containing a HAMP domain (mediate input-output signaling in histidine kinases, adenylyl cyclases, methyl-accepting chemotaxis proteins, and phosphatases) and a C-terminal GGDEF domain indicating a DGC’s function (Giardina et al.,; Malone et al.,). INTRO 161 172 HAMP domain structure_element YfiN is an integral inner-membrane protein with two potential transmembrane helices, a periplasmic Per-Arnt-Sim (PAS) domain, and cytosolic domains containing a HAMP domain (mediate input-output signaling in histidine kinases, adenylyl cyclases, methyl-accepting chemotaxis proteins, and phosphatases) and a C-terminal GGDEF domain indicating a DGC’s function (Giardina et al.,; Malone et al.,). INTRO 208 225 histidine kinases protein_type YfiN is an integral inner-membrane protein with two potential transmembrane helices, a periplasmic Per-Arnt-Sim (PAS) domain, and cytosolic domains containing a HAMP domain (mediate input-output signaling in histidine kinases, adenylyl cyclases, methyl-accepting chemotaxis proteins, and phosphatases) and a C-terminal GGDEF domain indicating a DGC’s function (Giardina et al.,; Malone et al.,). INTRO 227 244 adenylyl cyclases protein_type YfiN is an integral inner-membrane protein with two potential transmembrane helices, a periplasmic Per-Arnt-Sim (PAS) domain, and cytosolic domains containing a HAMP domain (mediate input-output signaling in histidine kinases, adenylyl cyclases, methyl-accepting chemotaxis proteins, and phosphatases) and a C-terminal GGDEF domain indicating a DGC’s function (Giardina et al.,; Malone et al.,). INTRO 246 282 methyl-accepting chemotaxis proteins protein_type YfiN is an integral inner-membrane protein with two potential transmembrane helices, a periplasmic Per-Arnt-Sim (PAS) domain, and cytosolic domains containing a HAMP domain (mediate input-output signaling in histidine kinases, adenylyl cyclases, methyl-accepting chemotaxis proteins, and phosphatases) and a C-terminal GGDEF domain indicating a DGC’s function (Giardina et al.,; Malone et al.,). INTRO 288 300 phosphatases protein_type YfiN is an integral inner-membrane protein with two potential transmembrane helices, a periplasmic Per-Arnt-Sim (PAS) domain, and cytosolic domains containing a HAMP domain (mediate input-output signaling in histidine kinases, adenylyl cyclases, methyl-accepting chemotaxis proteins, and phosphatases) and a C-terminal GGDEF domain indicating a DGC’s function (Giardina et al.,; Malone et al.,). INTRO 319 331 GGDEF domain structure_element YfiN is an integral inner-membrane protein with two potential transmembrane helices, a periplasmic Per-Arnt-Sim (PAS) domain, and cytosolic domains containing a HAMP domain (mediate input-output signaling in histidine kinases, adenylyl cyclases, methyl-accepting chemotaxis proteins, and phosphatases) and a C-terminal GGDEF domain indicating a DGC’s function (Giardina et al.,; Malone et al.,). INTRO 345 348 DGC protein_type YfiN is an integral inner-membrane protein with two potential transmembrane helices, a periplasmic Per-Arnt-Sim (PAS) domain, and cytosolic domains containing a HAMP domain (mediate input-output signaling in histidine kinases, adenylyl cyclases, methyl-accepting chemotaxis proteins, and phosphatases) and a C-terminal GGDEF domain indicating a DGC’s function (Giardina et al.,; Malone et al.,). INTRO 0 4 YfiN protein YfiN is repressed by specific interaction between its periplasmic PAS domain and the periplasmic protein YfiR (Malone et al.,). INTRO 8 20 repressed by protein_state YfiN is repressed by specific interaction between its periplasmic PAS domain and the periplasmic protein YfiR (Malone et al.,). INTRO 66 76 PAS domain structure_element YfiN is repressed by specific interaction between its periplasmic PAS domain and the periplasmic protein YfiR (Malone et al.,). INTRO 105 109 YfiR protein YfiN is repressed by specific interaction between its periplasmic PAS domain and the periplasmic protein YfiR (Malone et al.,). INTRO 0 4 YfiB protein YfiB is an OmpA/Pal-like outer-membrane lipoprotein (Parsons et al.,) that can activate YfiN by sequestering YfiR (Malone et al.,) in an unknown manner. INTRO 11 24 OmpA/Pal-like protein_type YfiB is an OmpA/Pal-like outer-membrane lipoprotein (Parsons et al.,) that can activate YfiN by sequestering YfiR (Malone et al.,) in an unknown manner. INTRO 40 51 lipoprotein protein_type YfiB is an OmpA/Pal-like outer-membrane lipoprotein (Parsons et al.,) that can activate YfiN by sequestering YfiR (Malone et al.,) in an unknown manner. INTRO 88 92 YfiN protein YfiB is an OmpA/Pal-like outer-membrane lipoprotein (Parsons et al.,) that can activate YfiN by sequestering YfiR (Malone et al.,) in an unknown manner. INTRO 109 113 YfiR protein YfiB is an OmpA/Pal-like outer-membrane lipoprotein (Parsons et al.,) that can activate YfiN by sequestering YfiR (Malone et al.,) in an unknown manner. INTRO 8 12 YfiB protein Whether YfiB directly recruits YfiR or recruits YfiR via a third partner is an open question. INTRO 31 35 YfiR protein Whether YfiB directly recruits YfiR or recruits YfiR via a third partner is an open question. INTRO 48 52 YfiR protein Whether YfiB directly recruits YfiR or recruits YfiR via a third partner is an open question. INTRO 27 31 YfiR protein After the sequestration of YfiR by YfiB, the c-di-GMP produced by activated YfiN increases the biosynthesis of the Pel and Psl EPSs, resulting in the appearance of the SCV phenotype, which indicates enhanced biofilm formation (Malone et al.,). INTRO 35 39 YfiB protein After the sequestration of YfiR by YfiB, the c-di-GMP produced by activated YfiN increases the biosynthesis of the Pel and Psl EPSs, resulting in the appearance of the SCV phenotype, which indicates enhanced biofilm formation (Malone et al.,). INTRO 45 53 c-di-GMP chemical After the sequestration of YfiR by YfiB, the c-di-GMP produced by activated YfiN increases the biosynthesis of the Pel and Psl EPSs, resulting in the appearance of the SCV phenotype, which indicates enhanced biofilm formation (Malone et al.,). INTRO 66 75 activated protein_state After the sequestration of YfiR by YfiB, the c-di-GMP produced by activated YfiN increases the biosynthesis of the Pel and Psl EPSs, resulting in the appearance of the SCV phenotype, which indicates enhanced biofilm formation (Malone et al.,). INTRO 76 80 YfiN protein After the sequestration of YfiR by YfiB, the c-di-GMP produced by activated YfiN increases the biosynthesis of the Pel and Psl EPSs, resulting in the appearance of the SCV phenotype, which indicates enhanced biofilm formation (Malone et al.,). INTRO 115 118 Pel chemical After the sequestration of YfiR by YfiB, the c-di-GMP produced by activated YfiN increases the biosynthesis of the Pel and Psl EPSs, resulting in the appearance of the SCV phenotype, which indicates enhanced biofilm formation (Malone et al.,). INTRO 123 126 Psl chemical After the sequestration of YfiR by YfiB, the c-di-GMP produced by activated YfiN increases the biosynthesis of the Pel and Psl EPSs, resulting in the appearance of the SCV phenotype, which indicates enhanced biofilm formation (Malone et al.,). INTRO 127 131 EPSs chemical After the sequestration of YfiR by YfiB, the c-di-GMP produced by activated YfiN increases the biosynthesis of the Pel and Psl EPSs, resulting in the appearance of the SCV phenotype, which indicates enhanced biofilm formation (Malone et al.,). INTRO 44 48 YfiN protein It has been reported that the activation of YfiN may be induced by redox-driven misfolding of YfiR (Giardina et al.,; Malone et al.,; Malone et al.,). INTRO 94 98 YfiR protein It has been reported that the activation of YfiN may be induced by redox-driven misfolding of YfiR (Giardina et al.,; Malone et al.,; Malone et al.,). INTRO 46 50 YfiR protein It is also proposed that the sequestration of YfiR by YfiB can be induced by certain YfiB-mediated cell wall stress, and mutagenesis studies revealed a number of activation residues of YfiB that were located in close proximity to the predicted first helix of the periplasmic domain (Malone et al.,). INTRO 54 58 YfiB protein It is also proposed that the sequestration of YfiR by YfiB can be induced by certain YfiB-mediated cell wall stress, and mutagenesis studies revealed a number of activation residues of YfiB that were located in close proximity to the predicted first helix of the periplasmic domain (Malone et al.,). INTRO 85 89 YfiB protein It is also proposed that the sequestration of YfiR by YfiB can be induced by certain YfiB-mediated cell wall stress, and mutagenesis studies revealed a number of activation residues of YfiB that were located in close proximity to the predicted first helix of the periplasmic domain (Malone et al.,). INTRO 121 140 mutagenesis studies experimental_method It is also proposed that the sequestration of YfiR by YfiB can be induced by certain YfiB-mediated cell wall stress, and mutagenesis studies revealed a number of activation residues of YfiB that were located in close proximity to the predicted first helix of the periplasmic domain (Malone et al.,). INTRO 162 181 activation residues structure_element It is also proposed that the sequestration of YfiR by YfiB can be induced by certain YfiB-mediated cell wall stress, and mutagenesis studies revealed a number of activation residues of YfiB that were located in close proximity to the predicted first helix of the periplasmic domain (Malone et al.,). INTRO 185 189 YfiB protein It is also proposed that the sequestration of YfiR by YfiB can be induced by certain YfiB-mediated cell wall stress, and mutagenesis studies revealed a number of activation residues of YfiB that were located in close proximity to the predicted first helix of the periplasmic domain (Malone et al.,). INTRO 234 243 predicted protein_state It is also proposed that the sequestration of YfiR by YfiB can be induced by certain YfiB-mediated cell wall stress, and mutagenesis studies revealed a number of activation residues of YfiB that were located in close proximity to the predicted first helix of the periplasmic domain (Malone et al.,). INTRO 244 255 first helix structure_element It is also proposed that the sequestration of YfiR by YfiB can be induced by certain YfiB-mediated cell wall stress, and mutagenesis studies revealed a number of activation residues of YfiB that were located in close proximity to the predicted first helix of the periplasmic domain (Malone et al.,). INTRO 263 281 periplasmic domain structure_element It is also proposed that the sequestration of YfiR by YfiB can be induced by certain YfiB-mediated cell wall stress, and mutagenesis studies revealed a number of activation residues of YfiB that were located in close proximity to the predicted first helix of the periplasmic domain (Malone et al.,). INTRO 61 71 PAS domain structure_element In addition, quorum sensing-related dephosphorylation of the PAS domain of YfiN may also be involved in the regulation (Ueda and Wood,; Xu et al.,). INTRO 75 79 YfiN protein In addition, quorum sensing-related dephosphorylation of the PAS domain of YfiN may also be involved in the regulation (Ueda and Wood,; Xu et al.,). INTRO 24 41 crystal structure evidence Recently, we solved the crystal structure of YfiR in both the non-oxidized and the oxidized states, revealing breakage/formation of one disulfide bond (Cys71-Cys110) and local conformational change around the other one (Cys145-Cys152), indicating that Cys145-Cys152 plays an important role in maintaining the correct folding of YfiR (Yang et al.,). INTRO 45 49 YfiR protein Recently, we solved the crystal structure of YfiR in both the non-oxidized and the oxidized states, revealing breakage/formation of one disulfide bond (Cys71-Cys110) and local conformational change around the other one (Cys145-Cys152), indicating that Cys145-Cys152 plays an important role in maintaining the correct folding of YfiR (Yang et al.,). INTRO 62 74 non-oxidized protein_state Recently, we solved the crystal structure of YfiR in both the non-oxidized and the oxidized states, revealing breakage/formation of one disulfide bond (Cys71-Cys110) and local conformational change around the other one (Cys145-Cys152), indicating that Cys145-Cys152 plays an important role in maintaining the correct folding of YfiR (Yang et al.,). INTRO 83 91 oxidized protein_state Recently, we solved the crystal structure of YfiR in both the non-oxidized and the oxidized states, revealing breakage/formation of one disulfide bond (Cys71-Cys110) and local conformational change around the other one (Cys145-Cys152), indicating that Cys145-Cys152 plays an important role in maintaining the correct folding of YfiR (Yang et al.,). INTRO 136 150 disulfide bond ptm Recently, we solved the crystal structure of YfiR in both the non-oxidized and the oxidized states, revealing breakage/formation of one disulfide bond (Cys71-Cys110) and local conformational change around the other one (Cys145-Cys152), indicating that Cys145-Cys152 plays an important role in maintaining the correct folding of YfiR (Yang et al.,). INTRO 152 157 Cys71 residue_name_number Recently, we solved the crystal structure of YfiR in both the non-oxidized and the oxidized states, revealing breakage/formation of one disulfide bond (Cys71-Cys110) and local conformational change around the other one (Cys145-Cys152), indicating that Cys145-Cys152 plays an important role in maintaining the correct folding of YfiR (Yang et al.,). INTRO 158 164 Cys110 residue_name_number Recently, we solved the crystal structure of YfiR in both the non-oxidized and the oxidized states, revealing breakage/formation of one disulfide bond (Cys71-Cys110) and local conformational change around the other one (Cys145-Cys152), indicating that Cys145-Cys152 plays an important role in maintaining the correct folding of YfiR (Yang et al.,). INTRO 220 226 Cys145 residue_name_number Recently, we solved the crystal structure of YfiR in both the non-oxidized and the oxidized states, revealing breakage/formation of one disulfide bond (Cys71-Cys110) and local conformational change around the other one (Cys145-Cys152), indicating that Cys145-Cys152 plays an important role in maintaining the correct folding of YfiR (Yang et al.,). INTRO 227 233 Cys152 residue_name_number Recently, we solved the crystal structure of YfiR in both the non-oxidized and the oxidized states, revealing breakage/formation of one disulfide bond (Cys71-Cys110) and local conformational change around the other one (Cys145-Cys152), indicating that Cys145-Cys152 plays an important role in maintaining the correct folding of YfiR (Yang et al.,). INTRO 252 258 Cys145 residue_name_number Recently, we solved the crystal structure of YfiR in both the non-oxidized and the oxidized states, revealing breakage/formation of one disulfide bond (Cys71-Cys110) and local conformational change around the other one (Cys145-Cys152), indicating that Cys145-Cys152 plays an important role in maintaining the correct folding of YfiR (Yang et al.,). INTRO 259 265 Cys152 residue_name_number Recently, we solved the crystal structure of YfiR in both the non-oxidized and the oxidized states, revealing breakage/formation of one disulfide bond (Cys71-Cys110) and local conformational change around the other one (Cys145-Cys152), indicating that Cys145-Cys152 plays an important role in maintaining the correct folding of YfiR (Yang et al.,). INTRO 328 332 YfiR protein Recently, we solved the crystal structure of YfiR in both the non-oxidized and the oxidized states, revealing breakage/formation of one disulfide bond (Cys71-Cys110) and local conformational change around the other one (Cys145-Cys152), indicating that Cys145-Cys152 plays an important role in maintaining the correct folding of YfiR (Yang et al.,). INTRO 36 54 crystal structures evidence In the present study, we solved the crystal structures of an N-terminal truncated form of YfiB (34–168) and YfiR in complex with an active mutant YfiBL43P. INTRO 72 81 truncated protein_state In the present study, we solved the crystal structures of an N-terminal truncated form of YfiB (34–168) and YfiR in complex with an active mutant YfiBL43P. INTRO 90 94 YfiB protein In the present study, we solved the crystal structures of an N-terminal truncated form of YfiB (34–168) and YfiR in complex with an active mutant YfiBL43P. INTRO 96 102 34–168 residue_range In the present study, we solved the crystal structures of an N-terminal truncated form of YfiB (34–168) and YfiR in complex with an active mutant YfiBL43P. INTRO 108 112 YfiR protein In the present study, we solved the crystal structures of an N-terminal truncated form of YfiB (34–168) and YfiR in complex with an active mutant YfiBL43P. INTRO 113 128 in complex with protein_state In the present study, we solved the crystal structures of an N-terminal truncated form of YfiB (34–168) and YfiR in complex with an active mutant YfiBL43P. INTRO 132 138 active protein_state In the present study, we solved the crystal structures of an N-terminal truncated form of YfiB (34–168) and YfiR in complex with an active mutant YfiBL43P. INTRO 139 145 mutant protein_state In the present study, we solved the crystal structures of an N-terminal truncated form of YfiB (34–168) and YfiR in complex with an active mutant YfiBL43P. INTRO 146 154 YfiBL43P mutant In the present study, we solved the crystal structures of an N-terminal truncated form of YfiB (34–168) and YfiR in complex with an active mutant YfiBL43P. INTRO 45 63 crystal structures evidence Most recently, Li and coworkers reported the crystal structures of YfiB (27–168) alone and YfiRC71S in complex with YfiB (59–168) (Li et al.,). INTRO 67 71 YfiB protein Most recently, Li and coworkers reported the crystal structures of YfiB (27–168) alone and YfiRC71S in complex with YfiB (59–168) (Li et al.,). INTRO 73 79 27–168 residue_range Most recently, Li and coworkers reported the crystal structures of YfiB (27–168) alone and YfiRC71S in complex with YfiB (59–168) (Li et al.,). INTRO 81 86 alone protein_state Most recently, Li and coworkers reported the crystal structures of YfiB (27–168) alone and YfiRC71S in complex with YfiB (59–168) (Li et al.,). INTRO 91 99 YfiRC71S mutant Most recently, Li and coworkers reported the crystal structures of YfiB (27–168) alone and YfiRC71S in complex with YfiB (59–168) (Li et al.,). INTRO 100 115 in complex with protein_state Most recently, Li and coworkers reported the crystal structures of YfiB (27–168) alone and YfiRC71S in complex with YfiB (59–168) (Li et al.,). INTRO 116 120 YfiB protein Most recently, Li and coworkers reported the crystal structures of YfiB (27–168) alone and YfiRC71S in complex with YfiB (59–168) (Li et al.,). INTRO 122 128 59–168 residue_range Most recently, Li and coworkers reported the crystal structures of YfiB (27–168) alone and YfiRC71S in complex with YfiB (59–168) (Li et al.,). INTRO 46 54 YfiBL43P mutant Compared with the reported complex structure, YfiBL43P in our YfiB-YfiR complex structure has additional visible N-terminal residues 44–58 that are shown to play essential roles in YfiB activation and biofilm formation. INTRO 62 71 YfiB-YfiR complex_assembly Compared with the reported complex structure, YfiBL43P in our YfiB-YfiR complex structure has additional visible N-terminal residues 44–58 that are shown to play essential roles in YfiB activation and biofilm formation. INTRO 80 89 structure evidence Compared with the reported complex structure, YfiBL43P in our YfiB-YfiR complex structure has additional visible N-terminal residues 44–58 that are shown to play essential roles in YfiB activation and biofilm formation. INTRO 133 138 44–58 residue_range Compared with the reported complex structure, YfiBL43P in our YfiB-YfiR complex structure has additional visible N-terminal residues 44–58 that are shown to play essential roles in YfiB activation and biofilm formation. INTRO 181 185 YfiB protein Compared with the reported complex structure, YfiBL43P in our YfiB-YfiR complex structure has additional visible N-terminal residues 44–58 that are shown to play essential roles in YfiB activation and biofilm formation. INTRO 103 107 YfiB protein Therefore, we are able to visualize the detailed allosteric arrangement of the N-terminal structure of YfiB and its important role in YfiB-YfiR interaction. INTRO 134 143 YfiB-YfiR complex_assembly Therefore, we are able to visualize the detailed allosteric arrangement of the N-terminal structure of YfiB and its important role in YfiB-YfiR interaction. INTRO 31 39 YfiBL43P mutant In addition, we found that the YfiBL43P shows a much higher PG-binding affinity than wild-type YfiB, most likely due to its more compact PG-binding pocket. INTRO 60 79 PG-binding affinity evidence In addition, we found that the YfiBL43P shows a much higher PG-binding affinity than wild-type YfiB, most likely due to its more compact PG-binding pocket. INTRO 85 94 wild-type protein_state In addition, we found that the YfiBL43P shows a much higher PG-binding affinity than wild-type YfiB, most likely due to its more compact PG-binding pocket. INTRO 95 99 YfiB protein In addition, we found that the YfiBL43P shows a much higher PG-binding affinity than wild-type YfiB, most likely due to its more compact PG-binding pocket. INTRO 137 154 PG-binding pocket site In addition, we found that the YfiBL43P shows a much higher PG-binding affinity than wild-type YfiB, most likely due to its more compact PG-binding pocket. INTRO 24 34 Vitamin B6 chemical Moreover, we found that Vitamin B6 (VB6) or L-Trp can bind YfiR with an affinity in the ten millimolar range. INTRO 36 39 VB6 chemical Moreover, we found that Vitamin B6 (VB6) or L-Trp can bind YfiR with an affinity in the ten millimolar range. INTRO 44 49 L-Trp chemical Moreover, we found that Vitamin B6 (VB6) or L-Trp can bind YfiR with an affinity in the ten millimolar range. INTRO 59 63 YfiR protein Moreover, we found that Vitamin B6 (VB6) or L-Trp can bind YfiR with an affinity in the ten millimolar range. INTRO 72 80 affinity evidence Moreover, we found that Vitamin B6 (VB6) or L-Trp can bind YfiR with an affinity in the ten millimolar range. INTRO 87 96 activated protein_state Together with functional data, these results provide new mechanistic insights into how activated YfiB sequesters YfiR and releases the suppression of YfiN. These findings may facilitate the development and optimization of anti-biofilm drugs for the treatment of chronic infections. INTRO 97 101 YfiB protein Together with functional data, these results provide new mechanistic insights into how activated YfiB sequesters YfiR and releases the suppression of YfiN. These findings may facilitate the development and optimization of anti-biofilm drugs for the treatment of chronic infections. INTRO 113 117 YfiR protein Together with functional data, these results provide new mechanistic insights into how activated YfiB sequesters YfiR and releases the suppression of YfiN. These findings may facilitate the development and optimization of anti-biofilm drugs for the treatment of chronic infections. INTRO 150 154 YfiN protein Together with functional data, these results provide new mechanistic insights into how activated YfiB sequesters YfiR and releases the suppression of YfiN. These findings may facilitate the development and optimization of anti-biofilm drugs for the treatment of chronic infections. INTRO 8 17 structure evidence Overall structure of YfiB RESULTS 21 25 YfiB protein Overall structure of YfiB RESULTS 16 29 crystal forms evidence We obtained two crystal forms of YfiB (residues 34–168, lacking the signal peptide from residues 1–26 and periplasmic residues 27–33), crystal forms I and II, belonging to space groups P21 and P41, respectively. RESULTS 33 37 YfiB protein We obtained two crystal forms of YfiB (residues 34–168, lacking the signal peptide from residues 1–26 and periplasmic residues 27–33), crystal forms I and II, belonging to space groups P21 and P41, respectively. RESULTS 48 54 34–168 residue_range We obtained two crystal forms of YfiB (residues 34–168, lacking the signal peptide from residues 1–26 and periplasmic residues 27–33), crystal forms I and II, belonging to space groups P21 and P41, respectively. RESULTS 56 63 lacking protein_state We obtained two crystal forms of YfiB (residues 34–168, lacking the signal peptide from residues 1–26 and periplasmic residues 27–33), crystal forms I and II, belonging to space groups P21 and P41, respectively. RESULTS 68 82 signal peptide structure_element We obtained two crystal forms of YfiB (residues 34–168, lacking the signal peptide from residues 1–26 and periplasmic residues 27–33), crystal forms I and II, belonging to space groups P21 and P41, respectively. RESULTS 97 101 1–26 residue_range We obtained two crystal forms of YfiB (residues 34–168, lacking the signal peptide from residues 1–26 and periplasmic residues 27–33), crystal forms I and II, belonging to space groups P21 and P41, respectively. RESULTS 127 132 27–33 residue_range We obtained two crystal forms of YfiB (residues 34–168, lacking the signal peptide from residues 1–26 and periplasmic residues 27–33), crystal forms I and II, belonging to space groups P21 and P41, respectively. RESULTS 8 17 structure evidence Overall structure of YfiB. (A) The overall structure of the YfiB monomer. (B) A topology diagram of the YfiB monomer. (C and D) The analytical ultracentrifugation experiment results for the wild-type YfiB and YfiBL43P FIG 21 25 YfiB protein Overall structure of YfiB. (A) The overall structure of the YfiB monomer. (B) A topology diagram of the YfiB monomer. (C and D) The analytical ultracentrifugation experiment results for the wild-type YfiB and YfiBL43P FIG 43 52 structure evidence Overall structure of YfiB. (A) The overall structure of the YfiB monomer. (B) A topology diagram of the YfiB monomer. (C and D) The analytical ultracentrifugation experiment results for the wild-type YfiB and YfiBL43P FIG 60 64 YfiB protein Overall structure of YfiB. (A) The overall structure of the YfiB monomer. (B) A topology diagram of the YfiB monomer. (C and D) The analytical ultracentrifugation experiment results for the wild-type YfiB and YfiBL43P FIG 65 72 monomer oligomeric_state Overall structure of YfiB. (A) The overall structure of the YfiB monomer. (B) A topology diagram of the YfiB monomer. (C and D) The analytical ultracentrifugation experiment results for the wild-type YfiB and YfiBL43P FIG 104 108 YfiB protein Overall structure of YfiB. (A) The overall structure of the YfiB monomer. (B) A topology diagram of the YfiB monomer. (C and D) The analytical ultracentrifugation experiment results for the wild-type YfiB and YfiBL43P FIG 109 116 monomer oligomeric_state Overall structure of YfiB. (A) The overall structure of the YfiB monomer. (B) A topology diagram of the YfiB monomer. (C and D) The analytical ultracentrifugation experiment results for the wild-type YfiB and YfiBL43P FIG 132 162 analytical ultracentrifugation experimental_method Overall structure of YfiB. (A) The overall structure of the YfiB monomer. (B) A topology diagram of the YfiB monomer. (C and D) The analytical ultracentrifugation experiment results for the wild-type YfiB and YfiBL43P FIG 190 199 wild-type protein_state Overall structure of YfiB. (A) The overall structure of the YfiB monomer. (B) A topology diagram of the YfiB monomer. (C and D) The analytical ultracentrifugation experiment results for the wild-type YfiB and YfiBL43P FIG 200 204 YfiB protein Overall structure of YfiB. (A) The overall structure of the YfiB monomer. (B) A topology diagram of the YfiB monomer. (C and D) The analytical ultracentrifugation experiment results for the wild-type YfiB and YfiBL43P FIG 209 217 YfiBL43P mutant Overall structure of YfiB. (A) The overall structure of the YfiB monomer. (B) A topology diagram of the YfiB monomer. (C and D) The analytical ultracentrifugation experiment results for the wild-type YfiB and YfiBL43P FIG 4 11 dimeric oligomeric_state Two dimeric types of YfiB dimer. (A–C) The “head to head” dimer. FIG 21 25 YfiB protein Two dimeric types of YfiB dimer. (A–C) The “head to head” dimer. FIG 26 31 dimer oligomeric_state Two dimeric types of YfiB dimer. (A–C) The “head to head” dimer. FIG 44 56 head to head protein_state Two dimeric types of YfiB dimer. (A–C) The “head to head” dimer. FIG 58 63 dimer oligomeric_state Two dimeric types of YfiB dimer. (A–C) The “head to head” dimer. FIG 5 17 back to back protein_state The “back to back” dimer. FIG 19 24 dimer oligomeric_state The “back to back” dimer. FIG 48 54 dimers oligomeric_state (A) and (E) indicate the front views of the two dimers, (B) and (F) indicate the top views of the two dimers, and (C) and (D) indicate the details of the two dimeric interfaces FIG 102 108 dimers oligomeric_state (A) and (E) indicate the front views of the two dimers, (B) and (F) indicate the top views of the two dimers, and (C) and (D) indicate the details of the two dimeric interfaces FIG 158 176 dimeric interfaces site (A) and (E) indicate the front views of the two dimers, (B) and (F) indicate the top views of the two dimers, and (C) and (D) indicate the details of the two dimeric interfaces FIG 4 21 crystal structure evidence The crystal structure of YfiB monomer consists of a five-stranded β-sheet (β1-2-5-3-4) flanked by five α-helices (α1–5) on one side. RESULTS 25 29 YfiB protein The crystal structure of YfiB monomer consists of a five-stranded β-sheet (β1-2-5-3-4) flanked by five α-helices (α1–5) on one side. RESULTS 30 37 monomer oligomeric_state The crystal structure of YfiB monomer consists of a five-stranded β-sheet (β1-2-5-3-4) flanked by five α-helices (α1–5) on one side. RESULTS 52 73 five-stranded β-sheet structure_element The crystal structure of YfiB monomer consists of a five-stranded β-sheet (β1-2-5-3-4) flanked by five α-helices (α1–5) on one side. RESULTS 75 85 β1-2-5-3-4 structure_element The crystal structure of YfiB monomer consists of a five-stranded β-sheet (β1-2-5-3-4) flanked by five α-helices (α1–5) on one side. RESULTS 98 112 five α-helices structure_element The crystal structure of YfiB monomer consists of a five-stranded β-sheet (β1-2-5-3-4) flanked by five α-helices (α1–5) on one side. RESULTS 114 118 α1–5 structure_element The crystal structure of YfiB monomer consists of a five-stranded β-sheet (β1-2-5-3-4) flanked by five α-helices (α1–5) on one side. RESULTS 30 40 helix turn structure_element In addition, there is a short helix turn connecting the β4 strand and α4 helix (Fig. 1A and 1B). RESULTS 56 65 β4 strand structure_element In addition, there is a short helix turn connecting the β4 strand and α4 helix (Fig. 1A and 1B). RESULTS 70 78 α4 helix structure_element In addition, there is a short helix turn connecting the β4 strand and α4 helix (Fig. 1A and 1B). RESULTS 43 50 dimeric oligomeric_state Each crystal form contains three different dimeric types of YfiB, two of which are present in both, suggesting that the rest of the dimeric types may result from crystal packing. RESULTS 60 64 YfiB protein Each crystal form contains three different dimeric types of YfiB, two of which are present in both, suggesting that the rest of the dimeric types may result from crystal packing. RESULTS 132 139 dimeric oligomeric_state Each crystal form contains three different dimeric types of YfiB, two of which are present in both, suggesting that the rest of the dimeric types may result from crystal packing. RESULTS 26 33 dimeric oligomeric_state Here, we refer to the two dimeric types as “head to head” and “back to back” according to the interacting mode (Fig. 2A and 2E), with the total buried surface areas being 316.8 Å2 and 554.3 Å2, respectively. RESULTS 44 56 head to head protein_state Here, we refer to the two dimeric types as “head to head” and “back to back” according to the interacting mode (Fig. 2A and 2E), with the total buried surface areas being 316.8 Å2 and 554.3 Å2, respectively. RESULTS 63 75 back to back protein_state Here, we refer to the two dimeric types as “head to head” and “back to back” according to the interacting mode (Fig. 2A and 2E), with the total buried surface areas being 316.8 Å2 and 554.3 Å2, respectively. RESULTS 5 17 head to head protein_state The “head to head” dimer exhibits a clamp shape. RESULTS 19 24 dimer oligomeric_state The “head to head” dimer exhibits a clamp shape. RESULTS 36 47 clamp shape protein_state The “head to head” dimer exhibits a clamp shape. RESULTS 35 59 hydrophobic interactions bond_interaction The dimerization occurs mainly via hydrophobic interactions formed by A37 and I40 on the α1 helices, L50 on the β1 strands, and W55 on the β2 strands of both molecules, making a hydrophobic interacting core (Fig. 2A–C). RESULTS 70 73 A37 residue_name_number The dimerization occurs mainly via hydrophobic interactions formed by A37 and I40 on the α1 helices, L50 on the β1 strands, and W55 on the β2 strands of both molecules, making a hydrophobic interacting core (Fig. 2A–C). RESULTS 78 81 I40 residue_name_number The dimerization occurs mainly via hydrophobic interactions formed by A37 and I40 on the α1 helices, L50 on the β1 strands, and W55 on the β2 strands of both molecules, making a hydrophobic interacting core (Fig. 2A–C). RESULTS 89 99 α1 helices structure_element The dimerization occurs mainly via hydrophobic interactions formed by A37 and I40 on the α1 helices, L50 on the β1 strands, and W55 on the β2 strands of both molecules, making a hydrophobic interacting core (Fig. 2A–C). RESULTS 101 104 L50 residue_name_number The dimerization occurs mainly via hydrophobic interactions formed by A37 and I40 on the α1 helices, L50 on the β1 strands, and W55 on the β2 strands of both molecules, making a hydrophobic interacting core (Fig. 2A–C). RESULTS 112 122 β1 strands structure_element The dimerization occurs mainly via hydrophobic interactions formed by A37 and I40 on the α1 helices, L50 on the β1 strands, and W55 on the β2 strands of both molecules, making a hydrophobic interacting core (Fig. 2A–C). RESULTS 128 131 W55 residue_name_number The dimerization occurs mainly via hydrophobic interactions formed by A37 and I40 on the α1 helices, L50 on the β1 strands, and W55 on the β2 strands of both molecules, making a hydrophobic interacting core (Fig. 2A–C). RESULTS 139 149 β2 strands structure_element The dimerization occurs mainly via hydrophobic interactions formed by A37 and I40 on the α1 helices, L50 on the β1 strands, and W55 on the β2 strands of both molecules, making a hydrophobic interacting core (Fig. 2A–C). RESULTS 178 206 hydrophobic interacting core site The dimerization occurs mainly via hydrophobic interactions formed by A37 and I40 on the α1 helices, L50 on the β1 strands, and W55 on the β2 strands of both molecules, making a hydrophobic interacting core (Fig. 2A–C). RESULTS 5 17 back to back protein_state The “back to back” dimer presents a Y shape. RESULTS 19 24 dimer oligomeric_state The “back to back” dimer presents a Y shape. RESULTS 36 43 Y shape protein_state The “back to back” dimer presents a Y shape. RESULTS 4 11 dimeric oligomeric_state The dimeric interaction is mainly hydrophilic, occurring among the main-chain and side-chain atoms of N68, L69, D70 and R71 on the α2-α3 loops and R116 and S120 on the α4 helices of both molecules, resulting in a complex hydrogen bond network (Fig. 2D–F). RESULTS 12 45 interaction is mainly hydrophilic bond_interaction The dimeric interaction is mainly hydrophilic, occurring among the main-chain and side-chain atoms of N68, L69, D70 and R71 on the α2-α3 loops and R116 and S120 on the α4 helices of both molecules, resulting in a complex hydrogen bond network (Fig. 2D–F). RESULTS 102 105 N68 residue_name_number The dimeric interaction is mainly hydrophilic, occurring among the main-chain and side-chain atoms of N68, L69, D70 and R71 on the α2-α3 loops and R116 and S120 on the α4 helices of both molecules, resulting in a complex hydrogen bond network (Fig. 2D–F). RESULTS 107 110 L69 residue_name_number The dimeric interaction is mainly hydrophilic, occurring among the main-chain and side-chain atoms of N68, L69, D70 and R71 on the α2-α3 loops and R116 and S120 on the α4 helices of both molecules, resulting in a complex hydrogen bond network (Fig. 2D–F). RESULTS 112 115 D70 residue_name_number The dimeric interaction is mainly hydrophilic, occurring among the main-chain and side-chain atoms of N68, L69, D70 and R71 on the α2-α3 loops and R116 and S120 on the α4 helices of both molecules, resulting in a complex hydrogen bond network (Fig. 2D–F). RESULTS 120 123 R71 residue_name_number The dimeric interaction is mainly hydrophilic, occurring among the main-chain and side-chain atoms of N68, L69, D70 and R71 on the α2-α3 loops and R116 and S120 on the α4 helices of both molecules, resulting in a complex hydrogen bond network (Fig. 2D–F). RESULTS 131 142 α2-α3 loops structure_element The dimeric interaction is mainly hydrophilic, occurring among the main-chain and side-chain atoms of N68, L69, D70 and R71 on the α2-α3 loops and R116 and S120 on the α4 helices of both molecules, resulting in a complex hydrogen bond network (Fig. 2D–F). RESULTS 147 151 R116 residue_name_number The dimeric interaction is mainly hydrophilic, occurring among the main-chain and side-chain atoms of N68, L69, D70 and R71 on the α2-α3 loops and R116 and S120 on the α4 helices of both molecules, resulting in a complex hydrogen bond network (Fig. 2D–F). RESULTS 156 160 S120 residue_name_number The dimeric interaction is mainly hydrophilic, occurring among the main-chain and side-chain atoms of N68, L69, D70 and R71 on the α2-α3 loops and R116 and S120 on the α4 helices of both molecules, resulting in a complex hydrogen bond network (Fig. 2D–F). RESULTS 168 178 α4 helices structure_element The dimeric interaction is mainly hydrophilic, occurring among the main-chain and side-chain atoms of N68, L69, D70 and R71 on the α2-α3 loops and R116 and S120 on the α4 helices of both molecules, resulting in a complex hydrogen bond network (Fig. 2D–F). RESULTS 221 242 hydrogen bond network site The dimeric interaction is mainly hydrophilic, occurring among the main-chain and side-chain atoms of N68, L69, D70 and R71 on the α2-α3 loops and R116 and S120 on the α4 helices of both molecules, resulting in a complex hydrogen bond network (Fig. 2D–F). RESULTS 4 13 YfiB-YfiR complex_assembly The YfiB-YfiR interaction RESULTS 8 17 structure evidence Overall structure of the YfiB-YfiR complex and the conserved surface in YfiR. (A) The overall structure of the YfiB-YfiR complex. FIG 25 34 YfiB-YfiR complex_assembly Overall structure of the YfiB-YfiR complex and the conserved surface in YfiR. (A) The overall structure of the YfiB-YfiR complex. FIG 51 68 conserved surface site Overall structure of the YfiB-YfiR complex and the conserved surface in YfiR. (A) The overall structure of the YfiB-YfiR complex. FIG 72 76 YfiR protein Overall structure of the YfiB-YfiR complex and the conserved surface in YfiR. (A) The overall structure of the YfiB-YfiR complex. FIG 94 103 structure evidence Overall structure of the YfiB-YfiR complex and the conserved surface in YfiR. (A) The overall structure of the YfiB-YfiR complex. FIG 111 120 YfiB-YfiR complex_assembly Overall structure of the YfiB-YfiR complex and the conserved surface in YfiR. (A) The overall structure of the YfiB-YfiR complex. FIG 4 12 YfiBL43P mutant The YfiBL43P molecules are shown in cyan and yellow. FIG 4 8 YfiR protein The YfiR molecules are shown in green and magenta. FIG 63 87 Structural superposition experimental_method Two interacting regions are highlighted by red rectangles. (B) Structural superposition of apo YfiB and YfiR-bound YfiBL43P. FIG 91 94 apo protein_state Two interacting regions are highlighted by red rectangles. (B) Structural superposition of apo YfiB and YfiR-bound YfiBL43P. FIG 95 99 YfiB protein Two interacting regions are highlighted by red rectangles. (B) Structural superposition of apo YfiB and YfiR-bound YfiBL43P. FIG 104 114 YfiR-bound protein_state Two interacting regions are highlighted by red rectangles. (B) Structural superposition of apo YfiB and YfiR-bound YfiBL43P. FIG 115 123 YfiBL43P mutant Two interacting regions are highlighted by red rectangles. (B) Structural superposition of apo YfiB and YfiR-bound YfiBL43P. FIG 38 41 apo protein_state To illustrate the differences between apo YfiB and YfiR-bound YfiBL43P, the apo YfiB is shown in pink, except residues 34–70 are shown in red, whereas the YfiR-bound YfiBL43P is shown in cyan, except residues 44–70 are shown in blue. (C) Close-up view of the differences between apo YfiB and YfiR-bound YfiBL43P. FIG 42 46 YfiB protein To illustrate the differences between apo YfiB and YfiR-bound YfiBL43P, the apo YfiB is shown in pink, except residues 34–70 are shown in red, whereas the YfiR-bound YfiBL43P is shown in cyan, except residues 44–70 are shown in blue. (C) Close-up view of the differences between apo YfiB and YfiR-bound YfiBL43P. FIG 51 61 YfiR-bound protein_state To illustrate the differences between apo YfiB and YfiR-bound YfiBL43P, the apo YfiB is shown in pink, except residues 34–70 are shown in red, whereas the YfiR-bound YfiBL43P is shown in cyan, except residues 44–70 are shown in blue. (C) Close-up view of the differences between apo YfiB and YfiR-bound YfiBL43P. FIG 62 70 YfiBL43P mutant To illustrate the differences between apo YfiB and YfiR-bound YfiBL43P, the apo YfiB is shown in pink, except residues 34–70 are shown in red, whereas the YfiR-bound YfiBL43P is shown in cyan, except residues 44–70 are shown in blue. (C) Close-up view of the differences between apo YfiB and YfiR-bound YfiBL43P. FIG 76 79 apo protein_state To illustrate the differences between apo YfiB and YfiR-bound YfiBL43P, the apo YfiB is shown in pink, except residues 34–70 are shown in red, whereas the YfiR-bound YfiBL43P is shown in cyan, except residues 44–70 are shown in blue. (C) Close-up view of the differences between apo YfiB and YfiR-bound YfiBL43P. FIG 80 84 YfiB protein To illustrate the differences between apo YfiB and YfiR-bound YfiBL43P, the apo YfiB is shown in pink, except residues 34–70 are shown in red, whereas the YfiR-bound YfiBL43P is shown in cyan, except residues 44–70 are shown in blue. (C) Close-up view of the differences between apo YfiB and YfiR-bound YfiBL43P. FIG 119 124 34–70 residue_range To illustrate the differences between apo YfiB and YfiR-bound YfiBL43P, the apo YfiB is shown in pink, except residues 34–70 are shown in red, whereas the YfiR-bound YfiBL43P is shown in cyan, except residues 44–70 are shown in blue. (C) Close-up view of the differences between apo YfiB and YfiR-bound YfiBL43P. FIG 155 165 YfiR-bound protein_state To illustrate the differences between apo YfiB and YfiR-bound YfiBL43P, the apo YfiB is shown in pink, except residues 34–70 are shown in red, whereas the YfiR-bound YfiBL43P is shown in cyan, except residues 44–70 are shown in blue. (C) Close-up view of the differences between apo YfiB and YfiR-bound YfiBL43P. FIG 166 174 YfiBL43P mutant To illustrate the differences between apo YfiB and YfiR-bound YfiBL43P, the apo YfiB is shown in pink, except residues 34–70 are shown in red, whereas the YfiR-bound YfiBL43P is shown in cyan, except residues 44–70 are shown in blue. (C) Close-up view of the differences between apo YfiB and YfiR-bound YfiBL43P. FIG 209 214 44–70 residue_range To illustrate the differences between apo YfiB and YfiR-bound YfiBL43P, the apo YfiB is shown in pink, except residues 34–70 are shown in red, whereas the YfiR-bound YfiBL43P is shown in cyan, except residues 44–70 are shown in blue. (C) Close-up view of the differences between apo YfiB and YfiR-bound YfiBL43P. FIG 279 282 apo protein_state To illustrate the differences between apo YfiB and YfiR-bound YfiBL43P, the apo YfiB is shown in pink, except residues 34–70 are shown in red, whereas the YfiR-bound YfiBL43P is shown in cyan, except residues 44–70 are shown in blue. (C) Close-up view of the differences between apo YfiB and YfiR-bound YfiBL43P. FIG 283 287 YfiB protein To illustrate the differences between apo YfiB and YfiR-bound YfiBL43P, the apo YfiB is shown in pink, except residues 34–70 are shown in red, whereas the YfiR-bound YfiBL43P is shown in cyan, except residues 44–70 are shown in blue. (C) Close-up view of the differences between apo YfiB and YfiR-bound YfiBL43P. FIG 292 302 YfiR-bound protein_state To illustrate the differences between apo YfiB and YfiR-bound YfiBL43P, the apo YfiB is shown in pink, except residues 34–70 are shown in red, whereas the YfiR-bound YfiBL43P is shown in cyan, except residues 44–70 are shown in blue. (C) Close-up view of the differences between apo YfiB and YfiR-bound YfiBL43P. FIG 303 311 YfiBL43P mutant To illustrate the differences between apo YfiB and YfiR-bound YfiBL43P, the apo YfiB is shown in pink, except residues 34–70 are shown in red, whereas the YfiR-bound YfiBL43P is shown in cyan, except residues 44–70 are shown in blue. (C) Close-up view of the differences between apo YfiB and YfiR-bound YfiBL43P. FIG 39 43 YfiB protein The residues proposed to contribute to YfiB activation are illustrated in sticks. FIG 20 23 apo protein_state The key residues in apo YfiB are shown in red and those in YfiBL43P are shown in blue. (D) Close-up views showing interactions in regions I and II. FIG 24 28 YfiB protein The key residues in apo YfiB are shown in red and those in YfiBL43P are shown in blue. (D) Close-up views showing interactions in regions I and II. FIG 59 67 YfiBL43P mutant The key residues in apo YfiB are shown in red and those in YfiBL43P are shown in blue. (D) Close-up views showing interactions in regions I and II. FIG 130 146 regions I and II structure_element The key residues in apo YfiB are shown in red and those in YfiBL43P are shown in blue. (D) Close-up views showing interactions in regions I and II. FIG 0 8 YfiBL43P mutant YfiBL43P and YfiR are shown in cyan and green, respectively. (E and F) The conserved surface in YfiR contributes to the interaction with YfiB. (G) The residues of YfiR responsible for interacting with YfiB are shown in green sticks, and the proposed YfiN-interacting residues are shown in yellow sticks. FIG 13 17 YfiR protein YfiBL43P and YfiR are shown in cyan and green, respectively. (E and F) The conserved surface in YfiR contributes to the interaction with YfiB. (G) The residues of YfiR responsible for interacting with YfiB are shown in green sticks, and the proposed YfiN-interacting residues are shown in yellow sticks. FIG 75 92 conserved surface site YfiBL43P and YfiR are shown in cyan and green, respectively. (E and F) The conserved surface in YfiR contributes to the interaction with YfiB. (G) The residues of YfiR responsible for interacting with YfiB are shown in green sticks, and the proposed YfiN-interacting residues are shown in yellow sticks. FIG 96 100 YfiR protein YfiBL43P and YfiR are shown in cyan and green, respectively. (E and F) The conserved surface in YfiR contributes to the interaction with YfiB. (G) The residues of YfiR responsible for interacting with YfiB are shown in green sticks, and the proposed YfiN-interacting residues are shown in yellow sticks. FIG 137 141 YfiB protein YfiBL43P and YfiR are shown in cyan and green, respectively. (E and F) The conserved surface in YfiR contributes to the interaction with YfiB. (G) The residues of YfiR responsible for interacting with YfiB are shown in green sticks, and the proposed YfiN-interacting residues are shown in yellow sticks. FIG 151 159 residues structure_element YfiBL43P and YfiR are shown in cyan and green, respectively. (E and F) The conserved surface in YfiR contributes to the interaction with YfiB. (G) The residues of YfiR responsible for interacting with YfiB are shown in green sticks, and the proposed YfiN-interacting residues are shown in yellow sticks. FIG 163 167 YfiR protein YfiBL43P and YfiR are shown in cyan and green, respectively. (E and F) The conserved surface in YfiR contributes to the interaction with YfiB. (G) The residues of YfiR responsible for interacting with YfiB are shown in green sticks, and the proposed YfiN-interacting residues are shown in yellow sticks. FIG 201 205 YfiB protein YfiBL43P and YfiR are shown in cyan and green, respectively. (E and F) The conserved surface in YfiR contributes to the interaction with YfiB. (G) The residues of YfiR responsible for interacting with YfiB are shown in green sticks, and the proposed YfiN-interacting residues are shown in yellow sticks. FIG 250 275 YfiN-interacting residues site YfiBL43P and YfiR are shown in cyan and green, respectively. (E and F) The conserved surface in YfiR contributes to the interaction with YfiB. (G) The residues of YfiR responsible for interacting with YfiB are shown in green sticks, and the proposed YfiN-interacting residues are shown in yellow sticks. FIG 36 61 YfiB-interacting residues site The red sticks, which represent the YfiB-interacting residues, are also responsible for the proposed interactions with YfiN FIG 119 123 YfiN protein The red sticks, which represent the YfiB-interacting residues, are also responsible for the proposed interactions with YfiN FIG 37 46 YfiB-YfiR complex_assembly To gain structural insights into the YfiB-YfiR interaction, we co-expressed YfiB (residues 34–168) and YfiR (residues 35–190, lacking the signal peptide), but failed to obtain the complex, in accordance with a previous report in which no stable complex of YfiB-YfiR was observed (Malone et al.,). RESULTS 63 75 co-expressed experimental_method To gain structural insights into the YfiB-YfiR interaction, we co-expressed YfiB (residues 34–168) and YfiR (residues 35–190, lacking the signal peptide), but failed to obtain the complex, in accordance with a previous report in which no stable complex of YfiB-YfiR was observed (Malone et al.,). RESULTS 76 80 YfiB protein To gain structural insights into the YfiB-YfiR interaction, we co-expressed YfiB (residues 34–168) and YfiR (residues 35–190, lacking the signal peptide), but failed to obtain the complex, in accordance with a previous report in which no stable complex of YfiB-YfiR was observed (Malone et al.,). RESULTS 91 97 34–168 residue_range To gain structural insights into the YfiB-YfiR interaction, we co-expressed YfiB (residues 34–168) and YfiR (residues 35–190, lacking the signal peptide), but failed to obtain the complex, in accordance with a previous report in which no stable complex of YfiB-YfiR was observed (Malone et al.,). RESULTS 103 107 YfiR protein To gain structural insights into the YfiB-YfiR interaction, we co-expressed YfiB (residues 34–168) and YfiR (residues 35–190, lacking the signal peptide), but failed to obtain the complex, in accordance with a previous report in which no stable complex of YfiB-YfiR was observed (Malone et al.,). RESULTS 118 124 35–190 residue_range To gain structural insights into the YfiB-YfiR interaction, we co-expressed YfiB (residues 34–168) and YfiR (residues 35–190, lacking the signal peptide), but failed to obtain the complex, in accordance with a previous report in which no stable complex of YfiB-YfiR was observed (Malone et al.,). RESULTS 126 133 lacking protein_state To gain structural insights into the YfiB-YfiR interaction, we co-expressed YfiB (residues 34–168) and YfiR (residues 35–190, lacking the signal peptide), but failed to obtain the complex, in accordance with a previous report in which no stable complex of YfiB-YfiR was observed (Malone et al.,). RESULTS 138 152 signal peptide structure_element To gain structural insights into the YfiB-YfiR interaction, we co-expressed YfiB (residues 34–168) and YfiR (residues 35–190, lacking the signal peptide), but failed to obtain the complex, in accordance with a previous report in which no stable complex of YfiB-YfiR was observed (Malone et al.,). RESULTS 235 244 no stable protein_state To gain structural insights into the YfiB-YfiR interaction, we co-expressed YfiB (residues 34–168) and YfiR (residues 35–190, lacking the signal peptide), but failed to obtain the complex, in accordance with a previous report in which no stable complex of YfiB-YfiR was observed (Malone et al.,). RESULTS 256 265 YfiB-YfiR complex_assembly To gain structural insights into the YfiB-YfiR interaction, we co-expressed YfiB (residues 34–168) and YfiR (residues 35–190, lacking the signal peptide), but failed to obtain the complex, in accordance with a previous report in which no stable complex of YfiB-YfiR was observed (Malone et al.,). RESULTS 26 43 single mutants of experimental_method It has been reported that single mutants of Q39, L43, F48 and W55 contribute to YfiB activation leading to the induction of the SCV phenotype in P. aeruginosa PAO1 (Malone et al.,). RESULTS 44 47 Q39 residue_name_number It has been reported that single mutants of Q39, L43, F48 and W55 contribute to YfiB activation leading to the induction of the SCV phenotype in P. aeruginosa PAO1 (Malone et al.,). RESULTS 49 52 L43 residue_name_number It has been reported that single mutants of Q39, L43, F48 and W55 contribute to YfiB activation leading to the induction of the SCV phenotype in P. aeruginosa PAO1 (Malone et al.,). RESULTS 54 57 F48 residue_name_number It has been reported that single mutants of Q39, L43, F48 and W55 contribute to YfiB activation leading to the induction of the SCV phenotype in P. aeruginosa PAO1 (Malone et al.,). RESULTS 62 65 W55 residue_name_number It has been reported that single mutants of Q39, L43, F48 and W55 contribute to YfiB activation leading to the induction of the SCV phenotype in P. aeruginosa PAO1 (Malone et al.,). RESULTS 80 84 YfiB protein It has been reported that single mutants of Q39, L43, F48 and W55 contribute to YfiB activation leading to the induction of the SCV phenotype in P. aeruginosa PAO1 (Malone et al.,). RESULTS 145 163 P. aeruginosa PAO1 species It has been reported that single mutants of Q39, L43, F48 and W55 contribute to YfiB activation leading to the induction of the SCV phenotype in P. aeruginosa PAO1 (Malone et al.,). RESULTS 82 86 YfiB protein It is likely that these residues may be involved in the conformational changes of YfiB that are related to YfiR sequestration (Fig. 3C). RESULTS 107 111 YfiR protein It is likely that these residues may be involved in the conformational changes of YfiB that are related to YfiR sequestration (Fig. 3C). RESULTS 14 49 constructed two such single mutants experimental_method Therefore, we constructed two such single mutants of YfiB (YfiBL43P and YfiBF48S). RESULTS 53 57 YfiB protein Therefore, we constructed two such single mutants of YfiB (YfiBL43P and YfiBF48S). RESULTS 59 67 YfiBL43P mutant Therefore, we constructed two such single mutants of YfiB (YfiBL43P and YfiBF48S). RESULTS 72 80 YfiBF48S mutant Therefore, we constructed two such single mutants of YfiB (YfiBL43P and YfiBF48S). RESULTS 33 39 stable protein_state As expected, both mutants form a stable complex with YfiR. Finally, we crystalized YfiR in complex with the YfiBL43P mutant and solved the structure at 1.78 Å resolution by molecular replacement using YfiR and YfiB as models. RESULTS 40 52 complex with protein_state As expected, both mutants form a stable complex with YfiR. Finally, we crystalized YfiR in complex with the YfiBL43P mutant and solved the structure at 1.78 Å resolution by molecular replacement using YfiR and YfiB as models. RESULTS 53 57 YfiR protein As expected, both mutants form a stable complex with YfiR. Finally, we crystalized YfiR in complex with the YfiBL43P mutant and solved the structure at 1.78 Å resolution by molecular replacement using YfiR and YfiB as models. RESULTS 71 82 crystalized experimental_method As expected, both mutants form a stable complex with YfiR. Finally, we crystalized YfiR in complex with the YfiBL43P mutant and solved the structure at 1.78 Å resolution by molecular replacement using YfiR and YfiB as models. RESULTS 83 87 YfiR protein As expected, both mutants form a stable complex with YfiR. Finally, we crystalized YfiR in complex with the YfiBL43P mutant and solved the structure at 1.78 Å resolution by molecular replacement using YfiR and YfiB as models. RESULTS 88 103 in complex with protein_state As expected, both mutants form a stable complex with YfiR. Finally, we crystalized YfiR in complex with the YfiBL43P mutant and solved the structure at 1.78 Å resolution by molecular replacement using YfiR and YfiB as models. RESULTS 108 116 YfiBL43P mutant As expected, both mutants form a stable complex with YfiR. Finally, we crystalized YfiR in complex with the YfiBL43P mutant and solved the structure at 1.78 Å resolution by molecular replacement using YfiR and YfiB as models. RESULTS 117 123 mutant protein_state As expected, both mutants form a stable complex with YfiR. Finally, we crystalized YfiR in complex with the YfiBL43P mutant and solved the structure at 1.78 Å resolution by molecular replacement using YfiR and YfiB as models. RESULTS 139 148 structure evidence As expected, both mutants form a stable complex with YfiR. Finally, we crystalized YfiR in complex with the YfiBL43P mutant and solved the structure at 1.78 Å resolution by molecular replacement using YfiR and YfiB as models. RESULTS 173 194 molecular replacement experimental_method As expected, both mutants form a stable complex with YfiR. Finally, we crystalized YfiR in complex with the YfiBL43P mutant and solved the structure at 1.78 Å resolution by molecular replacement using YfiR and YfiB as models. RESULTS 201 205 YfiR protein As expected, both mutants form a stable complex with YfiR. Finally, we crystalized YfiR in complex with the YfiBL43P mutant and solved the structure at 1.78 Å resolution by molecular replacement using YfiR and YfiB as models. RESULTS 210 214 YfiB protein As expected, both mutants form a stable complex with YfiR. Finally, we crystalized YfiR in complex with the YfiBL43P mutant and solved the structure at 1.78 Å resolution by molecular replacement using YfiR and YfiB as models. RESULTS 4 13 YfiB-YfiR complex_assembly The YfiB-YfiR complex is a 2:2 heterotetramer (Fig. 3A) in which the YfiR dimer is clamped by two separated YfiBL43P molecules with a total buried surface area of 3161.2 Å2. RESULTS 31 45 heterotetramer oligomeric_state The YfiB-YfiR complex is a 2:2 heterotetramer (Fig. 3A) in which the YfiR dimer is clamped by two separated YfiBL43P molecules with a total buried surface area of 3161.2 Å2. RESULTS 69 73 YfiR protein The YfiB-YfiR complex is a 2:2 heterotetramer (Fig. 3A) in which the YfiR dimer is clamped by two separated YfiBL43P molecules with a total buried surface area of 3161.2 Å2. RESULTS 74 79 dimer oligomeric_state The YfiB-YfiR complex is a 2:2 heterotetramer (Fig. 3A) in which the YfiR dimer is clamped by two separated YfiBL43P molecules with a total buried surface area of 3161.2 Å2. RESULTS 108 116 YfiBL43P mutant The YfiB-YfiR complex is a 2:2 heterotetramer (Fig. 3A) in which the YfiR dimer is clamped by two separated YfiBL43P molecules with a total buried surface area of 3161.2 Å2. RESULTS 4 8 YfiR protein The YfiR dimer in the complex is identical to the non-oxidized YfiR dimer alone (Yang et al.,), with only Cys145-Cys152 of the two disulfide bonds well formed, suggesting Cys71-Cys110 disulfide bond formation is not essential for forming YfiB-YfiR complex. RESULTS 9 14 dimer oligomeric_state The YfiR dimer in the complex is identical to the non-oxidized YfiR dimer alone (Yang et al.,), with only Cys145-Cys152 of the two disulfide bonds well formed, suggesting Cys71-Cys110 disulfide bond formation is not essential for forming YfiB-YfiR complex. RESULTS 50 62 non-oxidized protein_state The YfiR dimer in the complex is identical to the non-oxidized YfiR dimer alone (Yang et al.,), with only Cys145-Cys152 of the two disulfide bonds well formed, suggesting Cys71-Cys110 disulfide bond formation is not essential for forming YfiB-YfiR complex. RESULTS 63 67 YfiR protein The YfiR dimer in the complex is identical to the non-oxidized YfiR dimer alone (Yang et al.,), with only Cys145-Cys152 of the two disulfide bonds well formed, suggesting Cys71-Cys110 disulfide bond formation is not essential for forming YfiB-YfiR complex. RESULTS 68 73 dimer oligomeric_state The YfiR dimer in the complex is identical to the non-oxidized YfiR dimer alone (Yang et al.,), with only Cys145-Cys152 of the two disulfide bonds well formed, suggesting Cys71-Cys110 disulfide bond formation is not essential for forming YfiB-YfiR complex. RESULTS 74 79 alone protein_state The YfiR dimer in the complex is identical to the non-oxidized YfiR dimer alone (Yang et al.,), with only Cys145-Cys152 of the two disulfide bonds well formed, suggesting Cys71-Cys110 disulfide bond formation is not essential for forming YfiB-YfiR complex. RESULTS 106 112 Cys145 residue_name_number The YfiR dimer in the complex is identical to the non-oxidized YfiR dimer alone (Yang et al.,), with only Cys145-Cys152 of the two disulfide bonds well formed, suggesting Cys71-Cys110 disulfide bond formation is not essential for forming YfiB-YfiR complex. RESULTS 113 119 Cys152 residue_name_number The YfiR dimer in the complex is identical to the non-oxidized YfiR dimer alone (Yang et al.,), with only Cys145-Cys152 of the two disulfide bonds well formed, suggesting Cys71-Cys110 disulfide bond formation is not essential for forming YfiB-YfiR complex. RESULTS 131 146 disulfide bonds ptm The YfiR dimer in the complex is identical to the non-oxidized YfiR dimer alone (Yang et al.,), with only Cys145-Cys152 of the two disulfide bonds well formed, suggesting Cys71-Cys110 disulfide bond formation is not essential for forming YfiB-YfiR complex. RESULTS 171 176 Cys71 residue_name_number The YfiR dimer in the complex is identical to the non-oxidized YfiR dimer alone (Yang et al.,), with only Cys145-Cys152 of the two disulfide bonds well formed, suggesting Cys71-Cys110 disulfide bond formation is not essential for forming YfiB-YfiR complex. RESULTS 177 183 Cys110 residue_name_number The YfiR dimer in the complex is identical to the non-oxidized YfiR dimer alone (Yang et al.,), with only Cys145-Cys152 of the two disulfide bonds well formed, suggesting Cys71-Cys110 disulfide bond formation is not essential for forming YfiB-YfiR complex. RESULTS 184 198 disulfide bond ptm The YfiR dimer in the complex is identical to the non-oxidized YfiR dimer alone (Yang et al.,), with only Cys145-Cys152 of the two disulfide bonds well formed, suggesting Cys71-Cys110 disulfide bond formation is not essential for forming YfiB-YfiR complex. RESULTS 238 247 YfiB-YfiR complex_assembly The YfiR dimer in the complex is identical to the non-oxidized YfiR dimer alone (Yang et al.,), with only Cys145-Cys152 of the two disulfide bonds well formed, suggesting Cys71-Cys110 disulfide bond formation is not essential for forming YfiB-YfiR complex. RESULTS 42 50 YfiBL43P mutant The N-terminal structural conformation of YfiBL43P, from the foremost N-terminus to residue D70, is significantly altered compared with that of the apo YfiB. The majority of the α1 helix (residues 34–43) is invisible on the electron density map, and the α2 helix and β1 and β2 strands are rearranged to form a long loop containing two short α-helix turns (Fig. 3B and 3C), thus embracing the YfiR dimer. RESULTS 92 95 D70 residue_name_number The N-terminal structural conformation of YfiBL43P, from the foremost N-terminus to residue D70, is significantly altered compared with that of the apo YfiB. The majority of the α1 helix (residues 34–43) is invisible on the electron density map, and the α2 helix and β1 and β2 strands are rearranged to form a long loop containing two short α-helix turns (Fig. 3B and 3C), thus embracing the YfiR dimer. RESULTS 148 151 apo protein_state The N-terminal structural conformation of YfiBL43P, from the foremost N-terminus to residue D70, is significantly altered compared with that of the apo YfiB. The majority of the α1 helix (residues 34–43) is invisible on the electron density map, and the α2 helix and β1 and β2 strands are rearranged to form a long loop containing two short α-helix turns (Fig. 3B and 3C), thus embracing the YfiR dimer. RESULTS 152 156 YfiB protein The N-terminal structural conformation of YfiBL43P, from the foremost N-terminus to residue D70, is significantly altered compared with that of the apo YfiB. The majority of the α1 helix (residues 34–43) is invisible on the electron density map, and the α2 helix and β1 and β2 strands are rearranged to form a long loop containing two short α-helix turns (Fig. 3B and 3C), thus embracing the YfiR dimer. RESULTS 178 186 α1 helix structure_element The N-terminal structural conformation of YfiBL43P, from the foremost N-terminus to residue D70, is significantly altered compared with that of the apo YfiB. The majority of the α1 helix (residues 34–43) is invisible on the electron density map, and the α2 helix and β1 and β2 strands are rearranged to form a long loop containing two short α-helix turns (Fig. 3B and 3C), thus embracing the YfiR dimer. RESULTS 197 202 34–43 residue_range The N-terminal structural conformation of YfiBL43P, from the foremost N-terminus to residue D70, is significantly altered compared with that of the apo YfiB. The majority of the α1 helix (residues 34–43) is invisible on the electron density map, and the α2 helix and β1 and β2 strands are rearranged to form a long loop containing two short α-helix turns (Fig. 3B and 3C), thus embracing the YfiR dimer. RESULTS 224 244 electron density map evidence The N-terminal structural conformation of YfiBL43P, from the foremost N-terminus to residue D70, is significantly altered compared with that of the apo YfiB. The majority of the α1 helix (residues 34–43) is invisible on the electron density map, and the α2 helix and β1 and β2 strands are rearranged to form a long loop containing two short α-helix turns (Fig. 3B and 3C), thus embracing the YfiR dimer. RESULTS 254 262 α2 helix structure_element The N-terminal structural conformation of YfiBL43P, from the foremost N-terminus to residue D70, is significantly altered compared with that of the apo YfiB. The majority of the α1 helix (residues 34–43) is invisible on the electron density map, and the α2 helix and β1 and β2 strands are rearranged to form a long loop containing two short α-helix turns (Fig. 3B and 3C), thus embracing the YfiR dimer. RESULTS 267 269 β1 structure_element The N-terminal structural conformation of YfiBL43P, from the foremost N-terminus to residue D70, is significantly altered compared with that of the apo YfiB. The majority of the α1 helix (residues 34–43) is invisible on the electron density map, and the α2 helix and β1 and β2 strands are rearranged to form a long loop containing two short α-helix turns (Fig. 3B and 3C), thus embracing the YfiR dimer. RESULTS 274 284 β2 strands structure_element The N-terminal structural conformation of YfiBL43P, from the foremost N-terminus to residue D70, is significantly altered compared with that of the apo YfiB. The majority of the α1 helix (residues 34–43) is invisible on the electron density map, and the α2 helix and β1 and β2 strands are rearranged to form a long loop containing two short α-helix turns (Fig. 3B and 3C), thus embracing the YfiR dimer. RESULTS 315 319 loop structure_element The N-terminal structural conformation of YfiBL43P, from the foremost N-terminus to residue D70, is significantly altered compared with that of the apo YfiB. The majority of the α1 helix (residues 34–43) is invisible on the electron density map, and the α2 helix and β1 and β2 strands are rearranged to form a long loop containing two short α-helix turns (Fig. 3B and 3C), thus embracing the YfiR dimer. RESULTS 341 354 α-helix turns structure_element The N-terminal structural conformation of YfiBL43P, from the foremost N-terminus to residue D70, is significantly altered compared with that of the apo YfiB. The majority of the α1 helix (residues 34–43) is invisible on the electron density map, and the α2 helix and β1 and β2 strands are rearranged to form a long loop containing two short α-helix turns (Fig. 3B and 3C), thus embracing the YfiR dimer. RESULTS 392 396 YfiR protein The N-terminal structural conformation of YfiBL43P, from the foremost N-terminus to residue D70, is significantly altered compared with that of the apo YfiB. The majority of the α1 helix (residues 34–43) is invisible on the electron density map, and the α2 helix and β1 and β2 strands are rearranged to form a long loop containing two short α-helix turns (Fig. 3B and 3C), thus embracing the YfiR dimer. RESULTS 397 402 dimer oligomeric_state The N-terminal structural conformation of YfiBL43P, from the foremost N-terminus to residue D70, is significantly altered compared with that of the apo YfiB. The majority of the α1 helix (residues 34–43) is invisible on the electron density map, and the α2 helix and β1 and β2 strands are rearranged to form a long loop containing two short α-helix turns (Fig. 3B and 3C), thus embracing the YfiR dimer. RESULTS 40 44 YfiB protein The observed changes in conformation of YfiB and the results of mutagenesis suggest a mechanism by which YfiB sequesters YfiR. RESULTS 64 75 mutagenesis experimental_method The observed changes in conformation of YfiB and the results of mutagenesis suggest a mechanism by which YfiB sequesters YfiR. RESULTS 105 109 YfiB protein The observed changes in conformation of YfiB and the results of mutagenesis suggest a mechanism by which YfiB sequesters YfiR. RESULTS 121 125 YfiR protein The observed changes in conformation of YfiB and the results of mutagenesis suggest a mechanism by which YfiB sequesters YfiR. RESULTS 4 23 YfiB-YfiR interface site The YfiB-YfiR interface can be divided into two regions (Fig. 3A and 3D). RESULTS 0 8 Region I structure_element Region I is formed by numerous main-chain and side-chain hydrophilic interactions between residues E45, G47 and E53 from the N-terminal extended loop of YfiB and residues S57, R60, A89 and H177 from YfiR (Fig. 3D-I(i)). RESULTS 57 81 hydrophilic interactions bond_interaction Region I is formed by numerous main-chain and side-chain hydrophilic interactions between residues E45, G47 and E53 from the N-terminal extended loop of YfiB and residues S57, R60, A89 and H177 from YfiR (Fig. 3D-I(i)). RESULTS 99 102 E45 residue_name_number Region I is formed by numerous main-chain and side-chain hydrophilic interactions between residues E45, G47 and E53 from the N-terminal extended loop of YfiB and residues S57, R60, A89 and H177 from YfiR (Fig. 3D-I(i)). RESULTS 104 107 G47 residue_name_number Region I is formed by numerous main-chain and side-chain hydrophilic interactions between residues E45, G47 and E53 from the N-terminal extended loop of YfiB and residues S57, R60, A89 and H177 from YfiR (Fig. 3D-I(i)). RESULTS 112 115 E53 residue_name_number Region I is formed by numerous main-chain and side-chain hydrophilic interactions between residues E45, G47 and E53 from the N-terminal extended loop of YfiB and residues S57, R60, A89 and H177 from YfiR (Fig. 3D-I(i)). RESULTS 145 149 loop structure_element Region I is formed by numerous main-chain and side-chain hydrophilic interactions between residues E45, G47 and E53 from the N-terminal extended loop of YfiB and residues S57, R60, A89 and H177 from YfiR (Fig. 3D-I(i)). RESULTS 153 157 YfiB protein Region I is formed by numerous main-chain and side-chain hydrophilic interactions between residues E45, G47 and E53 from the N-terminal extended loop of YfiB and residues S57, R60, A89 and H177 from YfiR (Fig. 3D-I(i)). RESULTS 171 174 S57 residue_name_number Region I is formed by numerous main-chain and side-chain hydrophilic interactions between residues E45, G47 and E53 from the N-terminal extended loop of YfiB and residues S57, R60, A89 and H177 from YfiR (Fig. 3D-I(i)). RESULTS 176 179 R60 residue_name_number Region I is formed by numerous main-chain and side-chain hydrophilic interactions between residues E45, G47 and E53 from the N-terminal extended loop of YfiB and residues S57, R60, A89 and H177 from YfiR (Fig. 3D-I(i)). RESULTS 181 184 A89 residue_name_number Region I is formed by numerous main-chain and side-chain hydrophilic interactions between residues E45, G47 and E53 from the N-terminal extended loop of YfiB and residues S57, R60, A89 and H177 from YfiR (Fig. 3D-I(i)). RESULTS 189 193 H177 residue_name_number Region I is formed by numerous main-chain and side-chain hydrophilic interactions between residues E45, G47 and E53 from the N-terminal extended loop of YfiB and residues S57, R60, A89 and H177 from YfiR (Fig. 3D-I(i)). RESULTS 199 203 YfiR protein Region I is formed by numerous main-chain and side-chain hydrophilic interactions between residues E45, G47 and E53 from the N-terminal extended loop of YfiB and residues S57, R60, A89 and H177 from YfiR (Fig. 3D-I(i)). RESULTS 20 47 hydrophobic anchoring sites site Additionally, three hydrophobic anchoring sites exist in region I. The residues F48 and W55 of YfiB are inserted into the hydrophobic cores mainly formed by the main chain and side chain carbon atoms of residues S57/Q88/A89/N90 and R60/R175/H177 of YfiR, respectively; and F57 of YfiB is inserted into the hydrophobic pocket formed by L166/I169/V176/P178/L181 of YfiR (Fig. 3D-I(ii)). RESULTS 57 65 region I structure_element Additionally, three hydrophobic anchoring sites exist in region I. The residues F48 and W55 of YfiB are inserted into the hydrophobic cores mainly formed by the main chain and side chain carbon atoms of residues S57/Q88/A89/N90 and R60/R175/H177 of YfiR, respectively; and F57 of YfiB is inserted into the hydrophobic pocket formed by L166/I169/V176/P178/L181 of YfiR (Fig. 3D-I(ii)). RESULTS 80 83 F48 residue_name_number Additionally, three hydrophobic anchoring sites exist in region I. The residues F48 and W55 of YfiB are inserted into the hydrophobic cores mainly formed by the main chain and side chain carbon atoms of residues S57/Q88/A89/N90 and R60/R175/H177 of YfiR, respectively; and F57 of YfiB is inserted into the hydrophobic pocket formed by L166/I169/V176/P178/L181 of YfiR (Fig. 3D-I(ii)). RESULTS 88 91 W55 residue_name_number Additionally, three hydrophobic anchoring sites exist in region I. The residues F48 and W55 of YfiB are inserted into the hydrophobic cores mainly formed by the main chain and side chain carbon atoms of residues S57/Q88/A89/N90 and R60/R175/H177 of YfiR, respectively; and F57 of YfiB is inserted into the hydrophobic pocket formed by L166/I169/V176/P178/L181 of YfiR (Fig. 3D-I(ii)). RESULTS 95 99 YfiB protein Additionally, three hydrophobic anchoring sites exist in region I. The residues F48 and W55 of YfiB are inserted into the hydrophobic cores mainly formed by the main chain and side chain carbon atoms of residues S57/Q88/A89/N90 and R60/R175/H177 of YfiR, respectively; and F57 of YfiB is inserted into the hydrophobic pocket formed by L166/I169/V176/P178/L181 of YfiR (Fig. 3D-I(ii)). RESULTS 122 139 hydrophobic cores site Additionally, three hydrophobic anchoring sites exist in region I. The residues F48 and W55 of YfiB are inserted into the hydrophobic cores mainly formed by the main chain and side chain carbon atoms of residues S57/Q88/A89/N90 and R60/R175/H177 of YfiR, respectively; and F57 of YfiB is inserted into the hydrophobic pocket formed by L166/I169/V176/P178/L181 of YfiR (Fig. 3D-I(ii)). RESULTS 212 215 S57 residue_name_number Additionally, three hydrophobic anchoring sites exist in region I. The residues F48 and W55 of YfiB are inserted into the hydrophobic cores mainly formed by the main chain and side chain carbon atoms of residues S57/Q88/A89/N90 and R60/R175/H177 of YfiR, respectively; and F57 of YfiB is inserted into the hydrophobic pocket formed by L166/I169/V176/P178/L181 of YfiR (Fig. 3D-I(ii)). RESULTS 216 219 Q88 residue_name_number Additionally, three hydrophobic anchoring sites exist in region I. The residues F48 and W55 of YfiB are inserted into the hydrophobic cores mainly formed by the main chain and side chain carbon atoms of residues S57/Q88/A89/N90 and R60/R175/H177 of YfiR, respectively; and F57 of YfiB is inserted into the hydrophobic pocket formed by L166/I169/V176/P178/L181 of YfiR (Fig. 3D-I(ii)). RESULTS 220 223 A89 residue_name_number Additionally, three hydrophobic anchoring sites exist in region I. The residues F48 and W55 of YfiB are inserted into the hydrophobic cores mainly formed by the main chain and side chain carbon atoms of residues S57/Q88/A89/N90 and R60/R175/H177 of YfiR, respectively; and F57 of YfiB is inserted into the hydrophobic pocket formed by L166/I169/V176/P178/L181 of YfiR (Fig. 3D-I(ii)). RESULTS 224 227 N90 residue_name_number Additionally, three hydrophobic anchoring sites exist in region I. The residues F48 and W55 of YfiB are inserted into the hydrophobic cores mainly formed by the main chain and side chain carbon atoms of residues S57/Q88/A89/N90 and R60/R175/H177 of YfiR, respectively; and F57 of YfiB is inserted into the hydrophobic pocket formed by L166/I169/V176/P178/L181 of YfiR (Fig. 3D-I(ii)). RESULTS 232 235 R60 residue_name_number Additionally, three hydrophobic anchoring sites exist in region I. The residues F48 and W55 of YfiB are inserted into the hydrophobic cores mainly formed by the main chain and side chain carbon atoms of residues S57/Q88/A89/N90 and R60/R175/H177 of YfiR, respectively; and F57 of YfiB is inserted into the hydrophobic pocket formed by L166/I169/V176/P178/L181 of YfiR (Fig. 3D-I(ii)). RESULTS 236 240 R175 residue_name_number Additionally, three hydrophobic anchoring sites exist in region I. The residues F48 and W55 of YfiB are inserted into the hydrophobic cores mainly formed by the main chain and side chain carbon atoms of residues S57/Q88/A89/N90 and R60/R175/H177 of YfiR, respectively; and F57 of YfiB is inserted into the hydrophobic pocket formed by L166/I169/V176/P178/L181 of YfiR (Fig. 3D-I(ii)). RESULTS 241 245 H177 residue_name_number Additionally, three hydrophobic anchoring sites exist in region I. The residues F48 and W55 of YfiB are inserted into the hydrophobic cores mainly formed by the main chain and side chain carbon atoms of residues S57/Q88/A89/N90 and R60/R175/H177 of YfiR, respectively; and F57 of YfiB is inserted into the hydrophobic pocket formed by L166/I169/V176/P178/L181 of YfiR (Fig. 3D-I(ii)). RESULTS 249 253 YfiR protein Additionally, three hydrophobic anchoring sites exist in region I. The residues F48 and W55 of YfiB are inserted into the hydrophobic cores mainly formed by the main chain and side chain carbon atoms of residues S57/Q88/A89/N90 and R60/R175/H177 of YfiR, respectively; and F57 of YfiB is inserted into the hydrophobic pocket formed by L166/I169/V176/P178/L181 of YfiR (Fig. 3D-I(ii)). RESULTS 273 276 F57 residue_name_number Additionally, three hydrophobic anchoring sites exist in region I. The residues F48 and W55 of YfiB are inserted into the hydrophobic cores mainly formed by the main chain and side chain carbon atoms of residues S57/Q88/A89/N90 and R60/R175/H177 of YfiR, respectively; and F57 of YfiB is inserted into the hydrophobic pocket formed by L166/I169/V176/P178/L181 of YfiR (Fig. 3D-I(ii)). RESULTS 280 284 YfiB protein Additionally, three hydrophobic anchoring sites exist in region I. The residues F48 and W55 of YfiB are inserted into the hydrophobic cores mainly formed by the main chain and side chain carbon atoms of residues S57/Q88/A89/N90 and R60/R175/H177 of YfiR, respectively; and F57 of YfiB is inserted into the hydrophobic pocket formed by L166/I169/V176/P178/L181 of YfiR (Fig. 3D-I(ii)). RESULTS 306 324 hydrophobic pocket site Additionally, three hydrophobic anchoring sites exist in region I. The residues F48 and W55 of YfiB are inserted into the hydrophobic cores mainly formed by the main chain and side chain carbon atoms of residues S57/Q88/A89/N90 and R60/R175/H177 of YfiR, respectively; and F57 of YfiB is inserted into the hydrophobic pocket formed by L166/I169/V176/P178/L181 of YfiR (Fig. 3D-I(ii)). RESULTS 335 339 L166 residue_name_number Additionally, three hydrophobic anchoring sites exist in region I. The residues F48 and W55 of YfiB are inserted into the hydrophobic cores mainly formed by the main chain and side chain carbon atoms of residues S57/Q88/A89/N90 and R60/R175/H177 of YfiR, respectively; and F57 of YfiB is inserted into the hydrophobic pocket formed by L166/I169/V176/P178/L181 of YfiR (Fig. 3D-I(ii)). RESULTS 340 344 I169 residue_name_number Additionally, three hydrophobic anchoring sites exist in region I. The residues F48 and W55 of YfiB are inserted into the hydrophobic cores mainly formed by the main chain and side chain carbon atoms of residues S57/Q88/A89/N90 and R60/R175/H177 of YfiR, respectively; and F57 of YfiB is inserted into the hydrophobic pocket formed by L166/I169/V176/P178/L181 of YfiR (Fig. 3D-I(ii)). RESULTS 345 349 V176 residue_name_number Additionally, three hydrophobic anchoring sites exist in region I. The residues F48 and W55 of YfiB are inserted into the hydrophobic cores mainly formed by the main chain and side chain carbon atoms of residues S57/Q88/A89/N90 and R60/R175/H177 of YfiR, respectively; and F57 of YfiB is inserted into the hydrophobic pocket formed by L166/I169/V176/P178/L181 of YfiR (Fig. 3D-I(ii)). RESULTS 350 354 P178 residue_name_number Additionally, three hydrophobic anchoring sites exist in region I. The residues F48 and W55 of YfiB are inserted into the hydrophobic cores mainly formed by the main chain and side chain carbon atoms of residues S57/Q88/A89/N90 and R60/R175/H177 of YfiR, respectively; and F57 of YfiB is inserted into the hydrophobic pocket formed by L166/I169/V176/P178/L181 of YfiR (Fig. 3D-I(ii)). RESULTS 355 359 L181 residue_name_number Additionally, three hydrophobic anchoring sites exist in region I. The residues F48 and W55 of YfiB are inserted into the hydrophobic cores mainly formed by the main chain and side chain carbon atoms of residues S57/Q88/A89/N90 and R60/R175/H177 of YfiR, respectively; and F57 of YfiB is inserted into the hydrophobic pocket formed by L166/I169/V176/P178/L181 of YfiR (Fig. 3D-I(ii)). RESULTS 363 367 YfiR protein Additionally, three hydrophobic anchoring sites exist in region I. The residues F48 and W55 of YfiB are inserted into the hydrophobic cores mainly formed by the main chain and side chain carbon atoms of residues S57/Q88/A89/N90 and R60/R175/H177 of YfiR, respectively; and F57 of YfiB is inserted into the hydrophobic pocket formed by L166/I169/V176/P178/L181 of YfiR (Fig. 3D-I(ii)). RESULTS 3 12 region II structure_element In region II, the side chains of R96, E98 and E157 from YfiB interact with the side chains of E163, S146 and R171 from YfiR, respectively. RESULTS 33 36 R96 residue_name_number In region II, the side chains of R96, E98 and E157 from YfiB interact with the side chains of E163, S146 and R171 from YfiR, respectively. RESULTS 38 41 E98 residue_name_number In region II, the side chains of R96, E98 and E157 from YfiB interact with the side chains of E163, S146 and R171 from YfiR, respectively. RESULTS 46 50 E157 residue_name_number In region II, the side chains of R96, E98 and E157 from YfiB interact with the side chains of E163, S146 and R171 from YfiR, respectively. RESULTS 56 60 YfiB protein In region II, the side chains of R96, E98 and E157 from YfiB interact with the side chains of E163, S146 and R171 from YfiR, respectively. RESULTS 94 98 E163 residue_name_number In region II, the side chains of R96, E98 and E157 from YfiB interact with the side chains of E163, S146 and R171 from YfiR, respectively. RESULTS 100 104 S146 residue_name_number In region II, the side chains of R96, E98 and E157 from YfiB interact with the side chains of E163, S146 and R171 from YfiR, respectively. RESULTS 109 113 R171 residue_name_number In region II, the side chains of R96, E98 and E157 from YfiB interact with the side chains of E163, S146 and R171 from YfiR, respectively. RESULTS 119 123 YfiR protein In region II, the side chains of R96, E98 and E157 from YfiB interact with the side chains of E163, S146 and R171 from YfiR, respectively. RESULTS 33 37 I163 residue_name_number Additionally, the main chains of I163 and V165 from YfiB form hydrogen bonds with the main chains of L166 and A164 from YfiR, respectively, and the main chain of P166 from YfiB interacts with the side chain of R185 from YfiR (Fig. 3D-II). RESULTS 42 46 V165 residue_name_number Additionally, the main chains of I163 and V165 from YfiB form hydrogen bonds with the main chains of L166 and A164 from YfiR, respectively, and the main chain of P166 from YfiB interacts with the side chain of R185 from YfiR (Fig. 3D-II). RESULTS 52 56 YfiB protein Additionally, the main chains of I163 and V165 from YfiB form hydrogen bonds with the main chains of L166 and A164 from YfiR, respectively, and the main chain of P166 from YfiB interacts with the side chain of R185 from YfiR (Fig. 3D-II). RESULTS 62 76 hydrogen bonds bond_interaction Additionally, the main chains of I163 and V165 from YfiB form hydrogen bonds with the main chains of L166 and A164 from YfiR, respectively, and the main chain of P166 from YfiB interacts with the side chain of R185 from YfiR (Fig. 3D-II). RESULTS 101 105 L166 residue_name_number Additionally, the main chains of I163 and V165 from YfiB form hydrogen bonds with the main chains of L166 and A164 from YfiR, respectively, and the main chain of P166 from YfiB interacts with the side chain of R185 from YfiR (Fig. 3D-II). RESULTS 110 114 A164 residue_name_number Additionally, the main chains of I163 and V165 from YfiB form hydrogen bonds with the main chains of L166 and A164 from YfiR, respectively, and the main chain of P166 from YfiB interacts with the side chain of R185 from YfiR (Fig. 3D-II). RESULTS 120 124 YfiR protein Additionally, the main chains of I163 and V165 from YfiB form hydrogen bonds with the main chains of L166 and A164 from YfiR, respectively, and the main chain of P166 from YfiB interacts with the side chain of R185 from YfiR (Fig. 3D-II). RESULTS 162 166 P166 residue_name_number Additionally, the main chains of I163 and V165 from YfiB form hydrogen bonds with the main chains of L166 and A164 from YfiR, respectively, and the main chain of P166 from YfiB interacts with the side chain of R185 from YfiR (Fig. 3D-II). RESULTS 172 176 YfiB protein Additionally, the main chains of I163 and V165 from YfiB form hydrogen bonds with the main chains of L166 and A164 from YfiR, respectively, and the main chain of P166 from YfiB interacts with the side chain of R185 from YfiR (Fig. 3D-II). RESULTS 210 214 R185 residue_name_number Additionally, the main chains of I163 and V165 from YfiB form hydrogen bonds with the main chains of L166 and A164 from YfiR, respectively, and the main chain of P166 from YfiB interacts with the side chain of R185 from YfiR (Fig. 3D-II). RESULTS 220 224 YfiR protein Additionally, the main chains of I163 and V165 from YfiB form hydrogen bonds with the main chains of L166 and A164 from YfiR, respectively, and the main chain of P166 from YfiB interacts with the side chain of R185 from YfiR (Fig. 3D-II). RESULTS 38 62 hydrogen-bonding network site These two regions contribute a robust hydrogen-bonding network to the YfiB-YfiR interface, resulting in a tightly bound complex. RESULTS 70 89 YfiB-YfiR interface site These two regions contribute a robust hydrogen-bonding network to the YfiB-YfiR interface, resulting in a tightly bound complex. RESULTS 45 53 YfiBL43P mutant Based on the observations that two separated YfiBL43P molecules form a 2:2 complex structure with YfiR dimer, we performed an analytical ultracentrifugation experiment to check the oligomeric states of wild-type YfiB and YfiBL43P. RESULTS 83 92 structure evidence Based on the observations that two separated YfiBL43P molecules form a 2:2 complex structure with YfiR dimer, we performed an analytical ultracentrifugation experiment to check the oligomeric states of wild-type YfiB and YfiBL43P. RESULTS 98 102 YfiR protein Based on the observations that two separated YfiBL43P molecules form a 2:2 complex structure with YfiR dimer, we performed an analytical ultracentrifugation experiment to check the oligomeric states of wild-type YfiB and YfiBL43P. RESULTS 103 108 dimer oligomeric_state Based on the observations that two separated YfiBL43P molecules form a 2:2 complex structure with YfiR dimer, we performed an analytical ultracentrifugation experiment to check the oligomeric states of wild-type YfiB and YfiBL43P. RESULTS 126 156 analytical ultracentrifugation experimental_method Based on the observations that two separated YfiBL43P molecules form a 2:2 complex structure with YfiR dimer, we performed an analytical ultracentrifugation experiment to check the oligomeric states of wild-type YfiB and YfiBL43P. RESULTS 202 211 wild-type protein_state Based on the observations that two separated YfiBL43P molecules form a 2:2 complex structure with YfiR dimer, we performed an analytical ultracentrifugation experiment to check the oligomeric states of wild-type YfiB and YfiBL43P. RESULTS 212 216 YfiB protein Based on the observations that two separated YfiBL43P molecules form a 2:2 complex structure with YfiR dimer, we performed an analytical ultracentrifugation experiment to check the oligomeric states of wild-type YfiB and YfiBL43P. RESULTS 221 229 YfiBL43P mutant Based on the observations that two separated YfiBL43P molecules form a 2:2 complex structure with YfiR dimer, we performed an analytical ultracentrifugation experiment to check the oligomeric states of wild-type YfiB and YfiBL43P. RESULTS 24 33 wild-type protein_state The results showed that wild-type YfiB exists in both monomeric and dimeric states in solution, while YfiBL43P primarily adopts the monomer state in solution (Fig. 1C–D). RESULTS 34 38 YfiB protein The results showed that wild-type YfiB exists in both monomeric and dimeric states in solution, while YfiBL43P primarily adopts the monomer state in solution (Fig. 1C–D). RESULTS 54 63 monomeric oligomeric_state The results showed that wild-type YfiB exists in both monomeric and dimeric states in solution, while YfiBL43P primarily adopts the monomer state in solution (Fig. 1C–D). RESULTS 68 75 dimeric oligomeric_state The results showed that wild-type YfiB exists in both monomeric and dimeric states in solution, while YfiBL43P primarily adopts the monomer state in solution (Fig. 1C–D). RESULTS 102 110 YfiBL43P mutant The results showed that wild-type YfiB exists in both monomeric and dimeric states in solution, while YfiBL43P primarily adopts the monomer state in solution (Fig. 1C–D). RESULTS 132 139 monomer oligomeric_state The results showed that wild-type YfiB exists in both monomeric and dimeric states in solution, while YfiBL43P primarily adopts the monomer state in solution (Fig. 1C–D). RESULTS 37 41 YfiB protein This suggests that the N-terminus of YfiB plays an important role in forming the dimeric YfiB in solution and that the conformational change of residue L43 is associated with the stretch of the N-terminus and opening of the dimer. RESULTS 81 88 dimeric oligomeric_state This suggests that the N-terminus of YfiB plays an important role in forming the dimeric YfiB in solution and that the conformational change of residue L43 is associated with the stretch of the N-terminus and opening of the dimer. RESULTS 89 93 YfiB protein This suggests that the N-terminus of YfiB plays an important role in forming the dimeric YfiB in solution and that the conformational change of residue L43 is associated with the stretch of the N-terminus and opening of the dimer. RESULTS 152 155 L43 residue_name_number This suggests that the N-terminus of YfiB plays an important role in forming the dimeric YfiB in solution and that the conformational change of residue L43 is associated with the stretch of the N-terminus and opening of the dimer. RESULTS 224 229 dimer oligomeric_state This suggests that the N-terminus of YfiB plays an important role in forming the dimeric YfiB in solution and that the conformational change of residue L43 is associated with the stretch of the N-terminus and opening of the dimer. RESULTS 36 43 dimeric oligomeric_state Therefore, it is possible that both dimeric types might exist in solution. RESULTS 37 49 head to head protein_state For simplicity, we only discuss the “head to head” dimer in the following text. RESULTS 51 56 dimer oligomeric_state For simplicity, we only discuss the “head to head” dimer in the following text. RESULTS 4 19 PG-binding site site The PG-binding site of YfiB RESULTS 23 27 YfiB protein The PG-binding site of YfiB RESULTS 4 19 PG-binding site site The PG-binding site in YfiB. (A) Structural superposition of the PG-binding sites of the H. influenzae Pal/PG-P complex and YfiR-bound YfiBL43P complexed with sulfate ions. FIG 23 27 YfiB protein The PG-binding site in YfiB. (A) Structural superposition of the PG-binding sites of the H. influenzae Pal/PG-P complex and YfiR-bound YfiBL43P complexed with sulfate ions. FIG 33 57 Structural superposition experimental_method The PG-binding site in YfiB. (A) Structural superposition of the PG-binding sites of the H. influenzae Pal/PG-P complex and YfiR-bound YfiBL43P complexed with sulfate ions. FIG 65 81 PG-binding sites site The PG-binding site in YfiB. (A) Structural superposition of the PG-binding sites of the H. influenzae Pal/PG-P complex and YfiR-bound YfiBL43P complexed with sulfate ions. FIG 89 102 H. influenzae species The PG-binding site in YfiB. (A) Structural superposition of the PG-binding sites of the H. influenzae Pal/PG-P complex and YfiR-bound YfiBL43P complexed with sulfate ions. FIG 103 111 Pal/PG-P complex_assembly The PG-binding site in YfiB. (A) Structural superposition of the PG-binding sites of the H. influenzae Pal/PG-P complex and YfiR-bound YfiBL43P complexed with sulfate ions. FIG 124 134 YfiR-bound protein_state The PG-binding site in YfiB. (A) Structural superposition of the PG-binding sites of the H. influenzae Pal/PG-P complex and YfiR-bound YfiBL43P complexed with sulfate ions. FIG 135 143 YfiBL43P mutant The PG-binding site in YfiB. (A) Structural superposition of the PG-binding sites of the H. influenzae Pal/PG-P complex and YfiR-bound YfiBL43P complexed with sulfate ions. FIG 144 158 complexed with protein_state The PG-binding site in YfiB. (A) Structural superposition of the PG-binding sites of the H. influenzae Pal/PG-P complex and YfiR-bound YfiBL43P complexed with sulfate ions. FIG 159 166 sulfate chemical The PG-binding site in YfiB. (A) Structural superposition of the PG-binding sites of the H. influenzae Pal/PG-P complex and YfiR-bound YfiBL43P complexed with sulfate ions. FIG 46 49 Pal protein_type (B) Close-up view showing the key residues of Pal interacting with the m-Dap5 ε-carboxylate group of PG-P. Pal is shown in wheat and PG-P is in magenta. FIG 71 91 m-Dap5 ε-carboxylate chemical (B) Close-up view showing the key residues of Pal interacting with the m-Dap5 ε-carboxylate group of PG-P. Pal is shown in wheat and PG-P is in magenta. FIG 101 105 PG-P chemical (B) Close-up view showing the key residues of Pal interacting with the m-Dap5 ε-carboxylate group of PG-P. Pal is shown in wheat and PG-P is in magenta. FIG 107 110 Pal protein_type (B) Close-up view showing the key residues of Pal interacting with the m-Dap5 ε-carboxylate group of PG-P. Pal is shown in wheat and PG-P is in magenta. FIG 133 137 PG-P chemical (B) Close-up view showing the key residues of Pal interacting with the m-Dap5 ε-carboxylate group of PG-P. Pal is shown in wheat and PG-P is in magenta. FIG 46 56 YfiR-bound protein_state (C) Close-up view showing the key residues of YfiR-bound YfiBL43P interacting with a sulfate ion. FIG 57 65 YfiBL43P mutant (C) Close-up view showing the key residues of YfiR-bound YfiBL43P interacting with a sulfate ion. FIG 85 92 sulfate chemical (C) Close-up view showing the key residues of YfiR-bound YfiBL43P interacting with a sulfate ion. FIG 0 10 YfiR-bound protein_state YfiR-bound YfiBL43P is shown in cyan; the sulfate ion, in green; and the water molecule, in yellow. (D) Structural superposition of the PG-binding sites of apo YfiB and YfiR-bound YfiBL43P, the key residues are shown in stick. FIG 11 19 YfiBL43P mutant YfiR-bound YfiBL43P is shown in cyan; the sulfate ion, in green; and the water molecule, in yellow. (D) Structural superposition of the PG-binding sites of apo YfiB and YfiR-bound YfiBL43P, the key residues are shown in stick. FIG 42 49 sulfate chemical YfiR-bound YfiBL43P is shown in cyan; the sulfate ion, in green; and the water molecule, in yellow. (D) Structural superposition of the PG-binding sites of apo YfiB and YfiR-bound YfiBL43P, the key residues are shown in stick. FIG 73 78 water chemical YfiR-bound YfiBL43P is shown in cyan; the sulfate ion, in green; and the water molecule, in yellow. (D) Structural superposition of the PG-binding sites of apo YfiB and YfiR-bound YfiBL43P, the key residues are shown in stick. FIG 104 128 Structural superposition experimental_method YfiR-bound YfiBL43P is shown in cyan; the sulfate ion, in green; and the water molecule, in yellow. (D) Structural superposition of the PG-binding sites of apo YfiB and YfiR-bound YfiBL43P, the key residues are shown in stick. FIG 136 152 PG-binding sites site YfiR-bound YfiBL43P is shown in cyan; the sulfate ion, in green; and the water molecule, in yellow. (D) Structural superposition of the PG-binding sites of apo YfiB and YfiR-bound YfiBL43P, the key residues are shown in stick. FIG 156 159 apo protein_state YfiR-bound YfiBL43P is shown in cyan; the sulfate ion, in green; and the water molecule, in yellow. (D) Structural superposition of the PG-binding sites of apo YfiB and YfiR-bound YfiBL43P, the key residues are shown in stick. FIG 160 164 YfiB protein YfiR-bound YfiBL43P is shown in cyan; the sulfate ion, in green; and the water molecule, in yellow. (D) Structural superposition of the PG-binding sites of apo YfiB and YfiR-bound YfiBL43P, the key residues are shown in stick. FIG 169 179 YfiR-bound protein_state YfiR-bound YfiBL43P is shown in cyan; the sulfate ion, in green; and the water molecule, in yellow. (D) Structural superposition of the PG-binding sites of apo YfiB and YfiR-bound YfiBL43P, the key residues are shown in stick. FIG 180 188 YfiBL43P mutant YfiR-bound YfiBL43P is shown in cyan; the sulfate ion, in green; and the water molecule, in yellow. (D) Structural superposition of the PG-binding sites of apo YfiB and YfiR-bound YfiBL43P, the key residues are shown in stick. FIG 0 3 Apo protein_state Apo YfiB is shown in yellow and YfiR-bound YfiBL43P in cyan. (E and F) MST data and analysis for binding affinities of (E) YfiB wild-type and (F) YfiBL43P with PG. (G) The sequence alignment of P. aeruginosa and E. coli sources of YfiB, Pal and the periplasmic domain of OmpA FIG 4 8 YfiB protein Apo YfiB is shown in yellow and YfiR-bound YfiBL43P in cyan. (E and F) MST data and analysis for binding affinities of (E) YfiB wild-type and (F) YfiBL43P with PG. (G) The sequence alignment of P. aeruginosa and E. coli sources of YfiB, Pal and the periplasmic domain of OmpA FIG 32 42 YfiR-bound protein_state Apo YfiB is shown in yellow and YfiR-bound YfiBL43P in cyan. (E and F) MST data and analysis for binding affinities of (E) YfiB wild-type and (F) YfiBL43P with PG. (G) The sequence alignment of P. aeruginosa and E. coli sources of YfiB, Pal and the periplasmic domain of OmpA FIG 43 51 YfiBL43P mutant Apo YfiB is shown in yellow and YfiR-bound YfiBL43P in cyan. (E and F) MST data and analysis for binding affinities of (E) YfiB wild-type and (F) YfiBL43P with PG. (G) The sequence alignment of P. aeruginosa and E. coli sources of YfiB, Pal and the periplasmic domain of OmpA FIG 71 74 MST experimental_method Apo YfiB is shown in yellow and YfiR-bound YfiBL43P in cyan. (E and F) MST data and analysis for binding affinities of (E) YfiB wild-type and (F) YfiBL43P with PG. (G) The sequence alignment of P. aeruginosa and E. coli sources of YfiB, Pal and the periplasmic domain of OmpA FIG 97 115 binding affinities evidence Apo YfiB is shown in yellow and YfiR-bound YfiBL43P in cyan. (E and F) MST data and analysis for binding affinities of (E) YfiB wild-type and (F) YfiBL43P with PG. (G) The sequence alignment of P. aeruginosa and E. coli sources of YfiB, Pal and the periplasmic domain of OmpA FIG 123 127 YfiB protein Apo YfiB is shown in yellow and YfiR-bound YfiBL43P in cyan. (E and F) MST data and analysis for binding affinities of (E) YfiB wild-type and (F) YfiBL43P with PG. (G) The sequence alignment of P. aeruginosa and E. coli sources of YfiB, Pal and the periplasmic domain of OmpA FIG 128 137 wild-type protein_state Apo YfiB is shown in yellow and YfiR-bound YfiBL43P in cyan. (E and F) MST data and analysis for binding affinities of (E) YfiB wild-type and (F) YfiBL43P with PG. (G) The sequence alignment of P. aeruginosa and E. coli sources of YfiB, Pal and the periplasmic domain of OmpA FIG 146 154 YfiBL43P mutant Apo YfiB is shown in yellow and YfiR-bound YfiBL43P in cyan. (E and F) MST data and analysis for binding affinities of (E) YfiB wild-type and (F) YfiBL43P with PG. (G) The sequence alignment of P. aeruginosa and E. coli sources of YfiB, Pal and the periplasmic domain of OmpA FIG 160 162 PG chemical Apo YfiB is shown in yellow and YfiR-bound YfiBL43P in cyan. (E and F) MST data and analysis for binding affinities of (E) YfiB wild-type and (F) YfiBL43P with PG. (G) The sequence alignment of P. aeruginosa and E. coli sources of YfiB, Pal and the periplasmic domain of OmpA FIG 172 190 sequence alignment experimental_method Apo YfiB is shown in yellow and YfiR-bound YfiBL43P in cyan. (E and F) MST data and analysis for binding affinities of (E) YfiB wild-type and (F) YfiBL43P with PG. (G) The sequence alignment of P. aeruginosa and E. coli sources of YfiB, Pal and the periplasmic domain of OmpA FIG 194 207 P. aeruginosa species Apo YfiB is shown in yellow and YfiR-bound YfiBL43P in cyan. (E and F) MST data and analysis for binding affinities of (E) YfiB wild-type and (F) YfiBL43P with PG. (G) The sequence alignment of P. aeruginosa and E. coli sources of YfiB, Pal and the periplasmic domain of OmpA FIG 212 219 E. coli species Apo YfiB is shown in yellow and YfiR-bound YfiBL43P in cyan. (E and F) MST data and analysis for binding affinities of (E) YfiB wild-type and (F) YfiBL43P with PG. (G) The sequence alignment of P. aeruginosa and E. coli sources of YfiB, Pal and the periplasmic domain of OmpA FIG 231 235 YfiB protein Apo YfiB is shown in yellow and YfiR-bound YfiBL43P in cyan. (E and F) MST data and analysis for binding affinities of (E) YfiB wild-type and (F) YfiBL43P with PG. (G) The sequence alignment of P. aeruginosa and E. coli sources of YfiB, Pal and the periplasmic domain of OmpA FIG 237 240 Pal protein_type Apo YfiB is shown in yellow and YfiR-bound YfiBL43P in cyan. (E and F) MST data and analysis for binding affinities of (E) YfiB wild-type and (F) YfiBL43P with PG. (G) The sequence alignment of P. aeruginosa and E. coli sources of YfiB, Pal and the periplasmic domain of OmpA FIG 249 267 periplasmic domain structure_element Apo YfiB is shown in yellow and YfiR-bound YfiBL43P in cyan. (E and F) MST data and analysis for binding affinities of (E) YfiB wild-type and (F) YfiBL43P with PG. (G) The sequence alignment of P. aeruginosa and E. coli sources of YfiB, Pal and the periplasmic domain of OmpA FIG 271 275 OmpA protein_type Apo YfiB is shown in yellow and YfiR-bound YfiBL43P in cyan. (E and F) MST data and analysis for binding affinities of (E) YfiB wild-type and (F) YfiBL43P with PG. (G) The sequence alignment of P. aeruginosa and E. coli sources of YfiB, Pal and the periplasmic domain of OmpA FIG 0 25 PG-associated lipoprotein protein_type PG-associated lipoprotein (Pal) is highly conserved in Gram-negative bacteria and anchors to the outer membrane through an N-terminal lipid attachment and to PG layer through its periplasmic domain, which is implicated in maintaining outer membrane integrity. RESULTS 27 30 Pal protein_type PG-associated lipoprotein (Pal) is highly conserved in Gram-negative bacteria and anchors to the outer membrane through an N-terminal lipid attachment and to PG layer through its periplasmic domain, which is implicated in maintaining outer membrane integrity. RESULTS 35 51 highly conserved protein_state PG-associated lipoprotein (Pal) is highly conserved in Gram-negative bacteria and anchors to the outer membrane through an N-terminal lipid attachment and to PG layer through its periplasmic domain, which is implicated in maintaining outer membrane integrity. RESULTS 55 77 Gram-negative bacteria taxonomy_domain PG-associated lipoprotein (Pal) is highly conserved in Gram-negative bacteria and anchors to the outer membrane through an N-terminal lipid attachment and to PG layer through its periplasmic domain, which is implicated in maintaining outer membrane integrity. RESULTS 158 160 PG chemical PG-associated lipoprotein (Pal) is highly conserved in Gram-negative bacteria and anchors to the outer membrane through an N-terminal lipid attachment and to PG layer through its periplasmic domain, which is implicated in maintaining outer membrane integrity. RESULTS 179 197 periplasmic domain structure_element PG-associated lipoprotein (Pal) is highly conserved in Gram-negative bacteria and anchors to the outer membrane through an N-terminal lipid attachment and to PG layer through its periplasmic domain, which is implicated in maintaining outer membrane integrity. RESULTS 9 26 homology modeling experimental_method Previous homology modeling studies suggested that YfiB contains a Pal-like PG-binding site (Parsons et al.,), and the mutation of two residues at this site, D102 and G105, reduces the ability for biofilm formation and surface attachment (Malone et al.,). RESULTS 50 54 YfiB protein Previous homology modeling studies suggested that YfiB contains a Pal-like PG-binding site (Parsons et al.,), and the mutation of two residues at this site, D102 and G105, reduces the ability for biofilm formation and surface attachment (Malone et al.,). RESULTS 66 90 Pal-like PG-binding site site Previous homology modeling studies suggested that YfiB contains a Pal-like PG-binding site (Parsons et al.,), and the mutation of two residues at this site, D102 and G105, reduces the ability for biofilm formation and surface attachment (Malone et al.,). RESULTS 118 142 mutation of two residues experimental_method Previous homology modeling studies suggested that YfiB contains a Pal-like PG-binding site (Parsons et al.,), and the mutation of two residues at this site, D102 and G105, reduces the ability for biofilm formation and surface attachment (Malone et al.,). RESULTS 157 161 D102 residue_name_number Previous homology modeling studies suggested that YfiB contains a Pal-like PG-binding site (Parsons et al.,), and the mutation of two residues at this site, D102 and G105, reduces the ability for biofilm formation and surface attachment (Malone et al.,). RESULTS 166 170 G105 residue_name_number Previous homology modeling studies suggested that YfiB contains a Pal-like PG-binding site (Parsons et al.,), and the mutation of two residues at this site, D102 and G105, reduces the ability for biofilm formation and surface attachment (Malone et al.,). RESULTS 7 16 YfiB-YfiR complex_assembly In the YfiB-YfiR complex, one sulfate ion is found at the bottom of each YfiBL43P molecule (Fig. 3A) and forms a strong hydrogen bond with D102 of YfiBL43P (Fig. 4A and 4C). RESULTS 30 37 sulfate chemical In the YfiB-YfiR complex, one sulfate ion is found at the bottom of each YfiBL43P molecule (Fig. 3A) and forms a strong hydrogen bond with D102 of YfiBL43P (Fig. 4A and 4C). RESULTS 73 81 YfiBL43P mutant In the YfiB-YfiR complex, one sulfate ion is found at the bottom of each YfiBL43P molecule (Fig. 3A) and forms a strong hydrogen bond with D102 of YfiBL43P (Fig. 4A and 4C). RESULTS 120 133 hydrogen bond bond_interaction In the YfiB-YfiR complex, one sulfate ion is found at the bottom of each YfiBL43P molecule (Fig. 3A) and forms a strong hydrogen bond with D102 of YfiBL43P (Fig. 4A and 4C). RESULTS 139 143 D102 residue_name_number In the YfiB-YfiR complex, one sulfate ion is found at the bottom of each YfiBL43P molecule (Fig. 3A) and forms a strong hydrogen bond with D102 of YfiBL43P (Fig. 4A and 4C). RESULTS 147 155 YfiBL43P mutant In the YfiB-YfiR complex, one sulfate ion is found at the bottom of each YfiBL43P molecule (Fig. 3A) and forms a strong hydrogen bond with D102 of YfiBL43P (Fig. 4A and 4C). RESULTS 0 24 Structural superposition experimental_method Structural superposition between YfiBL43P and Haemophilus influenzae Pal complexed with biosynthetic peptidoglycan precursor (PG-P), UDP-N-acetylmuramyl-L-Ala-α-D-Glu-m-Dap-D-Ala-D-Ala (m-Dap is meso-diaminopimelate) (PDB code: 2aiz) (Parsons et al.,), revealed that the sulfate ion is located at the position of the m-Dap5 ϵ-carboxylate group in the Pal/PG-P complex (Fig. 4A). RESULTS 33 41 YfiBL43P mutant Structural superposition between YfiBL43P and Haemophilus influenzae Pal complexed with biosynthetic peptidoglycan precursor (PG-P), UDP-N-acetylmuramyl-L-Ala-α-D-Glu-m-Dap-D-Ala-D-Ala (m-Dap is meso-diaminopimelate) (PDB code: 2aiz) (Parsons et al.,), revealed that the sulfate ion is located at the position of the m-Dap5 ϵ-carboxylate group in the Pal/PG-P complex (Fig. 4A). RESULTS 46 68 Haemophilus influenzae species Structural superposition between YfiBL43P and Haemophilus influenzae Pal complexed with biosynthetic peptidoglycan precursor (PG-P), UDP-N-acetylmuramyl-L-Ala-α-D-Glu-m-Dap-D-Ala-D-Ala (m-Dap is meso-diaminopimelate) (PDB code: 2aiz) (Parsons et al.,), revealed that the sulfate ion is located at the position of the m-Dap5 ϵ-carboxylate group in the Pal/PG-P complex (Fig. 4A). RESULTS 69 72 Pal protein_type Structural superposition between YfiBL43P and Haemophilus influenzae Pal complexed with biosynthetic peptidoglycan precursor (PG-P), UDP-N-acetylmuramyl-L-Ala-α-D-Glu-m-Dap-D-Ala-D-Ala (m-Dap is meso-diaminopimelate) (PDB code: 2aiz) (Parsons et al.,), revealed that the sulfate ion is located at the position of the m-Dap5 ϵ-carboxylate group in the Pal/PG-P complex (Fig. 4A). RESULTS 73 87 complexed with protein_state Structural superposition between YfiBL43P and Haemophilus influenzae Pal complexed with biosynthetic peptidoglycan precursor (PG-P), UDP-N-acetylmuramyl-L-Ala-α-D-Glu-m-Dap-D-Ala-D-Ala (m-Dap is meso-diaminopimelate) (PDB code: 2aiz) (Parsons et al.,), revealed that the sulfate ion is located at the position of the m-Dap5 ϵ-carboxylate group in the Pal/PG-P complex (Fig. 4A). RESULTS 101 124 peptidoglycan precursor chemical Structural superposition between YfiBL43P and Haemophilus influenzae Pal complexed with biosynthetic peptidoglycan precursor (PG-P), UDP-N-acetylmuramyl-L-Ala-α-D-Glu-m-Dap-D-Ala-D-Ala (m-Dap is meso-diaminopimelate) (PDB code: 2aiz) (Parsons et al.,), revealed that the sulfate ion is located at the position of the m-Dap5 ϵ-carboxylate group in the Pal/PG-P complex (Fig. 4A). RESULTS 126 130 PG-P chemical Structural superposition between YfiBL43P and Haemophilus influenzae Pal complexed with biosynthetic peptidoglycan precursor (PG-P), UDP-N-acetylmuramyl-L-Ala-α-D-Glu-m-Dap-D-Ala-D-Ala (m-Dap is meso-diaminopimelate) (PDB code: 2aiz) (Parsons et al.,), revealed that the sulfate ion is located at the position of the m-Dap5 ϵ-carboxylate group in the Pal/PG-P complex (Fig. 4A). RESULTS 133 184 UDP-N-acetylmuramyl-L-Ala-α-D-Glu-m-Dap-D-Ala-D-Ala chemical Structural superposition between YfiBL43P and Haemophilus influenzae Pal complexed with biosynthetic peptidoglycan precursor (PG-P), UDP-N-acetylmuramyl-L-Ala-α-D-Glu-m-Dap-D-Ala-D-Ala (m-Dap is meso-diaminopimelate) (PDB code: 2aiz) (Parsons et al.,), revealed that the sulfate ion is located at the position of the m-Dap5 ϵ-carboxylate group in the Pal/PG-P complex (Fig. 4A). RESULTS 186 191 m-Dap chemical Structural superposition between YfiBL43P and Haemophilus influenzae Pal complexed with biosynthetic peptidoglycan precursor (PG-P), UDP-N-acetylmuramyl-L-Ala-α-D-Glu-m-Dap-D-Ala-D-Ala (m-Dap is meso-diaminopimelate) (PDB code: 2aiz) (Parsons et al.,), revealed that the sulfate ion is located at the position of the m-Dap5 ϵ-carboxylate group in the Pal/PG-P complex (Fig. 4A). RESULTS 195 215 meso-diaminopimelate chemical Structural superposition between YfiBL43P and Haemophilus influenzae Pal complexed with biosynthetic peptidoglycan precursor (PG-P), UDP-N-acetylmuramyl-L-Ala-α-D-Glu-m-Dap-D-Ala-D-Ala (m-Dap is meso-diaminopimelate) (PDB code: 2aiz) (Parsons et al.,), revealed that the sulfate ion is located at the position of the m-Dap5 ϵ-carboxylate group in the Pal/PG-P complex (Fig. 4A). RESULTS 271 278 sulfate chemical Structural superposition between YfiBL43P and Haemophilus influenzae Pal complexed with biosynthetic peptidoglycan precursor (PG-P), UDP-N-acetylmuramyl-L-Ala-α-D-Glu-m-Dap-D-Ala-D-Ala (m-Dap is meso-diaminopimelate) (PDB code: 2aiz) (Parsons et al.,), revealed that the sulfate ion is located at the position of the m-Dap5 ϵ-carboxylate group in the Pal/PG-P complex (Fig. 4A). RESULTS 317 337 m-Dap5 ϵ-carboxylate chemical Structural superposition between YfiBL43P and Haemophilus influenzae Pal complexed with biosynthetic peptidoglycan precursor (PG-P), UDP-N-acetylmuramyl-L-Ala-α-D-Glu-m-Dap-D-Ala-D-Ala (m-Dap is meso-diaminopimelate) (PDB code: 2aiz) (Parsons et al.,), revealed that the sulfate ion is located at the position of the m-Dap5 ϵ-carboxylate group in the Pal/PG-P complex (Fig. 4A). RESULTS 351 359 Pal/PG-P complex_assembly Structural superposition between YfiBL43P and Haemophilus influenzae Pal complexed with biosynthetic peptidoglycan precursor (PG-P), UDP-N-acetylmuramyl-L-Ala-α-D-Glu-m-Dap-D-Ala-D-Ala (m-Dap is meso-diaminopimelate) (PDB code: 2aiz) (Parsons et al.,), revealed that the sulfate ion is located at the position of the m-Dap5 ϵ-carboxylate group in the Pal/PG-P complex (Fig. 4A). RESULTS 7 15 Pal/PG-P complex_assembly In the Pal/PG-P complex structure, the m-Dap5 ϵ-carboxylate group interacts with the side-chain atoms of D71 and the main-chain amide of D37 (Fig. 4B). RESULTS 24 33 structure evidence In the Pal/PG-P complex structure, the m-Dap5 ϵ-carboxylate group interacts with the side-chain atoms of D71 and the main-chain amide of D37 (Fig. 4B). RESULTS 39 59 m-Dap5 ϵ-carboxylate chemical In the Pal/PG-P complex structure, the m-Dap5 ϵ-carboxylate group interacts with the side-chain atoms of D71 and the main-chain amide of D37 (Fig. 4B). RESULTS 105 108 D71 residue_name_number In the Pal/PG-P complex structure, the m-Dap5 ϵ-carboxylate group interacts with the side-chain atoms of D71 and the main-chain amide of D37 (Fig. 4B). RESULTS 137 140 D37 residue_name_number In the Pal/PG-P complex structure, the m-Dap5 ϵ-carboxylate group interacts with the side-chain atoms of D71 and the main-chain amide of D37 (Fig. 4B). RESULTS 18 28 YfiR-bound protein_state Similarly, in the YfiR-bound YfiBL43P structure, the sulfate ion interacts with the side-chain atoms of D102 (corresponding to D71 in Pal) and R117 (corresponding to R86 in Pal) and the main-chain amide of N68 (corresponding to D37 in Pal). RESULTS 29 37 YfiBL43P mutant Similarly, in the YfiR-bound YfiBL43P structure, the sulfate ion interacts with the side-chain atoms of D102 (corresponding to D71 in Pal) and R117 (corresponding to R86 in Pal) and the main-chain amide of N68 (corresponding to D37 in Pal). RESULTS 38 47 structure evidence Similarly, in the YfiR-bound YfiBL43P structure, the sulfate ion interacts with the side-chain atoms of D102 (corresponding to D71 in Pal) and R117 (corresponding to R86 in Pal) and the main-chain amide of N68 (corresponding to D37 in Pal). RESULTS 53 60 sulfate chemical Similarly, in the YfiR-bound YfiBL43P structure, the sulfate ion interacts with the side-chain atoms of D102 (corresponding to D71 in Pal) and R117 (corresponding to R86 in Pal) and the main-chain amide of N68 (corresponding to D37 in Pal). RESULTS 104 108 D102 residue_name_number Similarly, in the YfiR-bound YfiBL43P structure, the sulfate ion interacts with the side-chain atoms of D102 (corresponding to D71 in Pal) and R117 (corresponding to R86 in Pal) and the main-chain amide of N68 (corresponding to D37 in Pal). RESULTS 127 130 D71 residue_name_number Similarly, in the YfiR-bound YfiBL43P structure, the sulfate ion interacts with the side-chain atoms of D102 (corresponding to D71 in Pal) and R117 (corresponding to R86 in Pal) and the main-chain amide of N68 (corresponding to D37 in Pal). RESULTS 134 137 Pal protein_type Similarly, in the YfiR-bound YfiBL43P structure, the sulfate ion interacts with the side-chain atoms of D102 (corresponding to D71 in Pal) and R117 (corresponding to R86 in Pal) and the main-chain amide of N68 (corresponding to D37 in Pal). RESULTS 143 147 R117 residue_name_number Similarly, in the YfiR-bound YfiBL43P structure, the sulfate ion interacts with the side-chain atoms of D102 (corresponding to D71 in Pal) and R117 (corresponding to R86 in Pal) and the main-chain amide of N68 (corresponding to D37 in Pal). RESULTS 166 169 R86 residue_name_number Similarly, in the YfiR-bound YfiBL43P structure, the sulfate ion interacts with the side-chain atoms of D102 (corresponding to D71 in Pal) and R117 (corresponding to R86 in Pal) and the main-chain amide of N68 (corresponding to D37 in Pal). RESULTS 173 176 Pal protein_type Similarly, in the YfiR-bound YfiBL43P structure, the sulfate ion interacts with the side-chain atoms of D102 (corresponding to D71 in Pal) and R117 (corresponding to R86 in Pal) and the main-chain amide of N68 (corresponding to D37 in Pal). RESULTS 206 209 N68 residue_name_number Similarly, in the YfiR-bound YfiBL43P structure, the sulfate ion interacts with the side-chain atoms of D102 (corresponding to D71 in Pal) and R117 (corresponding to R86 in Pal) and the main-chain amide of N68 (corresponding to D37 in Pal). RESULTS 228 231 D37 residue_name_number Similarly, in the YfiR-bound YfiBL43P structure, the sulfate ion interacts with the side-chain atoms of D102 (corresponding to D71 in Pal) and R117 (corresponding to R86 in Pal) and the main-chain amide of N68 (corresponding to D37 in Pal). RESULTS 235 238 Pal protein_type Similarly, in the YfiR-bound YfiBL43P structure, the sulfate ion interacts with the side-chain atoms of D102 (corresponding to D71 in Pal) and R117 (corresponding to R86 in Pal) and the main-chain amide of N68 (corresponding to D37 in Pal). RESULTS 12 17 water chemical Moreover, a water molecule was found to bridge the sulfate ion and the side chains of N67 and D102, strengthening the hydrogen bond network (Fig. 4C). RESULTS 51 58 sulfate chemical Moreover, a water molecule was found to bridge the sulfate ion and the side chains of N67 and D102, strengthening the hydrogen bond network (Fig. 4C). RESULTS 86 89 N67 residue_name_number Moreover, a water molecule was found to bridge the sulfate ion and the side chains of N67 and D102, strengthening the hydrogen bond network (Fig. 4C). RESULTS 94 98 D102 residue_name_number Moreover, a water molecule was found to bridge the sulfate ion and the side chains of N67 and D102, strengthening the hydrogen bond network (Fig. 4C). RESULTS 118 139 hydrogen bond network site Moreover, a water molecule was found to bridge the sulfate ion and the side chains of N67 and D102, strengthening the hydrogen bond network (Fig. 4C). RESULTS 13 31 sequence alignment experimental_method In addition, sequence alignment of YfiB with Pal and the periplasmic domain of OmpA (proteins containing PG-binding site) showed that N68 and D102 are highly conserved (Fig. 4G, blue stars), suggesting that these residues contribute to the PG-binding ability of YfiB. RESULTS 35 39 YfiB protein In addition, sequence alignment of YfiB with Pal and the periplasmic domain of OmpA (proteins containing PG-binding site) showed that N68 and D102 are highly conserved (Fig. 4G, blue stars), suggesting that these residues contribute to the PG-binding ability of YfiB. RESULTS 45 48 Pal protein_type In addition, sequence alignment of YfiB with Pal and the periplasmic domain of OmpA (proteins containing PG-binding site) showed that N68 and D102 are highly conserved (Fig. 4G, blue stars), suggesting that these residues contribute to the PG-binding ability of YfiB. RESULTS 57 75 periplasmic domain structure_element In addition, sequence alignment of YfiB with Pal and the periplasmic domain of OmpA (proteins containing PG-binding site) showed that N68 and D102 are highly conserved (Fig. 4G, blue stars), suggesting that these residues contribute to the PG-binding ability of YfiB. RESULTS 79 83 OmpA protein_type In addition, sequence alignment of YfiB with Pal and the periplasmic domain of OmpA (proteins containing PG-binding site) showed that N68 and D102 are highly conserved (Fig. 4G, blue stars), suggesting that these residues contribute to the PG-binding ability of YfiB. RESULTS 105 120 PG-binding site site In addition, sequence alignment of YfiB with Pal and the periplasmic domain of OmpA (proteins containing PG-binding site) showed that N68 and D102 are highly conserved (Fig. 4G, blue stars), suggesting that these residues contribute to the PG-binding ability of YfiB. RESULTS 134 137 N68 residue_name_number In addition, sequence alignment of YfiB with Pal and the periplasmic domain of OmpA (proteins containing PG-binding site) showed that N68 and D102 are highly conserved (Fig. 4G, blue stars), suggesting that these residues contribute to the PG-binding ability of YfiB. RESULTS 142 146 D102 residue_name_number In addition, sequence alignment of YfiB with Pal and the periplasmic domain of OmpA (proteins containing PG-binding site) showed that N68 and D102 are highly conserved (Fig. 4G, blue stars), suggesting that these residues contribute to the PG-binding ability of YfiB. RESULTS 151 167 highly conserved protein_state In addition, sequence alignment of YfiB with Pal and the periplasmic domain of OmpA (proteins containing PG-binding site) showed that N68 and D102 are highly conserved (Fig. 4G, blue stars), suggesting that these residues contribute to the PG-binding ability of YfiB. RESULTS 262 266 YfiB protein In addition, sequence alignment of YfiB with Pal and the periplasmic domain of OmpA (proteins containing PG-binding site) showed that N68 and D102 are highly conserved (Fig. 4G, blue stars), suggesting that these residues contribute to the PG-binding ability of YfiB. RESULTS 15 28 superposition experimental_method Interestingly, superposition of apo YfiB with YfiR-bound YfiBL43P revealed that the PG-binding region is largely altered mainly due to different conformation of the N68 containing loop. RESULTS 32 35 apo protein_state Interestingly, superposition of apo YfiB with YfiR-bound YfiBL43P revealed that the PG-binding region is largely altered mainly due to different conformation of the N68 containing loop. RESULTS 36 40 YfiB protein Interestingly, superposition of apo YfiB with YfiR-bound YfiBL43P revealed that the PG-binding region is largely altered mainly due to different conformation of the N68 containing loop. RESULTS 46 56 YfiR-bound protein_state Interestingly, superposition of apo YfiB with YfiR-bound YfiBL43P revealed that the PG-binding region is largely altered mainly due to different conformation of the N68 containing loop. RESULTS 57 65 YfiBL43P mutant Interestingly, superposition of apo YfiB with YfiR-bound YfiBL43P revealed that the PG-binding region is largely altered mainly due to different conformation of the N68 containing loop. RESULTS 84 101 PG-binding region site Interestingly, superposition of apo YfiB with YfiR-bound YfiBL43P revealed that the PG-binding region is largely altered mainly due to different conformation of the N68 containing loop. RESULTS 135 157 different conformation protein_state Interestingly, superposition of apo YfiB with YfiR-bound YfiBL43P revealed that the PG-binding region is largely altered mainly due to different conformation of the N68 containing loop. RESULTS 165 168 N68 residue_name_number Interestingly, superposition of apo YfiB with YfiR-bound YfiBL43P revealed that the PG-binding region is largely altered mainly due to different conformation of the N68 containing loop. RESULTS 180 184 loop structure_element Interestingly, superposition of apo YfiB with YfiR-bound YfiBL43P revealed that the PG-binding region is largely altered mainly due to different conformation of the N68 containing loop. RESULTS 12 20 YfiBL43P mutant Compared to YfiBL43P, the N68-containing loop of the apo YfiB flips away about 7 Å, and D102 and R117 swing slightly outward; thus, the PG-binding pocket is enlarged with no sulfate ion or water bound (Fig. 4D). RESULTS 26 29 N68 residue_name_number Compared to YfiBL43P, the N68-containing loop of the apo YfiB flips away about 7 Å, and D102 and R117 swing slightly outward; thus, the PG-binding pocket is enlarged with no sulfate ion or water bound (Fig. 4D). RESULTS 41 45 loop structure_element Compared to YfiBL43P, the N68-containing loop of the apo YfiB flips away about 7 Å, and D102 and R117 swing slightly outward; thus, the PG-binding pocket is enlarged with no sulfate ion or water bound (Fig. 4D). RESULTS 53 56 apo protein_state Compared to YfiBL43P, the N68-containing loop of the apo YfiB flips away about 7 Å, and D102 and R117 swing slightly outward; thus, the PG-binding pocket is enlarged with no sulfate ion or water bound (Fig. 4D). RESULTS 57 61 YfiB protein Compared to YfiBL43P, the N68-containing loop of the apo YfiB flips away about 7 Å, and D102 and R117 swing slightly outward; thus, the PG-binding pocket is enlarged with no sulfate ion or water bound (Fig. 4D). RESULTS 88 92 D102 residue_name_number Compared to YfiBL43P, the N68-containing loop of the apo YfiB flips away about 7 Å, and D102 and R117 swing slightly outward; thus, the PG-binding pocket is enlarged with no sulfate ion or water bound (Fig. 4D). RESULTS 97 101 R117 residue_name_number Compared to YfiBL43P, the N68-containing loop of the apo YfiB flips away about 7 Å, and D102 and R117 swing slightly outward; thus, the PG-binding pocket is enlarged with no sulfate ion or water bound (Fig. 4D). RESULTS 136 153 PG-binding pocket site Compared to YfiBL43P, the N68-containing loop of the apo YfiB flips away about 7 Å, and D102 and R117 swing slightly outward; thus, the PG-binding pocket is enlarged with no sulfate ion or water bound (Fig. 4D). RESULTS 174 181 sulfate chemical Compared to YfiBL43P, the N68-containing loop of the apo YfiB flips away about 7 Å, and D102 and R117 swing slightly outward; thus, the PG-binding pocket is enlarged with no sulfate ion or water bound (Fig. 4D). RESULTS 189 194 water chemical Compared to YfiBL43P, the N68-containing loop of the apo YfiB flips away about 7 Å, and D102 and R117 swing slightly outward; thus, the PG-binding pocket is enlarged with no sulfate ion or water bound (Fig. 4D). RESULTS 32 34 PG chemical Therefore, we proposed that the PG-binding ability of inactive YfiB might be weaker than that of active YfiB. To validate this, we performed a microscale thermophoresis (MST) assay to measure the binding affinities of PG to wild-type YfiB and YfiBL43P, respectively. RESULTS 54 62 inactive protein_state Therefore, we proposed that the PG-binding ability of inactive YfiB might be weaker than that of active YfiB. To validate this, we performed a microscale thermophoresis (MST) assay to measure the binding affinities of PG to wild-type YfiB and YfiBL43P, respectively. RESULTS 63 67 YfiB protein Therefore, we proposed that the PG-binding ability of inactive YfiB might be weaker than that of active YfiB. To validate this, we performed a microscale thermophoresis (MST) assay to measure the binding affinities of PG to wild-type YfiB and YfiBL43P, respectively. RESULTS 97 103 active protein_state Therefore, we proposed that the PG-binding ability of inactive YfiB might be weaker than that of active YfiB. To validate this, we performed a microscale thermophoresis (MST) assay to measure the binding affinities of PG to wild-type YfiB and YfiBL43P, respectively. RESULTS 104 108 YfiB protein Therefore, we proposed that the PG-binding ability of inactive YfiB might be weaker than that of active YfiB. To validate this, we performed a microscale thermophoresis (MST) assay to measure the binding affinities of PG to wild-type YfiB and YfiBL43P, respectively. RESULTS 143 168 microscale thermophoresis experimental_method Therefore, we proposed that the PG-binding ability of inactive YfiB might be weaker than that of active YfiB. To validate this, we performed a microscale thermophoresis (MST) assay to measure the binding affinities of PG to wild-type YfiB and YfiBL43P, respectively. RESULTS 170 173 MST experimental_method Therefore, we proposed that the PG-binding ability of inactive YfiB might be weaker than that of active YfiB. To validate this, we performed a microscale thermophoresis (MST) assay to measure the binding affinities of PG to wild-type YfiB and YfiBL43P, respectively. RESULTS 196 214 binding affinities evidence Therefore, we proposed that the PG-binding ability of inactive YfiB might be weaker than that of active YfiB. To validate this, we performed a microscale thermophoresis (MST) assay to measure the binding affinities of PG to wild-type YfiB and YfiBL43P, respectively. RESULTS 218 220 PG chemical Therefore, we proposed that the PG-binding ability of inactive YfiB might be weaker than that of active YfiB. To validate this, we performed a microscale thermophoresis (MST) assay to measure the binding affinities of PG to wild-type YfiB and YfiBL43P, respectively. RESULTS 224 233 wild-type protein_state Therefore, we proposed that the PG-binding ability of inactive YfiB might be weaker than that of active YfiB. To validate this, we performed a microscale thermophoresis (MST) assay to measure the binding affinities of PG to wild-type YfiB and YfiBL43P, respectively. RESULTS 234 238 YfiB protein Therefore, we proposed that the PG-binding ability of inactive YfiB might be weaker than that of active YfiB. To validate this, we performed a microscale thermophoresis (MST) assay to measure the binding affinities of PG to wild-type YfiB and YfiBL43P, respectively. RESULTS 243 251 YfiBL43P mutant Therefore, we proposed that the PG-binding ability of inactive YfiB might be weaker than that of active YfiB. To validate this, we performed a microscale thermophoresis (MST) assay to measure the binding affinities of PG to wild-type YfiB and YfiBL43P, respectively. RESULTS 31 50 PG-binding affinity evidence The results indicated that the PG-binding affinity of YfiBL43P is 65.5 μmol/L, which is about 16-fold stronger than that of wild-type YfiB (Kd = 1.1 mmol/L) (Fig. 4E–F). RESULTS 54 62 YfiBL43P mutant The results indicated that the PG-binding affinity of YfiBL43P is 65.5 μmol/L, which is about 16-fold stronger than that of wild-type YfiB (Kd = 1.1 mmol/L) (Fig. 4E–F). RESULTS 124 133 wild-type protein_state The results indicated that the PG-binding affinity of YfiBL43P is 65.5 μmol/L, which is about 16-fold stronger than that of wild-type YfiB (Kd = 1.1 mmol/L) (Fig. 4E–F). RESULTS 134 138 YfiB protein The results indicated that the PG-binding affinity of YfiBL43P is 65.5 μmol/L, which is about 16-fold stronger than that of wild-type YfiB (Kd = 1.1 mmol/L) (Fig. 4E–F). RESULTS 140 142 Kd evidence The results indicated that the PG-binding affinity of YfiBL43P is 65.5 μmol/L, which is about 16-fold stronger than that of wild-type YfiB (Kd = 1.1 mmol/L) (Fig. 4E–F). RESULTS 31 48 in the absence of protein_state As the experiment is performed in the absence of YfiR, it suggests that an increase in the PG-binding affinity of YfiB is not a result of YfiB-YfiR interaction and is highly coupled to the activation of YfiB characterized by a stretched N-terminal conformation. RESULTS 49 53 YfiR protein As the experiment is performed in the absence of YfiR, it suggests that an increase in the PG-binding affinity of YfiB is not a result of YfiB-YfiR interaction and is highly coupled to the activation of YfiB characterized by a stretched N-terminal conformation. RESULTS 91 110 PG-binding affinity evidence As the experiment is performed in the absence of YfiR, it suggests that an increase in the PG-binding affinity of YfiB is not a result of YfiB-YfiR interaction and is highly coupled to the activation of YfiB characterized by a stretched N-terminal conformation. RESULTS 114 118 YfiB protein As the experiment is performed in the absence of YfiR, it suggests that an increase in the PG-binding affinity of YfiB is not a result of YfiB-YfiR interaction and is highly coupled to the activation of YfiB characterized by a stretched N-terminal conformation. RESULTS 138 147 YfiB-YfiR complex_assembly As the experiment is performed in the absence of YfiR, it suggests that an increase in the PG-binding affinity of YfiB is not a result of YfiB-YfiR interaction and is highly coupled to the activation of YfiB characterized by a stretched N-terminal conformation. RESULTS 203 207 YfiB protein As the experiment is performed in the absence of YfiR, it suggests that an increase in the PG-binding affinity of YfiB is not a result of YfiB-YfiR interaction and is highly coupled to the activation of YfiB characterized by a stretched N-terminal conformation. RESULTS 227 260 stretched N-terminal conformation protein_state As the experiment is performed in the absence of YfiR, it suggests that an increase in the PG-binding affinity of YfiB is not a result of YfiB-YfiR interaction and is highly coupled to the activation of YfiB characterized by a stretched N-terminal conformation. RESULTS 4 21 conserved surface site The conserved surface in YfiR is functional for binding YfiB and YfiN RESULTS 25 29 YfiR protein The conserved surface in YfiR is functional for binding YfiB and YfiN RESULTS 56 60 YfiB protein The conserved surface in YfiR is functional for binding YfiB and YfiN RESULTS 65 69 YfiN protein The conserved surface in YfiR is functional for binding YfiB and YfiN RESULTS 22 36 ConSurf Server experimental_method Calculation using the ConSurf Server (http://consurf.tau.ac.il/), which estimates the evolutionary conservation of amino acid positions and visualizes information on the structure surface, revealed a conserved surface on YfiR that contributes to the interaction with YfiB (Fig. 3E and 3F). RESULTS 86 111 evolutionary conservation evidence Calculation using the ConSurf Server (http://consurf.tau.ac.il/), which estimates the evolutionary conservation of amino acid positions and visualizes information on the structure surface, revealed a conserved surface on YfiR that contributes to the interaction with YfiB (Fig. 3E and 3F). RESULTS 170 187 structure surface site Calculation using the ConSurf Server (http://consurf.tau.ac.il/), which estimates the evolutionary conservation of amino acid positions and visualizes information on the structure surface, revealed a conserved surface on YfiR that contributes to the interaction with YfiB (Fig. 3E and 3F). RESULTS 200 217 conserved surface site Calculation using the ConSurf Server (http://consurf.tau.ac.il/), which estimates the evolutionary conservation of amino acid positions and visualizes information on the structure surface, revealed a conserved surface on YfiR that contributes to the interaction with YfiB (Fig. 3E and 3F). RESULTS 221 225 YfiR protein Calculation using the ConSurf Server (http://consurf.tau.ac.il/), which estimates the evolutionary conservation of amino acid positions and visualizes information on the structure surface, revealed a conserved surface on YfiR that contributes to the interaction with YfiB (Fig. 3E and 3F). RESULTS 267 271 YfiB protein Calculation using the ConSurf Server (http://consurf.tau.ac.il/), which estimates the evolutionary conservation of amino acid positions and visualizes information on the structure surface, revealed a conserved surface on YfiR that contributes to the interaction with YfiB (Fig. 3E and 3F). RESULTS 36 53 conserved surface site Interestingly, the majority of this conserved surface contributes to the interaction with YfiB (Fig. 3E and 3F). RESULTS 90 94 YfiB protein Interestingly, the majority of this conserved surface contributes to the interaction with YfiB (Fig. 3E and 3F). RESULTS 36 40 F151 residue_name_number Malone JG et al. have reported that F151, E163, I169 and Q187, located near the C-terminus of YfiR, comprise a putative YfiN binding site (Malone et al.,). RESULTS 42 46 E163 residue_name_number Malone JG et al. have reported that F151, E163, I169 and Q187, located near the C-terminus of YfiR, comprise a putative YfiN binding site (Malone et al.,). RESULTS 48 52 I169 residue_name_number Malone JG et al. have reported that F151, E163, I169 and Q187, located near the C-terminus of YfiR, comprise a putative YfiN binding site (Malone et al.,). RESULTS 57 61 Q187 residue_name_number Malone JG et al. have reported that F151, E163, I169 and Q187, located near the C-terminus of YfiR, comprise a putative YfiN binding site (Malone et al.,). RESULTS 94 98 YfiR protein Malone JG et al. have reported that F151, E163, I169 and Q187, located near the C-terminus of YfiR, comprise a putative YfiN binding site (Malone et al.,). RESULTS 120 137 YfiN binding site site Malone JG et al. have reported that F151, E163, I169 and Q187, located near the C-terminus of YfiR, comprise a putative YfiN binding site (Malone et al.,). RESULTS 46 63 conserved surface site Interestingly, these residues are part of the conserved surface of YfiR (Fig. 3G). RESULTS 67 71 YfiR protein Interestingly, these residues are part of the conserved surface of YfiR (Fig. 3G). RESULTS 0 4 F151 residue_name_number F151, E163 and I169 form a hydrophobic core while, Q187 is located at the end of the α6 helix. RESULTS 6 10 E163 residue_name_number F151, E163 and I169 form a hydrophobic core while, Q187 is located at the end of the α6 helix. RESULTS 15 19 I169 residue_name_number F151, E163 and I169 form a hydrophobic core while, Q187 is located at the end of the α6 helix. RESULTS 27 43 hydrophobic core site F151, E163 and I169 form a hydrophobic core while, Q187 is located at the end of the α6 helix. RESULTS 51 55 Q187 residue_name_number F151, E163 and I169 form a hydrophobic core while, Q187 is located at the end of the α6 helix. RESULTS 85 93 α6 helix structure_element F151, E163 and I169 form a hydrophobic core while, Q187 is located at the end of the α6 helix. RESULTS 0 4 E163 residue_name_number E163 and I169 are YfiB-interacting residues of YfiR, in which E163 forms a hydrogen bond with R96 of YfiB (Fig. 3D-II) and I169 is involved in forming the L166/I169/V176/P178/L181 hydrophobic core for anchoring F57 of YfiB (Fig. 3D-I(ii)). RESULTS 9 13 I169 residue_name_number E163 and I169 are YfiB-interacting residues of YfiR, in which E163 forms a hydrogen bond with R96 of YfiB (Fig. 3D-II) and I169 is involved in forming the L166/I169/V176/P178/L181 hydrophobic core for anchoring F57 of YfiB (Fig. 3D-I(ii)). RESULTS 18 43 YfiB-interacting residues site E163 and I169 are YfiB-interacting residues of YfiR, in which E163 forms a hydrogen bond with R96 of YfiB (Fig. 3D-II) and I169 is involved in forming the L166/I169/V176/P178/L181 hydrophobic core for anchoring F57 of YfiB (Fig. 3D-I(ii)). RESULTS 47 51 YfiR protein E163 and I169 are YfiB-interacting residues of YfiR, in which E163 forms a hydrogen bond with R96 of YfiB (Fig. 3D-II) and I169 is involved in forming the L166/I169/V176/P178/L181 hydrophobic core for anchoring F57 of YfiB (Fig. 3D-I(ii)). RESULTS 62 66 E163 residue_name_number E163 and I169 are YfiB-interacting residues of YfiR, in which E163 forms a hydrogen bond with R96 of YfiB (Fig. 3D-II) and I169 is involved in forming the L166/I169/V176/P178/L181 hydrophobic core for anchoring F57 of YfiB (Fig. 3D-I(ii)). RESULTS 75 88 hydrogen bond bond_interaction E163 and I169 are YfiB-interacting residues of YfiR, in which E163 forms a hydrogen bond with R96 of YfiB (Fig. 3D-II) and I169 is involved in forming the L166/I169/V176/P178/L181 hydrophobic core for anchoring F57 of YfiB (Fig. 3D-I(ii)). RESULTS 94 97 R96 residue_name_number E163 and I169 are YfiB-interacting residues of YfiR, in which E163 forms a hydrogen bond with R96 of YfiB (Fig. 3D-II) and I169 is involved in forming the L166/I169/V176/P178/L181 hydrophobic core for anchoring F57 of YfiB (Fig. 3D-I(ii)). RESULTS 101 105 YfiB protein E163 and I169 are YfiB-interacting residues of YfiR, in which E163 forms a hydrogen bond with R96 of YfiB (Fig. 3D-II) and I169 is involved in forming the L166/I169/V176/P178/L181 hydrophobic core for anchoring F57 of YfiB (Fig. 3D-I(ii)). RESULTS 123 127 I169 residue_name_number E163 and I169 are YfiB-interacting residues of YfiR, in which E163 forms a hydrogen bond with R96 of YfiB (Fig. 3D-II) and I169 is involved in forming the L166/I169/V176/P178/L181 hydrophobic core for anchoring F57 of YfiB (Fig. 3D-I(ii)). RESULTS 155 159 L166 residue_name_number E163 and I169 are YfiB-interacting residues of YfiR, in which E163 forms a hydrogen bond with R96 of YfiB (Fig. 3D-II) and I169 is involved in forming the L166/I169/V176/P178/L181 hydrophobic core for anchoring F57 of YfiB (Fig. 3D-I(ii)). RESULTS 160 164 I169 residue_name_number E163 and I169 are YfiB-interacting residues of YfiR, in which E163 forms a hydrogen bond with R96 of YfiB (Fig. 3D-II) and I169 is involved in forming the L166/I169/V176/P178/L181 hydrophobic core for anchoring F57 of YfiB (Fig. 3D-I(ii)). RESULTS 165 169 V176 residue_name_number E163 and I169 are YfiB-interacting residues of YfiR, in which E163 forms a hydrogen bond with R96 of YfiB (Fig. 3D-II) and I169 is involved in forming the L166/I169/V176/P178/L181 hydrophobic core for anchoring F57 of YfiB (Fig. 3D-I(ii)). RESULTS 170 174 P178 residue_name_number E163 and I169 are YfiB-interacting residues of YfiR, in which E163 forms a hydrogen bond with R96 of YfiB (Fig. 3D-II) and I169 is involved in forming the L166/I169/V176/P178/L181 hydrophobic core for anchoring F57 of YfiB (Fig. 3D-I(ii)). RESULTS 175 179 L181 residue_name_number E163 and I169 are YfiB-interacting residues of YfiR, in which E163 forms a hydrogen bond with R96 of YfiB (Fig. 3D-II) and I169 is involved in forming the L166/I169/V176/P178/L181 hydrophobic core for anchoring F57 of YfiB (Fig. 3D-I(ii)). RESULTS 180 196 hydrophobic core site E163 and I169 are YfiB-interacting residues of YfiR, in which E163 forms a hydrogen bond with R96 of YfiB (Fig. 3D-II) and I169 is involved in forming the L166/I169/V176/P178/L181 hydrophobic core for anchoring F57 of YfiB (Fig. 3D-I(ii)). RESULTS 211 214 F57 residue_name_number E163 and I169 are YfiB-interacting residues of YfiR, in which E163 forms a hydrogen bond with R96 of YfiB (Fig. 3D-II) and I169 is involved in forming the L166/I169/V176/P178/L181 hydrophobic core for anchoring F57 of YfiB (Fig. 3D-I(ii)). RESULTS 218 222 YfiB protein E163 and I169 are YfiB-interacting residues of YfiR, in which E163 forms a hydrogen bond with R96 of YfiB (Fig. 3D-II) and I169 is involved in forming the L166/I169/V176/P178/L181 hydrophobic core for anchoring F57 of YfiB (Fig. 3D-I(ii)). RESULTS 28 47 YfiB-YfiR interface site Collectively, a part of the YfiB-YfiR interface overlaps with the proposed YfiR-YfiN interface, suggesting alteration in the association-disassociation equilibrium of YfiR-YfiN and hence the ability of YfiB to sequester YfiR. RESULTS 75 94 YfiR-YfiN interface site Collectively, a part of the YfiB-YfiR interface overlaps with the proposed YfiR-YfiN interface, suggesting alteration in the association-disassociation equilibrium of YfiR-YfiN and hence the ability of YfiB to sequester YfiR. RESULTS 167 171 YfiR protein Collectively, a part of the YfiB-YfiR interface overlaps with the proposed YfiR-YfiN interface, suggesting alteration in the association-disassociation equilibrium of YfiR-YfiN and hence the ability of YfiB to sequester YfiR. RESULTS 172 176 YfiN protein Collectively, a part of the YfiB-YfiR interface overlaps with the proposed YfiR-YfiN interface, suggesting alteration in the association-disassociation equilibrium of YfiR-YfiN and hence the ability of YfiB to sequester YfiR. RESULTS 202 206 YfiB protein Collectively, a part of the YfiB-YfiR interface overlaps with the proposed YfiR-YfiN interface, suggesting alteration in the association-disassociation equilibrium of YfiR-YfiN and hence the ability of YfiB to sequester YfiR. RESULTS 220 224 YfiR protein Collectively, a part of the YfiB-YfiR interface overlaps with the proposed YfiR-YfiN interface, suggesting alteration in the association-disassociation equilibrium of YfiR-YfiN and hence the ability of YfiB to sequester YfiR. RESULTS 0 4 YfiR protein YfiR binds small molecules RESULTS 32 36 YfiR protein Previous studies indicated that YfiR constitutes a YfiB-independent sensing device that can activate YfiN in response to the redox status of the periplasm, and we have reported YfiR structures in both the non-oxidized and the oxidized states earlier, revealing that the Cys145-Cys152 disulfide bond plays an essential role in maintaining the correct folding of YfiR (Yang et al.,). RESULTS 51 55 YfiB protein Previous studies indicated that YfiR constitutes a YfiB-independent sensing device that can activate YfiN in response to the redox status of the periplasm, and we have reported YfiR structures in both the non-oxidized and the oxidized states earlier, revealing that the Cys145-Cys152 disulfide bond plays an essential role in maintaining the correct folding of YfiR (Yang et al.,). RESULTS 101 105 YfiN protein Previous studies indicated that YfiR constitutes a YfiB-independent sensing device that can activate YfiN in response to the redox status of the periplasm, and we have reported YfiR structures in both the non-oxidized and the oxidized states earlier, revealing that the Cys145-Cys152 disulfide bond plays an essential role in maintaining the correct folding of YfiR (Yang et al.,). RESULTS 177 181 YfiR protein Previous studies indicated that YfiR constitutes a YfiB-independent sensing device that can activate YfiN in response to the redox status of the periplasm, and we have reported YfiR structures in both the non-oxidized and the oxidized states earlier, revealing that the Cys145-Cys152 disulfide bond plays an essential role in maintaining the correct folding of YfiR (Yang et al.,). RESULTS 182 192 structures evidence Previous studies indicated that YfiR constitutes a YfiB-independent sensing device that can activate YfiN in response to the redox status of the periplasm, and we have reported YfiR structures in both the non-oxidized and the oxidized states earlier, revealing that the Cys145-Cys152 disulfide bond plays an essential role in maintaining the correct folding of YfiR (Yang et al.,). RESULTS 205 217 non-oxidized protein_state Previous studies indicated that YfiR constitutes a YfiB-independent sensing device that can activate YfiN in response to the redox status of the periplasm, and we have reported YfiR structures in both the non-oxidized and the oxidized states earlier, revealing that the Cys145-Cys152 disulfide bond plays an essential role in maintaining the correct folding of YfiR (Yang et al.,). RESULTS 226 234 oxidized protein_state Previous studies indicated that YfiR constitutes a YfiB-independent sensing device that can activate YfiN in response to the redox status of the periplasm, and we have reported YfiR structures in both the non-oxidized and the oxidized states earlier, revealing that the Cys145-Cys152 disulfide bond plays an essential role in maintaining the correct folding of YfiR (Yang et al.,). RESULTS 270 276 Cys145 residue_name_number Previous studies indicated that YfiR constitutes a YfiB-independent sensing device that can activate YfiN in response to the redox status of the periplasm, and we have reported YfiR structures in both the non-oxidized and the oxidized states earlier, revealing that the Cys145-Cys152 disulfide bond plays an essential role in maintaining the correct folding of YfiR (Yang et al.,). RESULTS 277 283 Cys152 residue_name_number Previous studies indicated that YfiR constitutes a YfiB-independent sensing device that can activate YfiN in response to the redox status of the periplasm, and we have reported YfiR structures in both the non-oxidized and the oxidized states earlier, revealing that the Cys145-Cys152 disulfide bond plays an essential role in maintaining the correct folding of YfiR (Yang et al.,). RESULTS 284 298 disulfide bond ptm Previous studies indicated that YfiR constitutes a YfiB-independent sensing device that can activate YfiN in response to the redox status of the periplasm, and we have reported YfiR structures in both the non-oxidized and the oxidized states earlier, revealing that the Cys145-Cys152 disulfide bond plays an essential role in maintaining the correct folding of YfiR (Yang et al.,). RESULTS 361 365 YfiR protein Previous studies indicated that YfiR constitutes a YfiB-independent sensing device that can activate YfiN in response to the redox status of the periplasm, and we have reported YfiR structures in both the non-oxidized and the oxidized states earlier, revealing that the Cys145-Cys152 disulfide bond plays an essential role in maintaining the correct folding of YfiR (Yang et al.,). RESULTS 17 21 YfiR protein However, whether YfiR is involved in other regulatory mechanisms is still an open question. RESULTS 8 18 Structures evidence Overall Structures of VB6-bound and Trp-bound YfiR. (A) Superposition of the overall structures of VB6-bound and Trp-bound YfiR. (B) Close-up views showing the key residues of YfiR that bind VB6 and L-Trp. FIG 22 31 VB6-bound protein_state Overall Structures of VB6-bound and Trp-bound YfiR. (A) Superposition of the overall structures of VB6-bound and Trp-bound YfiR. (B) Close-up views showing the key residues of YfiR that bind VB6 and L-Trp. FIG 36 45 Trp-bound protein_state Overall Structures of VB6-bound and Trp-bound YfiR. (A) Superposition of the overall structures of VB6-bound and Trp-bound YfiR. (B) Close-up views showing the key residues of YfiR that bind VB6 and L-Trp. FIG 46 50 YfiR protein Overall Structures of VB6-bound and Trp-bound YfiR. (A) Superposition of the overall structures of VB6-bound and Trp-bound YfiR. (B) Close-up views showing the key residues of YfiR that bind VB6 and L-Trp. FIG 56 69 Superposition experimental_method Overall Structures of VB6-bound and Trp-bound YfiR. (A) Superposition of the overall structures of VB6-bound and Trp-bound YfiR. (B) Close-up views showing the key residues of YfiR that bind VB6 and L-Trp. FIG 85 95 structures evidence Overall Structures of VB6-bound and Trp-bound YfiR. (A) Superposition of the overall structures of VB6-bound and Trp-bound YfiR. (B) Close-up views showing the key residues of YfiR that bind VB6 and L-Trp. FIG 99 108 VB6-bound protein_state Overall Structures of VB6-bound and Trp-bound YfiR. (A) Superposition of the overall structures of VB6-bound and Trp-bound YfiR. (B) Close-up views showing the key residues of YfiR that bind VB6 and L-Trp. FIG 113 122 Trp-bound protein_state Overall Structures of VB6-bound and Trp-bound YfiR. (A) Superposition of the overall structures of VB6-bound and Trp-bound YfiR. (B) Close-up views showing the key residues of YfiR that bind VB6 and L-Trp. FIG 123 127 YfiR protein Overall Structures of VB6-bound and Trp-bound YfiR. (A) Superposition of the overall structures of VB6-bound and Trp-bound YfiR. (B) Close-up views showing the key residues of YfiR that bind VB6 and L-Trp. FIG 176 180 YfiR protein Overall Structures of VB6-bound and Trp-bound YfiR. (A) Superposition of the overall structures of VB6-bound and Trp-bound YfiR. (B) Close-up views showing the key residues of YfiR that bind VB6 and L-Trp. FIG 191 194 VB6 chemical Overall Structures of VB6-bound and Trp-bound YfiR. (A) Superposition of the overall structures of VB6-bound and Trp-bound YfiR. (B) Close-up views showing the key residues of YfiR that bind VB6 and L-Trp. FIG 199 204 L-Trp chemical Overall Structures of VB6-bound and Trp-bound YfiR. (A) Superposition of the overall structures of VB6-bound and Trp-bound YfiR. (B) Close-up views showing the key residues of YfiR that bind VB6 and L-Trp. FIG 4 22 electron densities evidence The electron densities of VB6 and Trp are countered at 3.0σ and 2.3σ, respectively, in |Fo|-|Fc| maps. (C) Superposition of the hydrophobic pocket of YfiR with VB6, L-Trp and F57 of YfiB FIG 26 29 VB6 chemical The electron densities of VB6 and Trp are countered at 3.0σ and 2.3σ, respectively, in |Fo|-|Fc| maps. (C) Superposition of the hydrophobic pocket of YfiR with VB6, L-Trp and F57 of YfiB FIG 34 37 Trp chemical The electron densities of VB6 and Trp are countered at 3.0σ and 2.3σ, respectively, in |Fo|-|Fc| maps. (C) Superposition of the hydrophobic pocket of YfiR with VB6, L-Trp and F57 of YfiB FIG 87 101 |Fo|-|Fc| maps evidence The electron densities of VB6 and Trp are countered at 3.0σ and 2.3σ, respectively, in |Fo|-|Fc| maps. (C) Superposition of the hydrophobic pocket of YfiR with VB6, L-Trp and F57 of YfiB FIG 107 120 Superposition experimental_method The electron densities of VB6 and Trp are countered at 3.0σ and 2.3σ, respectively, in |Fo|-|Fc| maps. (C) Superposition of the hydrophobic pocket of YfiR with VB6, L-Trp and F57 of YfiB FIG 128 146 hydrophobic pocket site The electron densities of VB6 and Trp are countered at 3.0σ and 2.3σ, respectively, in |Fo|-|Fc| maps. (C) Superposition of the hydrophobic pocket of YfiR with VB6, L-Trp and F57 of YfiB FIG 150 154 YfiR protein The electron densities of VB6 and Trp are countered at 3.0σ and 2.3σ, respectively, in |Fo|-|Fc| maps. (C) Superposition of the hydrophobic pocket of YfiR with VB6, L-Trp and F57 of YfiB FIG 160 163 VB6 chemical The electron densities of VB6 and Trp are countered at 3.0σ and 2.3σ, respectively, in |Fo|-|Fc| maps. (C) Superposition of the hydrophobic pocket of YfiR with VB6, L-Trp and F57 of YfiB FIG 165 170 L-Trp chemical The electron densities of VB6 and Trp are countered at 3.0σ and 2.3σ, respectively, in |Fo|-|Fc| maps. (C) Superposition of the hydrophobic pocket of YfiR with VB6, L-Trp and F57 of YfiB FIG 175 178 F57 residue_name_number The electron densities of VB6 and Trp are countered at 3.0σ and 2.3σ, respectively, in |Fo|-|Fc| maps. (C) Superposition of the hydrophobic pocket of YfiR with VB6, L-Trp and F57 of YfiB FIG 182 186 YfiB protein The electron densities of VB6 and Trp are countered at 3.0σ and 2.3σ, respectively, in |Fo|-|Fc| maps. (C) Superposition of the hydrophobic pocket of YfiR with VB6, L-Trp and F57 of YfiB FIG 16 27 Dali search experimental_method Intriguingly, a Dali search (Holm and Rosenstrom,) indicated that the closest homologs of YfiR shared the characteristic of being able to bind several structurally similar small molecules, such as L-Trp, L-Phe, B-group vitamins and their analogs, encouraging us to test whether YfiR can recognize these molecules. RESULTS 90 94 YfiR protein Intriguingly, a Dali search (Holm and Rosenstrom,) indicated that the closest homologs of YfiR shared the characteristic of being able to bind several structurally similar small molecules, such as L-Trp, L-Phe, B-group vitamins and their analogs, encouraging us to test whether YfiR can recognize these molecules. RESULTS 197 202 L-Trp chemical Intriguingly, a Dali search (Holm and Rosenstrom,) indicated that the closest homologs of YfiR shared the characteristic of being able to bind several structurally similar small molecules, such as L-Trp, L-Phe, B-group vitamins and their analogs, encouraging us to test whether YfiR can recognize these molecules. RESULTS 204 209 L-Phe chemical Intriguingly, a Dali search (Holm and Rosenstrom,) indicated that the closest homologs of YfiR shared the characteristic of being able to bind several structurally similar small molecules, such as L-Trp, L-Phe, B-group vitamins and their analogs, encouraging us to test whether YfiR can recognize these molecules. RESULTS 278 282 YfiR protein Intriguingly, a Dali search (Holm and Rosenstrom,) indicated that the closest homologs of YfiR shared the characteristic of being able to bind several structurally similar small molecules, such as L-Trp, L-Phe, B-group vitamins and their analogs, encouraging us to test whether YfiR can recognize these molecules. RESULTS 21 36 co-crystallized experimental_method For this purpose, we co-crystallized YfiR or soaked YfiR crystals with different small molecules, including L-Trp and B-group vitamins. RESULTS 37 41 YfiR protein For this purpose, we co-crystallized YfiR or soaked YfiR crystals with different small molecules, including L-Trp and B-group vitamins. RESULTS 45 51 soaked experimental_method For this purpose, we co-crystallized YfiR or soaked YfiR crystals with different small molecules, including L-Trp and B-group vitamins. RESULTS 52 56 YfiR protein For this purpose, we co-crystallized YfiR or soaked YfiR crystals with different small molecules, including L-Trp and B-group vitamins. RESULTS 57 65 crystals evidence For this purpose, we co-crystallized YfiR or soaked YfiR crystals with different small molecules, including L-Trp and B-group vitamins. RESULTS 108 113 L-Trp chemical For this purpose, we co-crystallized YfiR or soaked YfiR crystals with different small molecules, including L-Trp and B-group vitamins. RESULTS 30 52 small-molecule density evidence Fortunately, we found obvious small-molecule density in the VB6-bound and Trp-bound YfiR crystal structures (Fig. 5A and 5B), and in both structures, the YfiR dimers resemble the oxidized YfiR structure in which both two disulfide bonds are well formed (Yang et al.,). RESULTS 60 69 VB6-bound protein_state Fortunately, we found obvious small-molecule density in the VB6-bound and Trp-bound YfiR crystal structures (Fig. 5A and 5B), and in both structures, the YfiR dimers resemble the oxidized YfiR structure in which both two disulfide bonds are well formed (Yang et al.,). RESULTS 74 83 Trp-bound protein_state Fortunately, we found obvious small-molecule density in the VB6-bound and Trp-bound YfiR crystal structures (Fig. 5A and 5B), and in both structures, the YfiR dimers resemble the oxidized YfiR structure in which both two disulfide bonds are well formed (Yang et al.,). RESULTS 84 88 YfiR protein Fortunately, we found obvious small-molecule density in the VB6-bound and Trp-bound YfiR crystal structures (Fig. 5A and 5B), and in both structures, the YfiR dimers resemble the oxidized YfiR structure in which both two disulfide bonds are well formed (Yang et al.,). RESULTS 89 107 crystal structures evidence Fortunately, we found obvious small-molecule density in the VB6-bound and Trp-bound YfiR crystal structures (Fig. 5A and 5B), and in both structures, the YfiR dimers resemble the oxidized YfiR structure in which both two disulfide bonds are well formed (Yang et al.,). RESULTS 138 148 structures evidence Fortunately, we found obvious small-molecule density in the VB6-bound and Trp-bound YfiR crystal structures (Fig. 5A and 5B), and in both structures, the YfiR dimers resemble the oxidized YfiR structure in which both two disulfide bonds are well formed (Yang et al.,). RESULTS 154 158 YfiR protein Fortunately, we found obvious small-molecule density in the VB6-bound and Trp-bound YfiR crystal structures (Fig. 5A and 5B), and in both structures, the YfiR dimers resemble the oxidized YfiR structure in which both two disulfide bonds are well formed (Yang et al.,). RESULTS 159 165 dimers oligomeric_state Fortunately, we found obvious small-molecule density in the VB6-bound and Trp-bound YfiR crystal structures (Fig. 5A and 5B), and in both structures, the YfiR dimers resemble the oxidized YfiR structure in which both two disulfide bonds are well formed (Yang et al.,). RESULTS 179 187 oxidized protein_state Fortunately, we found obvious small-molecule density in the VB6-bound and Trp-bound YfiR crystal structures (Fig. 5A and 5B), and in both structures, the YfiR dimers resemble the oxidized YfiR structure in which both two disulfide bonds are well formed (Yang et al.,). RESULTS 188 192 YfiR protein Fortunately, we found obvious small-molecule density in the VB6-bound and Trp-bound YfiR crystal structures (Fig. 5A and 5B), and in both structures, the YfiR dimers resemble the oxidized YfiR structure in which both two disulfide bonds are well formed (Yang et al.,). RESULTS 193 202 structure evidence Fortunately, we found obvious small-molecule density in the VB6-bound and Trp-bound YfiR crystal structures (Fig. 5A and 5B), and in both structures, the YfiR dimers resemble the oxidized YfiR structure in which both two disulfide bonds are well formed (Yang et al.,). RESULTS 221 236 disulfide bonds ptm Fortunately, we found obvious small-molecule density in the VB6-bound and Trp-bound YfiR crystal structures (Fig. 5A and 5B), and in both structures, the YfiR dimers resemble the oxidized YfiR structure in which both two disulfide bonds are well formed (Yang et al.,). RESULTS 23 26 VB6 chemical Functional analysis of VB6 and L-Trp. (A and B) The effect of increasing concentrations of VB6 or L-Trp on YfiBL43P-induced attachment (bars). FIG 31 36 L-Trp chemical Functional analysis of VB6 and L-Trp. (A and B) The effect of increasing concentrations of VB6 or L-Trp on YfiBL43P-induced attachment (bars). FIG 52 87 effect of increasing concentrations experimental_method Functional analysis of VB6 and L-Trp. (A and B) The effect of increasing concentrations of VB6 or L-Trp on YfiBL43P-induced attachment (bars). FIG 91 94 VB6 chemical Functional analysis of VB6 and L-Trp. (A and B) The effect of increasing concentrations of VB6 or L-Trp on YfiBL43P-induced attachment (bars). FIG 98 103 L-Trp chemical Functional analysis of VB6 and L-Trp. (A and B) The effect of increasing concentrations of VB6 or L-Trp on YfiBL43P-induced attachment (bars). FIG 107 115 YfiBL43P mutant Functional analysis of VB6 and L-Trp. (A and B) The effect of increasing concentrations of VB6 or L-Trp on YfiBL43P-induced attachment (bars). FIG 4 28 relative optical density evidence The relative optical density is represented as curves. FIG 0 9 Wild-type protein_state Wild-type YfiB is used as negative control. FIG 10 14 YfiB protein Wild-type YfiB is used as negative control. FIG 10 17 BIAcore experimental_method (C and D) BIAcore data and analysis for binding affinities of (C) VB6 and (D) L-Trp with YfiR. (E–G) ITC data and analysis for titration of (E) YfiB wild-type, (F) YfiBL43P, and (G) YfiBL43P/F57A into YfiR FIG 40 58 binding affinities evidence (C and D) BIAcore data and analysis for binding affinities of (C) VB6 and (D) L-Trp with YfiR. (E–G) ITC data and analysis for titration of (E) YfiB wild-type, (F) YfiBL43P, and (G) YfiBL43P/F57A into YfiR FIG 66 69 VB6 chemical (C and D) BIAcore data and analysis for binding affinities of (C) VB6 and (D) L-Trp with YfiR. (E–G) ITC data and analysis for titration of (E) YfiB wild-type, (F) YfiBL43P, and (G) YfiBL43P/F57A into YfiR FIG 78 83 L-Trp chemical (C and D) BIAcore data and analysis for binding affinities of (C) VB6 and (D) L-Trp with YfiR. (E–G) ITC data and analysis for titration of (E) YfiB wild-type, (F) YfiBL43P, and (G) YfiBL43P/F57A into YfiR FIG 89 93 YfiR protein (C and D) BIAcore data and analysis for binding affinities of (C) VB6 and (D) L-Trp with YfiR. (E–G) ITC data and analysis for titration of (E) YfiB wild-type, (F) YfiBL43P, and (G) YfiBL43P/F57A into YfiR FIG 101 104 ITC experimental_method (C and D) BIAcore data and analysis for binding affinities of (C) VB6 and (D) L-Trp with YfiR. (E–G) ITC data and analysis for titration of (E) YfiB wild-type, (F) YfiBL43P, and (G) YfiBL43P/F57A into YfiR FIG 127 136 titration experimental_method (C and D) BIAcore data and analysis for binding affinities of (C) VB6 and (D) L-Trp with YfiR. (E–G) ITC data and analysis for titration of (E) YfiB wild-type, (F) YfiBL43P, and (G) YfiBL43P/F57A into YfiR FIG 144 148 YfiB protein (C and D) BIAcore data and analysis for binding affinities of (C) VB6 and (D) L-Trp with YfiR. (E–G) ITC data and analysis for titration of (E) YfiB wild-type, (F) YfiBL43P, and (G) YfiBL43P/F57A into YfiR FIG 149 158 wild-type protein_state (C and D) BIAcore data and analysis for binding affinities of (C) VB6 and (D) L-Trp with YfiR. (E–G) ITC data and analysis for titration of (E) YfiB wild-type, (F) YfiBL43P, and (G) YfiBL43P/F57A into YfiR FIG 182 190 YfiBL43P mutant (C and D) BIAcore data and analysis for binding affinities of (C) VB6 and (D) L-Trp with YfiR. (E–G) ITC data and analysis for titration of (E) YfiB wild-type, (F) YfiBL43P, and (G) YfiBL43P/F57A into YfiR FIG 191 195 F57A mutant (C and D) BIAcore data and analysis for binding affinities of (C) VB6 and (D) L-Trp with YfiR. (E–G) ITC data and analysis for titration of (E) YfiB wild-type, (F) YfiBL43P, and (G) YfiBL43P/F57A into YfiR FIG 201 205 YfiR protein (C and D) BIAcore data and analysis for binding affinities of (C) VB6 and (D) L-Trp with YfiR. (E–G) ITC data and analysis for titration of (E) YfiB wild-type, (F) YfiBL43P, and (G) YfiBL43P/F57A into YfiR FIG 0 19 Structural analyses experimental_method Structural analyses revealed that the VB6 and L-Trp molecules are bound at the periphery of the YfiR dimer, but not at the dimer interface. RESULTS 38 41 VB6 chemical Structural analyses revealed that the VB6 and L-Trp molecules are bound at the periphery of the YfiR dimer, but not at the dimer interface. RESULTS 46 51 L-Trp chemical Structural analyses revealed that the VB6 and L-Trp molecules are bound at the periphery of the YfiR dimer, but not at the dimer interface. RESULTS 66 74 bound at protein_state Structural analyses revealed that the VB6 and L-Trp molecules are bound at the periphery of the YfiR dimer, but not at the dimer interface. RESULTS 96 100 YfiR protein Structural analyses revealed that the VB6 and L-Trp molecules are bound at the periphery of the YfiR dimer, but not at the dimer interface. RESULTS 101 106 dimer oligomeric_state Structural analyses revealed that the VB6 and L-Trp molecules are bound at the periphery of the YfiR dimer, but not at the dimer interface. RESULTS 123 138 dimer interface site Structural analyses revealed that the VB6 and L-Trp molecules are bound at the periphery of the YfiR dimer, but not at the dimer interface. RESULTS 15 18 VB6 chemical Interestingly, VB6 and L-Trp were found to occupy the same hydrophobic pocket, formed by L166/I169/V176/P178/L181 of YfiR, which is also a binding pocket for F57 of YfiB, as observed in the YfiB-YfiR complex (Fig. 5C). RESULTS 23 28 L-Trp chemical Interestingly, VB6 and L-Trp were found to occupy the same hydrophobic pocket, formed by L166/I169/V176/P178/L181 of YfiR, which is also a binding pocket for F57 of YfiB, as observed in the YfiB-YfiR complex (Fig. 5C). RESULTS 59 77 hydrophobic pocket site Interestingly, VB6 and L-Trp were found to occupy the same hydrophobic pocket, formed by L166/I169/V176/P178/L181 of YfiR, which is also a binding pocket for F57 of YfiB, as observed in the YfiB-YfiR complex (Fig. 5C). RESULTS 89 93 L166 residue_name_number Interestingly, VB6 and L-Trp were found to occupy the same hydrophobic pocket, formed by L166/I169/V176/P178/L181 of YfiR, which is also a binding pocket for F57 of YfiB, as observed in the YfiB-YfiR complex (Fig. 5C). RESULTS 94 98 I169 residue_name_number Interestingly, VB6 and L-Trp were found to occupy the same hydrophobic pocket, formed by L166/I169/V176/P178/L181 of YfiR, which is also a binding pocket for F57 of YfiB, as observed in the YfiB-YfiR complex (Fig. 5C). RESULTS 99 103 V176 residue_name_number Interestingly, VB6 and L-Trp were found to occupy the same hydrophobic pocket, formed by L166/I169/V176/P178/L181 of YfiR, which is also a binding pocket for F57 of YfiB, as observed in the YfiB-YfiR complex (Fig. 5C). RESULTS 104 108 P178 residue_name_number Interestingly, VB6 and L-Trp were found to occupy the same hydrophobic pocket, formed by L166/I169/V176/P178/L181 of YfiR, which is also a binding pocket for F57 of YfiB, as observed in the YfiB-YfiR complex (Fig. 5C). RESULTS 109 113 L181 residue_name_number Interestingly, VB6 and L-Trp were found to occupy the same hydrophobic pocket, formed by L166/I169/V176/P178/L181 of YfiR, which is also a binding pocket for F57 of YfiB, as observed in the YfiB-YfiR complex (Fig. 5C). RESULTS 117 121 YfiR protein Interestingly, VB6 and L-Trp were found to occupy the same hydrophobic pocket, formed by L166/I169/V176/P178/L181 of YfiR, which is also a binding pocket for F57 of YfiB, as observed in the YfiB-YfiR complex (Fig. 5C). RESULTS 139 153 binding pocket site Interestingly, VB6 and L-Trp were found to occupy the same hydrophobic pocket, formed by L166/I169/V176/P178/L181 of YfiR, which is also a binding pocket for F57 of YfiB, as observed in the YfiB-YfiR complex (Fig. 5C). RESULTS 158 161 F57 residue_name_number Interestingly, VB6 and L-Trp were found to occupy the same hydrophobic pocket, formed by L166/I169/V176/P178/L181 of YfiR, which is also a binding pocket for F57 of YfiB, as observed in the YfiB-YfiR complex (Fig. 5C). RESULTS 165 169 YfiB protein Interestingly, VB6 and L-Trp were found to occupy the same hydrophobic pocket, formed by L166/I169/V176/P178/L181 of YfiR, which is also a binding pocket for F57 of YfiB, as observed in the YfiB-YfiR complex (Fig. 5C). RESULTS 190 199 YfiB-YfiR complex_assembly Interestingly, VB6 and L-Trp were found to occupy the same hydrophobic pocket, formed by L166/I169/V176/P178/L181 of YfiR, which is also a binding pocket for F57 of YfiB, as observed in the YfiB-YfiR complex (Fig. 5C). RESULTS 30 33 F57 residue_name_number To evaluate the importance of F57 in YfiBL43P-YfiR interaction, the binding affinities of YfiBL43P and YfiBL43P/F57A for YfiR were measured by isothermal titration calorimetry (ITC). RESULTS 37 50 YfiBL43P-YfiR complex_assembly To evaluate the importance of F57 in YfiBL43P-YfiR interaction, the binding affinities of YfiBL43P and YfiBL43P/F57A for YfiR were measured by isothermal titration calorimetry (ITC). RESULTS 68 86 binding affinities evidence To evaluate the importance of F57 in YfiBL43P-YfiR interaction, the binding affinities of YfiBL43P and YfiBL43P/F57A for YfiR were measured by isothermal titration calorimetry (ITC). RESULTS 90 98 YfiBL43P mutant To evaluate the importance of F57 in YfiBL43P-YfiR interaction, the binding affinities of YfiBL43P and YfiBL43P/F57A for YfiR were measured by isothermal titration calorimetry (ITC). RESULTS 103 111 YfiBL43P mutant To evaluate the importance of F57 in YfiBL43P-YfiR interaction, the binding affinities of YfiBL43P and YfiBL43P/F57A for YfiR were measured by isothermal titration calorimetry (ITC). RESULTS 112 116 F57A mutant To evaluate the importance of F57 in YfiBL43P-YfiR interaction, the binding affinities of YfiBL43P and YfiBL43P/F57A for YfiR were measured by isothermal titration calorimetry (ITC). RESULTS 121 125 YfiR protein To evaluate the importance of F57 in YfiBL43P-YfiR interaction, the binding affinities of YfiBL43P and YfiBL43P/F57A for YfiR were measured by isothermal titration calorimetry (ITC). RESULTS 143 175 isothermal titration calorimetry experimental_method To evaluate the importance of F57 in YfiBL43P-YfiR interaction, the binding affinities of YfiBL43P and YfiBL43P/F57A for YfiR were measured by isothermal titration calorimetry (ITC). RESULTS 177 180 ITC experimental_method To evaluate the importance of F57 in YfiBL43P-YfiR interaction, the binding affinities of YfiBL43P and YfiBL43P/F57A for YfiR were measured by isothermal titration calorimetry (ITC). RESULTS 19 21 Kd evidence The results showed Kd values of 1.4 × 10−7 mol/L and 5.3 × 10−7 mol/L for YfiBL43P and YfiBL43P/F57A, respectively, revealing that the YfiBL43P/F57A mutant caused a 3.8-fold reduction in the binding affinity compared with the YfiBL43P mutant (Fig. 6F and 6G). RESULTS 74 82 YfiBL43P mutant The results showed Kd values of 1.4 × 10−7 mol/L and 5.3 × 10−7 mol/L for YfiBL43P and YfiBL43P/F57A, respectively, revealing that the YfiBL43P/F57A mutant caused a 3.8-fold reduction in the binding affinity compared with the YfiBL43P mutant (Fig. 6F and 6G). RESULTS 87 95 YfiBL43P mutant The results showed Kd values of 1.4 × 10−7 mol/L and 5.3 × 10−7 mol/L for YfiBL43P and YfiBL43P/F57A, respectively, revealing that the YfiBL43P/F57A mutant caused a 3.8-fold reduction in the binding affinity compared with the YfiBL43P mutant (Fig. 6F and 6G). RESULTS 96 100 F57A mutant The results showed Kd values of 1.4 × 10−7 mol/L and 5.3 × 10−7 mol/L for YfiBL43P and YfiBL43P/F57A, respectively, revealing that the YfiBL43P/F57A mutant caused a 3.8-fold reduction in the binding affinity compared with the YfiBL43P mutant (Fig. 6F and 6G). RESULTS 135 143 YfiBL43P mutant The results showed Kd values of 1.4 × 10−7 mol/L and 5.3 × 10−7 mol/L for YfiBL43P and YfiBL43P/F57A, respectively, revealing that the YfiBL43P/F57A mutant caused a 3.8-fold reduction in the binding affinity compared with the YfiBL43P mutant (Fig. 6F and 6G). RESULTS 144 148 F57A mutant The results showed Kd values of 1.4 × 10−7 mol/L and 5.3 × 10−7 mol/L for YfiBL43P and YfiBL43P/F57A, respectively, revealing that the YfiBL43P/F57A mutant caused a 3.8-fold reduction in the binding affinity compared with the YfiBL43P mutant (Fig. 6F and 6G). RESULTS 149 155 mutant protein_state The results showed Kd values of 1.4 × 10−7 mol/L and 5.3 × 10−7 mol/L for YfiBL43P and YfiBL43P/F57A, respectively, revealing that the YfiBL43P/F57A mutant caused a 3.8-fold reduction in the binding affinity compared with the YfiBL43P mutant (Fig. 6F and 6G). RESULTS 191 207 binding affinity evidence The results showed Kd values of 1.4 × 10−7 mol/L and 5.3 × 10−7 mol/L for YfiBL43P and YfiBL43P/F57A, respectively, revealing that the YfiBL43P/F57A mutant caused a 3.8-fold reduction in the binding affinity compared with the YfiBL43P mutant (Fig. 6F and 6G). RESULTS 226 234 YfiBL43P mutant The results showed Kd values of 1.4 × 10−7 mol/L and 5.3 × 10−7 mol/L for YfiBL43P and YfiBL43P/F57A, respectively, revealing that the YfiBL43P/F57A mutant caused a 3.8-fold reduction in the binding affinity compared with the YfiBL43P mutant (Fig. 6F and 6G). RESULTS 235 241 mutant protein_state The results showed Kd values of 1.4 × 10−7 mol/L and 5.3 × 10−7 mol/L for YfiBL43P and YfiBL43P/F57A, respectively, revealing that the YfiBL43P/F57A mutant caused a 3.8-fold reduction in the binding affinity compared with the YfiBL43P mutant (Fig. 6F and 6G). RESULTS 66 69 VB6 chemical In parallel, to better understand the putative functional role of VB6 and L-Trp, yfiB was deleted in a PAO1 wild-type strain, and a construct expressing the YfiBL43P mutant was transformed into the PAO1 ΔyfiB strain to trigger YfiBL43P-induced biofilm formation. RESULTS 74 79 L-Trp chemical In parallel, to better understand the putative functional role of VB6 and L-Trp, yfiB was deleted in a PAO1 wild-type strain, and a construct expressing the YfiBL43P mutant was transformed into the PAO1 ΔyfiB strain to trigger YfiBL43P-induced biofilm formation. RESULTS 81 85 yfiB gene In parallel, to better understand the putative functional role of VB6 and L-Trp, yfiB was deleted in a PAO1 wild-type strain, and a construct expressing the YfiBL43P mutant was transformed into the PAO1 ΔyfiB strain to trigger YfiBL43P-induced biofilm formation. RESULTS 90 97 deleted experimental_method In parallel, to better understand the putative functional role of VB6 and L-Trp, yfiB was deleted in a PAO1 wild-type strain, and a construct expressing the YfiBL43P mutant was transformed into the PAO1 ΔyfiB strain to trigger YfiBL43P-induced biofilm formation. RESULTS 103 107 PAO1 species In parallel, to better understand the putative functional role of VB6 and L-Trp, yfiB was deleted in a PAO1 wild-type strain, and a construct expressing the YfiBL43P mutant was transformed into the PAO1 ΔyfiB strain to trigger YfiBL43P-induced biofilm formation. RESULTS 108 117 wild-type protein_state In parallel, to better understand the putative functional role of VB6 and L-Trp, yfiB was deleted in a PAO1 wild-type strain, and a construct expressing the YfiBL43P mutant was transformed into the PAO1 ΔyfiB strain to trigger YfiBL43P-induced biofilm formation. RESULTS 132 152 construct expressing experimental_method In parallel, to better understand the putative functional role of VB6 and L-Trp, yfiB was deleted in a PAO1 wild-type strain, and a construct expressing the YfiBL43P mutant was transformed into the PAO1 ΔyfiB strain to trigger YfiBL43P-induced biofilm formation. RESULTS 157 165 YfiBL43P mutant In parallel, to better understand the putative functional role of VB6 and L-Trp, yfiB was deleted in a PAO1 wild-type strain, and a construct expressing the YfiBL43P mutant was transformed into the PAO1 ΔyfiB strain to trigger YfiBL43P-induced biofilm formation. RESULTS 166 172 mutant protein_state In parallel, to better understand the putative functional role of VB6 and L-Trp, yfiB was deleted in a PAO1 wild-type strain, and a construct expressing the YfiBL43P mutant was transformed into the PAO1 ΔyfiB strain to trigger YfiBL43P-induced biofilm formation. RESULTS 177 193 transformed into experimental_method In parallel, to better understand the putative functional role of VB6 and L-Trp, yfiB was deleted in a PAO1 wild-type strain, and a construct expressing the YfiBL43P mutant was transformed into the PAO1 ΔyfiB strain to trigger YfiBL43P-induced biofilm formation. RESULTS 198 202 PAO1 species In parallel, to better understand the putative functional role of VB6 and L-Trp, yfiB was deleted in a PAO1 wild-type strain, and a construct expressing the YfiBL43P mutant was transformed into the PAO1 ΔyfiB strain to trigger YfiBL43P-induced biofilm formation. RESULTS 203 208 ΔyfiB mutant In parallel, to better understand the putative functional role of VB6 and L-Trp, yfiB was deleted in a PAO1 wild-type strain, and a construct expressing the YfiBL43P mutant was transformed into the PAO1 ΔyfiB strain to trigger YfiBL43P-induced biofilm formation. RESULTS 227 235 YfiBL43P mutant In parallel, to better understand the putative functional role of VB6 and L-Trp, yfiB was deleted in a PAO1 wild-type strain, and a construct expressing the YfiBL43P mutant was transformed into the PAO1 ΔyfiB strain to trigger YfiBL43P-induced biofilm formation. RESULTS 0 36 Growth and surface attachment assays experimental_method Growth and surface attachment assays were carried out for the yfiB-L43P strain in the presence of increasing concentrations of VB6 or L-Trp. RESULTS 62 71 yfiB-L43P mutant Growth and surface attachment assays were carried out for the yfiB-L43P strain in the presence of increasing concentrations of VB6 or L-Trp. RESULTS 98 123 increasing concentrations experimental_method Growth and surface attachment assays were carried out for the yfiB-L43P strain in the presence of increasing concentrations of VB6 or L-Trp. RESULTS 127 130 VB6 chemical Growth and surface attachment assays were carried out for the yfiB-L43P strain in the presence of increasing concentrations of VB6 or L-Trp. RESULTS 134 139 L-Trp chemical Growth and surface attachment assays were carried out for the yfiB-L43P strain in the presence of increasing concentrations of VB6 or L-Trp. RESULTS 32 47 over-expression experimental_method As shown in Fig. 6A and 6B, the over-expression of YfiBL43P induced strong surface attachment and much slower growth of the yfiB-L43P strain, and as expected, a certain amount of VB6 or L-Trp (4–6 mmol/L for VB6 and 6–10 mmol/L for L-Trp) could reduce the surface attachment. RESULTS 51 59 YfiBL43P mutant As shown in Fig. 6A and 6B, the over-expression of YfiBL43P induced strong surface attachment and much slower growth of the yfiB-L43P strain, and as expected, a certain amount of VB6 or L-Trp (4–6 mmol/L for VB6 and 6–10 mmol/L for L-Trp) could reduce the surface attachment. RESULTS 124 133 yfiB-L43P mutant As shown in Fig. 6A and 6B, the over-expression of YfiBL43P induced strong surface attachment and much slower growth of the yfiB-L43P strain, and as expected, a certain amount of VB6 or L-Trp (4–6 mmol/L for VB6 and 6–10 mmol/L for L-Trp) could reduce the surface attachment. RESULTS 179 182 VB6 chemical As shown in Fig. 6A and 6B, the over-expression of YfiBL43P induced strong surface attachment and much slower growth of the yfiB-L43P strain, and as expected, a certain amount of VB6 or L-Trp (4–6 mmol/L for VB6 and 6–10 mmol/L for L-Trp) could reduce the surface attachment. RESULTS 186 191 L-Trp chemical As shown in Fig. 6A and 6B, the over-expression of YfiBL43P induced strong surface attachment and much slower growth of the yfiB-L43P strain, and as expected, a certain amount of VB6 or L-Trp (4–6 mmol/L for VB6 and 6–10 mmol/L for L-Trp) could reduce the surface attachment. RESULTS 208 211 VB6 chemical As shown in Fig. 6A and 6B, the over-expression of YfiBL43P induced strong surface attachment and much slower growth of the yfiB-L43P strain, and as expected, a certain amount of VB6 or L-Trp (4–6 mmol/L for VB6 and 6–10 mmol/L for L-Trp) could reduce the surface attachment. RESULTS 232 237 L-Trp chemical As shown in Fig. 6A and 6B, the over-expression of YfiBL43P induced strong surface attachment and much slower growth of the yfiB-L43P strain, and as expected, a certain amount of VB6 or L-Trp (4–6 mmol/L for VB6 and 6–10 mmol/L for L-Trp) could reduce the surface attachment. RESULTS 56 59 VB6 chemical Interestingly, at a concentration higher than 8 mmol/L, VB6 lost its ability to inhibit biofilm formation, implying that the VB6-involving regulatory mechanism is highly complicated and remains to be further investigated. RESULTS 125 128 VB6 chemical Interestingly, at a concentration higher than 8 mmol/L, VB6 lost its ability to inhibit biofilm formation, implying that the VB6-involving regulatory mechanism is highly complicated and remains to be further investigated. RESULTS 14 17 VB6 chemical Of note, both VB6 and L-Trp have been reported to correlate with biofilm formation in certain Gram-negative bacteria (Grubman et al.,; Shimazaki et al.,). RESULTS 22 27 L-Trp chemical Of note, both VB6 and L-Trp have been reported to correlate with biofilm formation in certain Gram-negative bacteria (Grubman et al.,; Shimazaki et al.,). RESULTS 94 116 Gram-negative bacteria taxonomy_domain Of note, both VB6 and L-Trp have been reported to correlate with biofilm formation in certain Gram-negative bacteria (Grubman et al.,; Shimazaki et al.,). RESULTS 3 22 Helicobacter pylori species In Helicobacter pylori in particular, VB6 biosynthetic enzymes act as novel virulence factors, and VB6 is required for full motility and virulence (Grubman et al.,). RESULTS 38 41 VB6 chemical In Helicobacter pylori in particular, VB6 biosynthetic enzymes act as novel virulence factors, and VB6 is required for full motility and virulence (Grubman et al.,). RESULTS 99 102 VB6 chemical In Helicobacter pylori in particular, VB6 biosynthetic enzymes act as novel virulence factors, and VB6 is required for full motility and virulence (Grubman et al.,). RESULTS 4 11 E. coli species  In E. coli, mutants with decreased tryptophan synthesis show greater biofilm formation, and matured biofilm is degraded by L-tryptophan addition (Shimazaki et al.,). RESULTS 36 46 tryptophan chemical  In E. coli, mutants with decreased tryptophan synthesis show greater biofilm formation, and matured biofilm is degraded by L-tryptophan addition (Shimazaki et al.,). RESULTS 124 136 L-tryptophan chemical  In E. coli, mutants with decreased tryptophan synthesis show greater biofilm formation, and matured biofilm is degraded by L-tryptophan addition (Shimazaki et al.,). RESULTS 46 49 VB6 chemical To answer the question whether competition of VB6 or L-Trp for the YfiB F57-binding pocket of YfiR plays an essential role in inhibiting biofilm formation, we measured the binding affinities of VB6 and L-Trp for YfiR via BIAcore experiments. RESULTS 53 58 L-Trp chemical To answer the question whether competition of VB6 or L-Trp for the YfiB F57-binding pocket of YfiR plays an essential role in inhibiting biofilm formation, we measured the binding affinities of VB6 and L-Trp for YfiR via BIAcore experiments. RESULTS 67 71 YfiB protein To answer the question whether competition of VB6 or L-Trp for the YfiB F57-binding pocket of YfiR plays an essential role in inhibiting biofilm formation, we measured the binding affinities of VB6 and L-Trp for YfiR via BIAcore experiments. RESULTS 72 90 F57-binding pocket site To answer the question whether competition of VB6 or L-Trp for the YfiB F57-binding pocket of YfiR plays an essential role in inhibiting biofilm formation, we measured the binding affinities of VB6 and L-Trp for YfiR via BIAcore experiments. RESULTS 94 98 YfiR protein To answer the question whether competition of VB6 or L-Trp for the YfiB F57-binding pocket of YfiR plays an essential role in inhibiting biofilm formation, we measured the binding affinities of VB6 and L-Trp for YfiR via BIAcore experiments. RESULTS 172 190 binding affinities evidence To answer the question whether competition of VB6 or L-Trp for the YfiB F57-binding pocket of YfiR plays an essential role in inhibiting biofilm formation, we measured the binding affinities of VB6 and L-Trp for YfiR via BIAcore experiments. RESULTS 194 197 VB6 chemical To answer the question whether competition of VB6 or L-Trp for the YfiB F57-binding pocket of YfiR plays an essential role in inhibiting biofilm formation, we measured the binding affinities of VB6 and L-Trp for YfiR via BIAcore experiments. RESULTS 202 207 L-Trp chemical To answer the question whether competition of VB6 or L-Trp for the YfiB F57-binding pocket of YfiR plays an essential role in inhibiting biofilm formation, we measured the binding affinities of VB6 and L-Trp for YfiR via BIAcore experiments. RESULTS 212 216 YfiR protein To answer the question whether competition of VB6 or L-Trp for the YfiB F57-binding pocket of YfiR plays an essential role in inhibiting biofilm formation, we measured the binding affinities of VB6 and L-Trp for YfiR via BIAcore experiments. RESULTS 221 228 BIAcore experimental_method To answer the question whether competition of VB6 or L-Trp for the YfiB F57-binding pocket of YfiR plays an essential role in inhibiting biofilm formation, we measured the binding affinities of VB6 and L-Trp for YfiR via BIAcore experiments. RESULTS 35 37 Kd evidence The results showed relatively weak Kd values of 35.2 mmol/L and 76.9 mmol/L for VB6 and L-Trp, respectively (Fig. 6C and 6D). RESULTS 80 83 VB6 chemical The results showed relatively weak Kd values of 35.2 mmol/L and 76.9 mmol/L for VB6 and L-Trp, respectively (Fig. 6C and 6D). RESULTS 88 93 L-Trp chemical The results showed relatively weak Kd values of 35.2 mmol/L and 76.9 mmol/L for VB6 and L-Trp, respectively (Fig. 6C and 6D). RESULTS 40 43 VB6 chemical Based on our results, we concluded that VB6 or L-Trp can bind to YfiR, however, VB6 or L-Trp alone may have little effects in interrupting the YfiB-YfiR interaction, the mechanism by which VB6 or L-Trp inhibits biofilm formation remains unclear and requires further investigation. RESULTS 47 52 L-Trp chemical Based on our results, we concluded that VB6 or L-Trp can bind to YfiR, however, VB6 or L-Trp alone may have little effects in interrupting the YfiB-YfiR interaction, the mechanism by which VB6 or L-Trp inhibits biofilm formation remains unclear and requires further investigation. RESULTS 65 69 YfiR protein Based on our results, we concluded that VB6 or L-Trp can bind to YfiR, however, VB6 or L-Trp alone may have little effects in interrupting the YfiB-YfiR interaction, the mechanism by which VB6 or L-Trp inhibits biofilm formation remains unclear and requires further investigation. RESULTS 80 83 VB6 chemical Based on our results, we concluded that VB6 or L-Trp can bind to YfiR, however, VB6 or L-Trp alone may have little effects in interrupting the YfiB-YfiR interaction, the mechanism by which VB6 or L-Trp inhibits biofilm formation remains unclear and requires further investigation. RESULTS 87 92 L-Trp chemical Based on our results, we concluded that VB6 or L-Trp can bind to YfiR, however, VB6 or L-Trp alone may have little effects in interrupting the YfiB-YfiR interaction, the mechanism by which VB6 or L-Trp inhibits biofilm formation remains unclear and requires further investigation. RESULTS 93 98 alone protein_state Based on our results, we concluded that VB6 or L-Trp can bind to YfiR, however, VB6 or L-Trp alone may have little effects in interrupting the YfiB-YfiR interaction, the mechanism by which VB6 or L-Trp inhibits biofilm formation remains unclear and requires further investigation. RESULTS 143 152 YfiB-YfiR complex_assembly Based on our results, we concluded that VB6 or L-Trp can bind to YfiR, however, VB6 or L-Trp alone may have little effects in interrupting the YfiB-YfiR interaction, the mechanism by which VB6 or L-Trp inhibits biofilm formation remains unclear and requires further investigation. RESULTS 189 192 VB6 chemical Based on our results, we concluded that VB6 or L-Trp can bind to YfiR, however, VB6 or L-Trp alone may have little effects in interrupting the YfiB-YfiR interaction, the mechanism by which VB6 or L-Trp inhibits biofilm formation remains unclear and requires further investigation. RESULTS 196 201 L-Trp chemical Based on our results, we concluded that VB6 or L-Trp can bind to YfiR, however, VB6 or L-Trp alone may have little effects in interrupting the YfiB-YfiR interaction, the mechanism by which VB6 or L-Trp inhibits biofilm formation remains unclear and requires further investigation. RESULTS 60 64 YfiB protein Previous studies suggested that in response to cell stress, YfiB in the outer membrane sequesters the periplasmic protein YfiR, releasing its inhibition of YfiN on the inner membrane and thus inducing the diguanylate cyclase activity of YfiN to allow c-di-GMP production (Giardina et al.,; Malone et al.,; Malone et al.,). DISCUSS 122 126 YfiR protein Previous studies suggested that in response to cell stress, YfiB in the outer membrane sequesters the periplasmic protein YfiR, releasing its inhibition of YfiN on the inner membrane and thus inducing the diguanylate cyclase activity of YfiN to allow c-di-GMP production (Giardina et al.,; Malone et al.,; Malone et al.,). DISCUSS 156 160 YfiN protein Previous studies suggested that in response to cell stress, YfiB in the outer membrane sequesters the periplasmic protein YfiR, releasing its inhibition of YfiN on the inner membrane and thus inducing the diguanylate cyclase activity of YfiN to allow c-di-GMP production (Giardina et al.,; Malone et al.,; Malone et al.,). DISCUSS 237 241 YfiN protein Previous studies suggested that in response to cell stress, YfiB in the outer membrane sequesters the periplasmic protein YfiR, releasing its inhibition of YfiN on the inner membrane and thus inducing the diguanylate cyclase activity of YfiN to allow c-di-GMP production (Giardina et al.,; Malone et al.,; Malone et al.,). DISCUSS 251 259 c-di-GMP chemical Previous studies suggested that in response to cell stress, YfiB in the outer membrane sequesters the periplasmic protein YfiR, releasing its inhibition of YfiN on the inner membrane and thus inducing the diguanylate cyclase activity of YfiN to allow c-di-GMP production (Giardina et al.,; Malone et al.,; Malone et al.,). DISCUSS 20 38 crystal structures evidence Here, we report the crystal structures of YfiB alone and an active mutant YfiBL43P in complex with YfiR, indicating that YfiR forms a 2:2 complex with YfiB via a region composed of conserved residues. DISCUSS 42 46 YfiB protein Here, we report the crystal structures of YfiB alone and an active mutant YfiBL43P in complex with YfiR, indicating that YfiR forms a 2:2 complex with YfiB via a region composed of conserved residues. DISCUSS 47 52 alone protein_state Here, we report the crystal structures of YfiB alone and an active mutant YfiBL43P in complex with YfiR, indicating that YfiR forms a 2:2 complex with YfiB via a region composed of conserved residues. DISCUSS 60 66 active protein_state Here, we report the crystal structures of YfiB alone and an active mutant YfiBL43P in complex with YfiR, indicating that YfiR forms a 2:2 complex with YfiB via a region composed of conserved residues. DISCUSS 67 73 mutant protein_state Here, we report the crystal structures of YfiB alone and an active mutant YfiBL43P in complex with YfiR, indicating that YfiR forms a 2:2 complex with YfiB via a region composed of conserved residues. DISCUSS 74 82 YfiBL43P mutant Here, we report the crystal structures of YfiB alone and an active mutant YfiBL43P in complex with YfiR, indicating that YfiR forms a 2:2 complex with YfiB via a region composed of conserved residues. DISCUSS 83 98 in complex with protein_state Here, we report the crystal structures of YfiB alone and an active mutant YfiBL43P in complex with YfiR, indicating that YfiR forms a 2:2 complex with YfiB via a region composed of conserved residues. DISCUSS 99 103 YfiR protein Here, we report the crystal structures of YfiB alone and an active mutant YfiBL43P in complex with YfiR, indicating that YfiR forms a 2:2 complex with YfiB via a region composed of conserved residues. DISCUSS 121 125 YfiR protein Here, we report the crystal structures of YfiB alone and an active mutant YfiBL43P in complex with YfiR, indicating that YfiR forms a 2:2 complex with YfiB via a region composed of conserved residues. DISCUSS 138 150 complex with protein_state Here, we report the crystal structures of YfiB alone and an active mutant YfiBL43P in complex with YfiR, indicating that YfiR forms a 2:2 complex with YfiB via a region composed of conserved residues. DISCUSS 151 155 YfiB protein Here, we report the crystal structures of YfiB alone and an active mutant YfiBL43P in complex with YfiR, indicating that YfiR forms a 2:2 complex with YfiB via a region composed of conserved residues. DISCUSS 4 28 structural data analysis experimental_method Our structural data analysis shows that the activated YfiB has an N-terminal portion that is largely altered, adopting a stretched conformation compared with the compact conformation of the apo YfiB. The apo YfiB structure constructed beginning at residue 34 has a compact conformation of approximately 45 Å in length. DISCUSS 44 53 activated protein_state Our structural data analysis shows that the activated YfiB has an N-terminal portion that is largely altered, adopting a stretched conformation compared with the compact conformation of the apo YfiB. The apo YfiB structure constructed beginning at residue 34 has a compact conformation of approximately 45 Å in length. DISCUSS 54 58 YfiB protein Our structural data analysis shows that the activated YfiB has an N-terminal portion that is largely altered, adopting a stretched conformation compared with the compact conformation of the apo YfiB. The apo YfiB structure constructed beginning at residue 34 has a compact conformation of approximately 45 Å in length. DISCUSS 66 84 N-terminal portion structure_element Our structural data analysis shows that the activated YfiB has an N-terminal portion that is largely altered, adopting a stretched conformation compared with the compact conformation of the apo YfiB. The apo YfiB structure constructed beginning at residue 34 has a compact conformation of approximately 45 Å in length. DISCUSS 121 143 stretched conformation protein_state Our structural data analysis shows that the activated YfiB has an N-terminal portion that is largely altered, adopting a stretched conformation compared with the compact conformation of the apo YfiB. The apo YfiB structure constructed beginning at residue 34 has a compact conformation of approximately 45 Å in length. DISCUSS 162 182 compact conformation protein_state Our structural data analysis shows that the activated YfiB has an N-terminal portion that is largely altered, adopting a stretched conformation compared with the compact conformation of the apo YfiB. The apo YfiB structure constructed beginning at residue 34 has a compact conformation of approximately 45 Å in length. DISCUSS 190 193 apo protein_state Our structural data analysis shows that the activated YfiB has an N-terminal portion that is largely altered, adopting a stretched conformation compared with the compact conformation of the apo YfiB. The apo YfiB structure constructed beginning at residue 34 has a compact conformation of approximately 45 Å in length. DISCUSS 194 198 YfiB protein Our structural data analysis shows that the activated YfiB has an N-terminal portion that is largely altered, adopting a stretched conformation compared with the compact conformation of the apo YfiB. The apo YfiB structure constructed beginning at residue 34 has a compact conformation of approximately 45 Å in length. DISCUSS 204 207 apo protein_state Our structural data analysis shows that the activated YfiB has an N-terminal portion that is largely altered, adopting a stretched conformation compared with the compact conformation of the apo YfiB. The apo YfiB structure constructed beginning at residue 34 has a compact conformation of approximately 45 Å in length. DISCUSS 208 212 YfiB protein Our structural data analysis shows that the activated YfiB has an N-terminal portion that is largely altered, adopting a stretched conformation compared with the compact conformation of the apo YfiB. The apo YfiB structure constructed beginning at residue 34 has a compact conformation of approximately 45 Å in length. DISCUSS 213 222 structure evidence Our structural data analysis shows that the activated YfiB has an N-terminal portion that is largely altered, adopting a stretched conformation compared with the compact conformation of the apo YfiB. The apo YfiB structure constructed beginning at residue 34 has a compact conformation of approximately 45 Å in length. DISCUSS 256 258 34 residue_number Our structural data analysis shows that the activated YfiB has an N-terminal portion that is largely altered, adopting a stretched conformation compared with the compact conformation of the apo YfiB. The apo YfiB structure constructed beginning at residue 34 has a compact conformation of approximately 45 Å in length. DISCUSS 265 285 compact conformation protein_state Our structural data analysis shows that the activated YfiB has an N-terminal portion that is largely altered, adopting a stretched conformation compared with the compact conformation of the apo YfiB. The apo YfiB structure constructed beginning at residue 34 has a compact conformation of approximately 45 Å in length. DISCUSS 19 33 preceding 8 aa residue_range In addition to the preceding 8 aa loop (from the lipid acceptor Cys26 to Gly34), the full length of the periplasmic portion of apo YfiB can reach approximately 60 Å. It was reported that the distance between the outer membrane and the cell wall is approximately 50 Å and that the thickness of the PG layer is approximately 70 Å (Matias et al.,). DISCUSS 34 38 loop structure_element In addition to the preceding 8 aa loop (from the lipid acceptor Cys26 to Gly34), the full length of the periplasmic portion of apo YfiB can reach approximately 60 Å. It was reported that the distance between the outer membrane and the cell wall is approximately 50 Å and that the thickness of the PG layer is approximately 70 Å (Matias et al.,). DISCUSS 64 78 Cys26 to Gly34 residue_range In addition to the preceding 8 aa loop (from the lipid acceptor Cys26 to Gly34), the full length of the periplasmic portion of apo YfiB can reach approximately 60 Å. It was reported that the distance between the outer membrane and the cell wall is approximately 50 Å and that the thickness of the PG layer is approximately 70 Å (Matias et al.,). DISCUSS 85 96 full length protein_state In addition to the preceding 8 aa loop (from the lipid acceptor Cys26 to Gly34), the full length of the periplasmic portion of apo YfiB can reach approximately 60 Å. It was reported that the distance between the outer membrane and the cell wall is approximately 50 Å and that the thickness of the PG layer is approximately 70 Å (Matias et al.,). DISCUSS 127 130 apo protein_state In addition to the preceding 8 aa loop (from the lipid acceptor Cys26 to Gly34), the full length of the periplasmic portion of apo YfiB can reach approximately 60 Å. It was reported that the distance between the outer membrane and the cell wall is approximately 50 Å and that the thickness of the PG layer is approximately 70 Å (Matias et al.,). DISCUSS 131 135 YfiB protein In addition to the preceding 8 aa loop (from the lipid acceptor Cys26 to Gly34), the full length of the periplasmic portion of apo YfiB can reach approximately 60 Å. It was reported that the distance between the outer membrane and the cell wall is approximately 50 Å and that the thickness of the PG layer is approximately 70 Å (Matias et al.,). DISCUSS 6 10 YfiB protein Thus, YfiB alone represents an inactive form that may only partially insert into the PG matrix. DISCUSS 11 16 alone protein_state Thus, YfiB alone represents an inactive form that may only partially insert into the PG matrix. DISCUSS 31 39 inactive protein_state Thus, YfiB alone represents an inactive form that may only partially insert into the PG matrix. DISCUSS 13 23 YfiR-bound protein_state By contrast, YfiR-bound YfiBL43P (residues 44–168) has a stretched conformation of approximately 55 Å in length. DISCUSS 24 32 YfiBL43P mutant By contrast, YfiR-bound YfiBL43P (residues 44–168) has a stretched conformation of approximately 55 Å in length. DISCUSS 43 49 44–168 residue_range By contrast, YfiR-bound YfiBL43P (residues 44–168) has a stretched conformation of approximately 55 Å in length. DISCUSS 57 79 stretched conformation protein_state By contrast, YfiR-bound YfiBL43P (residues 44–168) has a stretched conformation of approximately 55 Å in length. DISCUSS 19 54 17 preceding intracellular residues residue_range In addition to the 17 preceding intracellular residues (from the lipid acceptor Cys26 to Leu43), the length of the intracellular portion of active YfiB may extend over 100 Å, assuming a fully stretched conformation. DISCUSS 80 94 Cys26 to Leu43 residue_range In addition to the 17 preceding intracellular residues (from the lipid acceptor Cys26 to Leu43), the length of the intracellular portion of active YfiB may extend over 100 Å, assuming a fully stretched conformation. DISCUSS 140 146 active protein_state In addition to the 17 preceding intracellular residues (from the lipid acceptor Cys26 to Leu43), the length of the intracellular portion of active YfiB may extend over 100 Å, assuming a fully stretched conformation. DISCUSS 147 151 YfiB protein In addition to the 17 preceding intracellular residues (from the lipid acceptor Cys26 to Leu43), the length of the intracellular portion of active YfiB may extend over 100 Å, assuming a fully stretched conformation. DISCUSS 186 214 fully stretched conformation protein_state In addition to the 17 preceding intracellular residues (from the lipid acceptor Cys26 to Leu43), the length of the intracellular portion of active YfiB may extend over 100 Å, assuming a fully stretched conformation. DISCUSS 53 57 YfiB protein Provided that the diameter of the widest part of the YfiB dimer is approximately 64 Å, which is slightly smaller than the smallest diameter of the PG pore (70 Å) (Meroueh et al.,), the YfiB dimer should be able to penetrate the PG layer. DISCUSS 58 63 dimer oligomeric_state Provided that the diameter of the widest part of the YfiB dimer is approximately 64 Å, which is slightly smaller than the smallest diameter of the PG pore (70 Å) (Meroueh et al.,), the YfiB dimer should be able to penetrate the PG layer. DISCUSS 185 189 YfiB protein Provided that the diameter of the widest part of the YfiB dimer is approximately 64 Å, which is slightly smaller than the smallest diameter of the PG pore (70 Å) (Meroueh et al.,), the YfiB dimer should be able to penetrate the PG layer. DISCUSS 190 195 dimer oligomeric_state Provided that the diameter of the widest part of the YfiB dimer is approximately 64 Å, which is slightly smaller than the smallest diameter of the PG pore (70 Å) (Meroueh et al.,), the YfiB dimer should be able to penetrate the PG layer. DISCUSS 24 30 YfiBNR complex_assembly Regulatory model of the YfiBNR tripartite system. FIG 31 41 tripartite protein_state Regulatory model of the YfiBNR tripartite system. FIG 4 22 periplasmic domain structure_element The periplasmic domain of YfiB and the YfiB-YfiR complex are depicted according to the crystal structures. FIG 26 30 YfiB protein The periplasmic domain of YfiB and the YfiB-YfiR complex are depicted according to the crystal structures. FIG 39 48 YfiB-YfiR complex_assembly The periplasmic domain of YfiB and the YfiB-YfiR complex are depicted according to the crystal structures. FIG 87 105 crystal structures evidence The periplasmic domain of YfiB and the YfiB-YfiR complex are depicted according to the crystal structures. FIG 19 24 Cys26 residue_name_number The lipid acceptor Cys26 is indicated as blue ball. FIG 4 8 loop structure_element The loop connecting Cys26 and Gly34 of YfiB is modeled. FIG 20 25 Cys26 residue_name_number The loop connecting Cys26 and Gly34 of YfiB is modeled. FIG 30 35 Gly34 residue_name_number The loop connecting Cys26 and Gly34 of YfiB is modeled. FIG 39 43 YfiB protein The loop connecting Cys26 and Gly34 of YfiB is modeled. FIG 4 14 PAS domain structure_element The PAS domain of YfiN is shown as pink oval. FIG 18 22 YfiN protein The PAS domain of YfiN is shown as pink oval. FIG 5 14 activated protein_state Once activated by certain cell stress, the dimeric YfiB transforms from a compact conformation to a stretched conformation, allowing the periplasmic domain of the membrane-anchored YfiB to penetrate the cell wall and sequester the YfiR dimer, thus relieving the repression of YfiN FIG 43 50 dimeric oligomeric_state Once activated by certain cell stress, the dimeric YfiB transforms from a compact conformation to a stretched conformation, allowing the periplasmic domain of the membrane-anchored YfiB to penetrate the cell wall and sequester the YfiR dimer, thus relieving the repression of YfiN FIG 51 55 YfiB protein Once activated by certain cell stress, the dimeric YfiB transforms from a compact conformation to a stretched conformation, allowing the periplasmic domain of the membrane-anchored YfiB to penetrate the cell wall and sequester the YfiR dimer, thus relieving the repression of YfiN FIG 74 94 compact conformation protein_state Once activated by certain cell stress, the dimeric YfiB transforms from a compact conformation to a stretched conformation, allowing the periplasmic domain of the membrane-anchored YfiB to penetrate the cell wall and sequester the YfiR dimer, thus relieving the repression of YfiN FIG 100 122 stretched conformation protein_state Once activated by certain cell stress, the dimeric YfiB transforms from a compact conformation to a stretched conformation, allowing the periplasmic domain of the membrane-anchored YfiB to penetrate the cell wall and sequester the YfiR dimer, thus relieving the repression of YfiN FIG 137 155 periplasmic domain structure_element Once activated by certain cell stress, the dimeric YfiB transforms from a compact conformation to a stretched conformation, allowing the periplasmic domain of the membrane-anchored YfiB to penetrate the cell wall and sequester the YfiR dimer, thus relieving the repression of YfiN FIG 163 180 membrane-anchored protein_state Once activated by certain cell stress, the dimeric YfiB transforms from a compact conformation to a stretched conformation, allowing the periplasmic domain of the membrane-anchored YfiB to penetrate the cell wall and sequester the YfiR dimer, thus relieving the repression of YfiN FIG 181 185 YfiB protein Once activated by certain cell stress, the dimeric YfiB transforms from a compact conformation to a stretched conformation, allowing the periplasmic domain of the membrane-anchored YfiB to penetrate the cell wall and sequester the YfiR dimer, thus relieving the repression of YfiN FIG 231 235 YfiR protein Once activated by certain cell stress, the dimeric YfiB transforms from a compact conformation to a stretched conformation, allowing the periplasmic domain of the membrane-anchored YfiB to penetrate the cell wall and sequester the YfiR dimer, thus relieving the repression of YfiN FIG 236 241 dimer oligomeric_state Once activated by certain cell stress, the dimeric YfiB transforms from a compact conformation to a stretched conformation, allowing the periplasmic domain of the membrane-anchored YfiB to penetrate the cell wall and sequester the YfiR dimer, thus relieving the repression of YfiN FIG 276 280 YfiN protein Once activated by certain cell stress, the dimeric YfiB transforms from a compact conformation to a stretched conformation, allowing the periplasmic domain of the membrane-anchored YfiB to penetrate the cell wall and sequester the YfiR dimer, thus relieving the repression of YfiN FIG 50 59 activated protein_state These results, together with our observation that activated YfiB has a much higher cell wall binding affinity, and previous mutagenesis data showing that (1) both PG binding and membrane anchoring are required for YfiB activity and (2) activating mutations possessing an altered N-terminal loop length are dominant over the loss of PG binding (Malone et al.,), suggest an updated regulatory model of the YfiBNR system (Fig. 7). DISCUSS 60 64 YfiB protein These results, together with our observation that activated YfiB has a much higher cell wall binding affinity, and previous mutagenesis data showing that (1) both PG binding and membrane anchoring are required for YfiB activity and (2) activating mutations possessing an altered N-terminal loop length are dominant over the loss of PG binding (Malone et al.,), suggest an updated regulatory model of the YfiBNR system (Fig. 7). DISCUSS 83 109 cell wall binding affinity evidence These results, together with our observation that activated YfiB has a much higher cell wall binding affinity, and previous mutagenesis data showing that (1) both PG binding and membrane anchoring are required for YfiB activity and (2) activating mutations possessing an altered N-terminal loop length are dominant over the loss of PG binding (Malone et al.,), suggest an updated regulatory model of the YfiBNR system (Fig. 7). DISCUSS 163 165 PG chemical These results, together with our observation that activated YfiB has a much higher cell wall binding affinity, and previous mutagenesis data showing that (1) both PG binding and membrane anchoring are required for YfiB activity and (2) activating mutations possessing an altered N-terminal loop length are dominant over the loss of PG binding (Malone et al.,), suggest an updated regulatory model of the YfiBNR system (Fig. 7). DISCUSS 214 218 YfiB protein These results, together with our observation that activated YfiB has a much higher cell wall binding affinity, and previous mutagenesis data showing that (1) both PG binding and membrane anchoring are required for YfiB activity and (2) activating mutations possessing an altered N-terminal loop length are dominant over the loss of PG binding (Malone et al.,), suggest an updated regulatory model of the YfiBNR system (Fig. 7). DISCUSS 290 294 loop structure_element These results, together with our observation that activated YfiB has a much higher cell wall binding affinity, and previous mutagenesis data showing that (1) both PG binding and membrane anchoring are required for YfiB activity and (2) activating mutations possessing an altered N-terminal loop length are dominant over the loss of PG binding (Malone et al.,), suggest an updated regulatory model of the YfiBNR system (Fig. 7). DISCUSS 332 334 PG chemical These results, together with our observation that activated YfiB has a much higher cell wall binding affinity, and previous mutagenesis data showing that (1) both PG binding and membrane anchoring are required for YfiB activity and (2) activating mutations possessing an altered N-terminal loop length are dominant over the loss of PG binding (Malone et al.,), suggest an updated regulatory model of the YfiBNR system (Fig. 7). DISCUSS 404 410 YfiBNR complex_assembly These results, together with our observation that activated YfiB has a much higher cell wall binding affinity, and previous mutagenesis data showing that (1) both PG binding and membrane anchoring are required for YfiB activity and (2) activating mutations possessing an altered N-terminal loop length are dominant over the loss of PG binding (Malone et al.,), suggest an updated regulatory model of the YfiBNR system (Fig. 7). DISCUSS 89 96 dimeric oligomeric_state In this model, in response to a particular cell stress that is yet to be identified, the dimeric YfiB is activated from a compact, inactive conformation to a stretched conformation, which possesses increased PG binding affinity. DISCUSS 97 101 YfiB protein In this model, in response to a particular cell stress that is yet to be identified, the dimeric YfiB is activated from a compact, inactive conformation to a stretched conformation, which possesses increased PG binding affinity. DISCUSS 105 114 activated protein_state In this model, in response to a particular cell stress that is yet to be identified, the dimeric YfiB is activated from a compact, inactive conformation to a stretched conformation, which possesses increased PG binding affinity. DISCUSS 122 129 compact protein_state In this model, in response to a particular cell stress that is yet to be identified, the dimeric YfiB is activated from a compact, inactive conformation to a stretched conformation, which possesses increased PG binding affinity. DISCUSS 131 139 inactive protein_state In this model, in response to a particular cell stress that is yet to be identified, the dimeric YfiB is activated from a compact, inactive conformation to a stretched conformation, which possesses increased PG binding affinity. DISCUSS 140 152 conformation protein_state In this model, in response to a particular cell stress that is yet to be identified, the dimeric YfiB is activated from a compact, inactive conformation to a stretched conformation, which possesses increased PG binding affinity. DISCUSS 158 180 stretched conformation protein_state In this model, in response to a particular cell stress that is yet to be identified, the dimeric YfiB is activated from a compact, inactive conformation to a stretched conformation, which possesses increased PG binding affinity. DISCUSS 208 210 PG chemical In this model, in response to a particular cell stress that is yet to be identified, the dimeric YfiB is activated from a compact, inactive conformation to a stretched conformation, which possesses increased PG binding affinity. DISCUSS 16 34 C-terminal portion structure_element This allows the C-terminal portion of the membrane-anchored YfiB to reach, bind and penetrate the cell wall and sequester the YfiR dimer. DISCUSS 42 59 membrane-anchored protein_state This allows the C-terminal portion of the membrane-anchored YfiB to reach, bind and penetrate the cell wall and sequester the YfiR dimer. DISCUSS 60 64 YfiB protein This allows the C-terminal portion of the membrane-anchored YfiB to reach, bind and penetrate the cell wall and sequester the YfiR dimer. DISCUSS 126 130 YfiR protein This allows the C-terminal portion of the membrane-anchored YfiB to reach, bind and penetrate the cell wall and sequester the YfiR dimer. DISCUSS 131 136 dimer oligomeric_state This allows the C-terminal portion of the membrane-anchored YfiB to reach, bind and penetrate the cell wall and sequester the YfiR dimer. DISCUSS 4 10 YfiBNR complex_assembly The YfiBNR system provides a good example of a delicate homeostatic system that integrates multiple signals to regulate the c-di-GMP level. DISCUSS 124 132 c-di-GMP chemical The YfiBNR system provides a good example of a delicate homeostatic system that integrates multiple signals to regulate the c-di-GMP level. DISCUSS 16 22 YfiBNR complex_assembly Homologs of the YfiBNR system are functionally conserved in P. aeruginosa (Malone et al.,; Malone et al.,), E. coli (Hufnagel et al.,; Raterman et al.,; Sanchez-Torres et al.,), K. pneumonia (Huertas et al.,) and Y. pestis (Ren et al.,), where they affect c-di-GMP production and biofilm formation. DISCUSS 34 56 functionally conserved protein_state Homologs of the YfiBNR system are functionally conserved in P. aeruginosa (Malone et al.,; Malone et al.,), E. coli (Hufnagel et al.,; Raterman et al.,; Sanchez-Torres et al.,), K. pneumonia (Huertas et al.,) and Y. pestis (Ren et al.,), where they affect c-di-GMP production and biofilm formation. DISCUSS 60 73 P. aeruginosa species Homologs of the YfiBNR system are functionally conserved in P. aeruginosa (Malone et al.,; Malone et al.,), E. coli (Hufnagel et al.,; Raterman et al.,; Sanchez-Torres et al.,), K. pneumonia (Huertas et al.,) and Y. pestis (Ren et al.,), where they affect c-di-GMP production and biofilm formation. DISCUSS 108 115 E. coli species Homologs of the YfiBNR system are functionally conserved in P. aeruginosa (Malone et al.,; Malone et al.,), E. coli (Hufnagel et al.,; Raterman et al.,; Sanchez-Torres et al.,), K. pneumonia (Huertas et al.,) and Y. pestis (Ren et al.,), where they affect c-di-GMP production and biofilm formation. DISCUSS 178 190 K. pneumonia species Homologs of the YfiBNR system are functionally conserved in P. aeruginosa (Malone et al.,; Malone et al.,), E. coli (Hufnagel et al.,; Raterman et al.,; Sanchez-Torres et al.,), K. pneumonia (Huertas et al.,) and Y. pestis (Ren et al.,), where they affect c-di-GMP production and biofilm formation. DISCUSS 213 222 Y. pestis species Homologs of the YfiBNR system are functionally conserved in P. aeruginosa (Malone et al.,; Malone et al.,), E. coli (Hufnagel et al.,; Raterman et al.,; Sanchez-Torres et al.,), K. pneumonia (Huertas et al.,) and Y. pestis (Ren et al.,), where they affect c-di-GMP production and biofilm formation. DISCUSS 256 264 c-di-GMP chemical Homologs of the YfiBNR system are functionally conserved in P. aeruginosa (Malone et al.,; Malone et al.,), E. coli (Hufnagel et al.,; Raterman et al.,; Sanchez-Torres et al.,), K. pneumonia (Huertas et al.,) and Y. pestis (Ren et al.,), where they affect c-di-GMP production and biofilm formation. DISCUSS 23 32 activated protein_state The mechanism by which activated YfiB relieves the repression of YfiN may be applicable to the YfiBNR system in other bacteria and to analogous outside-in signaling for c-di-GMP production, which in turn may be relevant to the development of drugs that can circumvent complicated antibiotic resistance. DISCUSS 33 37 YfiB protein The mechanism by which activated YfiB relieves the repression of YfiN may be applicable to the YfiBNR system in other bacteria and to analogous outside-in signaling for c-di-GMP production, which in turn may be relevant to the development of drugs that can circumvent complicated antibiotic resistance. DISCUSS 65 69 YfiN protein The mechanism by which activated YfiB relieves the repression of YfiN may be applicable to the YfiBNR system in other bacteria and to analogous outside-in signaling for c-di-GMP production, which in turn may be relevant to the development of drugs that can circumvent complicated antibiotic resistance. DISCUSS 95 101 YfiBNR complex_assembly The mechanism by which activated YfiB relieves the repression of YfiN may be applicable to the YfiBNR system in other bacteria and to analogous outside-in signaling for c-di-GMP production, which in turn may be relevant to the development of drugs that can circumvent complicated antibiotic resistance. DISCUSS 118 126 bacteria taxonomy_domain The mechanism by which activated YfiB relieves the repression of YfiN may be applicable to the YfiBNR system in other bacteria and to analogous outside-in signaling for c-di-GMP production, which in turn may be relevant to the development of drugs that can circumvent complicated antibiotic resistance. DISCUSS 169 177 c-di-GMP chemical The mechanism by which activated YfiB relieves the repression of YfiN may be applicable to the YfiBNR system in other bacteria and to analogous outside-in signaling for c-di-GMP production, which in turn may be relevant to the development of drugs that can circumvent complicated antibiotic resistance. DISCUSS