4zhu

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of a bacterial repressor protein

Structural highlights

4zhu 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 2.3968Å
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 tripartite signalling system in Pseudomonas aeruginosa that modulates intracellular c-di-GMP levels in response to signals received in the periplasm. YfiB is an outer membrane lipoprotein and presumed sensor protein that sequesters the repressor protein YfiR. To provide insights into YfiBNR function, we have determined three-dimensional crystal structures of YfiB and YfiR from P. aeruginosa PAO1 alone and as a 1:1 complex. A YfiB(27-168) construct is predominantly dimeric, whereas a YfiB(59-168) is monomeric, indicating that YfiB can dimerize via its N-terminal region. YfiR forms a stable complex with YfiB(59-168), while the YfiR binding interface is obstructed by the N-terminal region in YfiB(27-168). The YfiB-YfiR complex reveals a conserved interaction surface on YfiR that overlaps with residues predicted to interact with the periplasmic PAS domain of YfiN. Comparison of native and YfiR-bound structures of YfiB suggests unwinding of the N-terminal linker region for attachment to the outer membrane. A model is thus proposed for YfiR sequestration at the outer membrane by YfiB. Our work provides the first detailed insights into the interaction between YfiB and YfiR at the molecular level and is a valuable starting point for further functional and mechanistic studies of the YfiBNR signalling system.

Structural insights into YfiR sequestering by YfiB in Pseudomonas aeruginosa PAO1.,Li S, Li T, Xu Y, Zhang Q, Zhang W, Che S, Liu R, Wang Y, Bartlam M Sci Rep. 2015 Nov 23;5:16915. doi: 10.1038/srep16915. PMID:26593397^[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
↑ Li S, Li T, Xu Y, Zhang Q, Zhang W, Che S, Liu R, Wang Y, Bartlam M. Structural insights into YfiR sequestering by YfiB in Pseudomonas aeruginosa PAO1. Sci Rep. 2015 Nov 23;5:16915. doi: 10.1038/srep16915. PMID:26593397 doi:http://dx.doi.org/10.1038/srep16915

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/4zhu"

@@ Line 1: / Line 1: @@
 ==Crystal structure of a bacterial repressor protein==
-<StructureSection load='4zhu' size='340' side='right' caption='[[4zhu]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
+<StructureSection load='4zhu' size='340' side='right'caption='[[4zhu]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4zhu]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ZHU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ZHU FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4zhu]] 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=4ZHU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4ZHU FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.3968&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4zhv|4zhv]], [[4zhw|4zhw]], [[4zhy|4zhy]]</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></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4zhu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zhu OCA], [http://pdbe.org/4zhu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4zhu RCSB], [http://www.ebi.ac.uk/pdbsum/4zhu PDBsum]</span></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=4zhu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zhu OCA], [https://pdbe.org/4zhu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4zhu RCSB], [https://www.ebi.ac.uk/pdbsum/4zhu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4zhu 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 21: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Bartlam, M]]
+[[Category: Large Structures]]
-[[Category: Li, S]]
+[[Category: Pseudomonas aeruginosa PAO1]]
-[[Category: Li, T]]
+[[Category: Bartlam M]]
-[[Category: Wang, Y]]
+[[Category: Li S]]
-[[Category: Periplasmic binding protein]]
+[[Category: Li T]]
-[[Category: Repressor]]
+[[Category: Wang Y]]
-[[Category: Transcription]]

4zhu

From Proteopedia

Current revision

Crystal structure of a bacterial repressor protein

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

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