5eb2

From Proteopedia

(Difference between revisions)

Current revision

Trp-bound YfiR

Structural highlights

5eb2 is a 2 chain structure with sequence from Pseudomonas aeruginosa PAO1. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.709Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

YFIR_PSEAE Negatively regulates the activity of the diguanylate cyclase TpbB/YfiN, leading to decreased c-di-GMP production (PubMed:20300602). Inhibits TpbB/YfiN allosterically, through a hydrophobic interaction between the C-terminus of YfiR and a conserved region of the periplasmic PAS domain of TpbB/YfiN (PubMed:22719254). Under reducing conditions, may also act as an YfiB-independent sensing device that is able to activate TpbB/YfiN in response to the redox status of the periplasm (PubMed:22719254).^[1] ^[2] Part of the YfiB-TpbB-YfiR (or yfiBNR) system, encoding a tripartite signaling module that modulates intracellular c-di-GMP levels (PubMed:20300602, PubMed:22719254). The system is a key regulator of the small colony variant (SCV) phenotype, and plays an important role in biofilm formation and in vivo persistence (PubMed:20300602). The c-di-GMP produced by TpbB/YfiN stimulates the production of the Pel and Psl exopolysaccharides, which promotes surface attachment, generates an SCV phenotype and confers resistance against phagocytosis (PubMed:20300602).^[3] ^[4]

Publication Abstract from PubMed

YfiBNR is a recently identified bis-(3'-5')-cyclic dimeric GMP (c-di-GMP) signaling system in opportunistic pathogens. It is a key regulator of biofilm formation, which is correlated with prolonged persistence of infection and antibiotic drug resistance. 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. However, the detailed regulatory mechanism remains elusive. Here, we report the crystal structures of YfiB alone and of an active mutant YfiBL43P complexed with YfiR with 2:2 stoichiometry. 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. 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. Based on the structural and biochemical data, we propose an updated regulatory model of the YfiBNR system.

Structural insights into the regulatory mechanism of the Pseudomonas aeruginosa YfiBNR system.,Xu M, Yang X, Yang XA, Zhou L, Liu TZ, Fan Z, Jiang T Protein Cell. 2016 Apr 25. PMID:27113583^[5]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Malone JG, Jaeger T, Spangler C, Ritz D, Spang A, Arrieumerlou C, Kaever V, Landmann R, Jenal U. YfiBNR mediates cyclic di-GMP dependent small colony variant formation and persistence in Pseudomonas aeruginosa. PLoS Pathog. 2010 Mar 12;6(3):e1000804. PMID:20300602 doi:10.1371/journal.ppat.1000804
↑ Malone JG, Jaeger T, Manfredi P, Dötsch A, Blanka A, Bos R, Cornelis GR, Häussler S, Jenal U. The YfiBNR signal transduction mechanism reveals novel targets for the evolution of persistent Pseudomonas aeruginosa in cystic fibrosis airways. PLoS Pathog. 2012;8(6):e1002760. PMID:22719254 doi:10.1371/journal.ppat.1002760
↑ Malone JG, Jaeger T, Spangler C, Ritz D, Spang A, Arrieumerlou C, Kaever V, Landmann R, Jenal U. YfiBNR mediates cyclic di-GMP dependent small colony variant formation and persistence in Pseudomonas aeruginosa. PLoS Pathog. 2010 Mar 12;6(3):e1000804. PMID:20300602 doi:10.1371/journal.ppat.1000804
↑ Malone JG, Jaeger T, Manfredi P, Dötsch A, Blanka A, Bos R, Cornelis GR, Häussler S, Jenal U. The YfiBNR signal transduction mechanism reveals novel targets for the evolution of persistent Pseudomonas aeruginosa in cystic fibrosis airways. PLoS Pathog. 2012;8(6):e1002760. PMID:22719254 doi:10.1371/journal.ppat.1002760
↑ Xu M, Yang X, Yang XA, Zhou L, Liu TZ, Fan Z, Jiang T. Structural insights into the regulatory mechanism of the Pseudomonas aeruginosa YfiBNR system. Protein Cell. 2016 Apr 25. PMID:27113583 doi:http://dx.doi.org/10.1007/s13238-016-0264-7

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5eb2"

@@ Line 3: / Line 3: @@
 <StructureSection load='5eb2' size='340' side='right'caption='[[5eb2]], [[Resolution|resolution]] 2.71&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5eb2]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseae Pseae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EB2 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5EB2 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5eb2]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_aeruginosa_PAO1 Pseudomonas aeruginosa PAO1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EB2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5EB2 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TRP:TRYPTOPHAN'>TRP</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.709&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5eaz|5eaz]], [[5eb0|5eb0]], [[5eb1|5eb1]], [[5eb3|5eb3]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TRP:TRYPTOPHAN'>TRP</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">yfiR, PA1121 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=208964 PSEAE])</td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5eb2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5eb2 OCA], [https://pdbe.org/5eb2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5eb2 RCSB], [https://www.ebi.ac.uk/pdbsum/5eb2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5eb2 ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5eb2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5eb2 OCA], [http://pdbe.org/5eb2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5eb2 RCSB], [http://www.ebi.ac.uk/pdbsum/5eb2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5eb2 ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/YFIR_PSEAE YFIR_PSEAE] Negatively regulates the activity of the diguanylate cyclase TpbB/YfiN, leading to decreased c-di-GMP production (PubMed:20300602). Inhibits TpbB/YfiN allosterically, through a hydrophobic interaction between the C-terminus of YfiR and a conserved region of the periplasmic PAS domain of TpbB/YfiN (PubMed:22719254). Under reducing conditions, may also act as an YfiB-independent sensing device that is able to activate TpbB/YfiN in response to the redox status of the periplasm (PubMed:22719254).<ref>PMID:20300602</ref> <ref>PMID:22719254</ref>   Part of the YfiB-TpbB-YfiR (or yfiBNR) system, encoding a tripartite signaling module that modulates intracellular c-di-GMP levels (PubMed:20300602, PubMed:22719254). The system is a key regulator of the small colony variant (SCV) phenotype, and plays an important role in biofilm formation and in vivo persistence (PubMed:20300602). The c-di-GMP produced by TpbB/YfiN stimulates the production of the Pel and Psl exopolysaccharides, which promotes surface attachment, generates an SCV phenotype and confers resistance against phagocytosis (PubMed:20300602).<ref>PMID:20300602</ref> <ref>PMID:22719254</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 23: / Line 24: @@
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Pseae]]
+[[Category: Pseudomonas aeruginosa PAO1]]
-[[Category: Fan, Z]]
+[[Category: Fan Z]]
-[[Category: Jiang, T]]
+[[Category: Jiang T]]
-[[Category: Liu, T Z]]
+[[Category: Liu T-Z]]
-[[Category: Xu, M]]
+[[Category: Xu M]]
-[[Category: Yang, X]]
+[[Category: Yang X]]
-[[Category: Yang, X A]]
+[[Category: Yang X-A]]
-[[Category: Zhou, L]]
+[[Category: Zhou L]]
-[[Category: Periplasmic repressor protein]]
-[[Category: Transcription]]

5eb2

From Proteopedia

Current revision

Trp-bound YfiR

Structural highlights

Function

Publication Abstract from PubMed

References

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