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3kyf

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Revision as of 15:17, 5 August 2016

Crystal structure of P4397 complexed with c-di-GMP

Structural highlights

3kyf is a 1 chain structure with sequence from Psepk. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Related:	3kyg
Gene:	PP4397 (PSEPK)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[YCGR_PSEPK] Acts as a flagellar brake, regulating swimming and swarming in a bis-(3'-5') cyclic diguanylic acid (c-di-GMP)-dependent manner. Increasing levels of c-di-GMP lead to decreased motility (By similarity). Binds c-di-GMP with a dissociation constant of 165 nM. Binds 2 intercalated (c-di-GMP) dimers per subunit.

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

Cyclic diguanylate (c-di-GMP) is a global regulator that modulates pathogen virulence and biofilm formation in bacteria. Although a bioinformatic study revealed that PilZ domain proteins are the long-sought c-di-GMP binding proteins, the mechanism by which c-di-GMP regulates them is uncertain. Pseudomonas putida PP4397 is one such protein that contains YcgR-N and PilZ domains and the apo-PP4397 structure was solved earlier by the Joint Center for Structural Genomics. We determined the crystal structure of holo-PP4397 and found that two intercalated c-di-GMPs fit into the junction of its YcgR-N and PilZ domains. Moreover, c-di-GMP binding induces PP4397 to undergo a dimer-to-monomer transition. Interestingly, another PilZ domain protein, VCA0042, binds to a single molecule of c-di-GMP, and both its apo and holo forms are dimeric. Mutational studies and the additional crystal structure of holo-VCA0042 (L135R) showed that the Arg122 residue of PP4397 is crucial for the recognition of two molecules of c-di-GMP. Thus, PilZ domain proteins exhibit different c-di-GMP binding stoichiometry and quaternary structure, and these differences are expected to play a role in generating diverse forms of c-di-GMP-mediated regulation.

Structure of PP4397 reveals the molecular basis for different c-di-GMP binding modes by Pilz domain proteins.,Ko J, Ryu KS, Kim H, Shin JS, Lee JO, Cheong C, Choi BS J Mol Biol. 2010 Apr 23;398(1):97-110. Epub 2010 Mar 10. PMID:20226196^[1]

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

References

↑ Ko J, Ryu KS, Kim H, Shin JS, Lee JO, Cheong C, Choi BS. Structure of PP4397 reveals the molecular basis for different c-di-GMP binding modes by Pilz domain proteins. J Mol Biol. 2010 Apr 23;398(1):97-110. Epub 2010 Mar 10. PMID:20226196 doi:10.1016/j.jmb.2010.03.007

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3kyf"

@@ Line 1: / Line 1: @@
 ==Crystal structure of P4397 complexed with c-di-GMP==
 <StructureSection load='3kyf' size='340' side='right' caption='[[3kyf]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3kyf]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_putida Pseudomonas putida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KYF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3KYF FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3kyf]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Psepk Psepk]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KYF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3KYF FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=5GP:GUANOSINE-5-MONOPHOSPHATE'>5GP</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3kyg|3kyg]]</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PP4397 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=303 Pseudomonas putida])</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PP4397 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=160488 PSEPK])</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=3kyf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kyf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3kyf RCSB], [http://www.ebi.ac.uk/pdbsum/3kyf PDBsum]</span></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=3kyf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kyf OCA], [http://pdbe.org/3kyf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3kyf RCSB], [http://www.ebi.ac.uk/pdbsum/3kyf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3kyf ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/Q88EQ6_PSEPK Q88EQ6_PSEPK]] Acts as a flagellar brake, regulating swimming and swarming in a bis-(3'-5') cyclic diguanylic acid (c-di-GMP)-dependent manner. Increasing levels of c-di-GMP lead to decreased motility (By similarity). Binds c-di-GMP with a dissociation constant of 165 nM.[HAMAP-Rule:MF_01457]
+[[http://www.uniprot.org/uniprot/YCGR_PSEPK YCGR_PSEPK]] Acts as a flagellar brake, regulating swimming and swarming in a bis-(3'-5') cyclic diguanylic acid (c-di-GMP)-dependent manner. Increasing levels of c-di-GMP lead to decreased motility (By similarity). Binds c-di-GMP with a dissociation constant of 165 nM. Binds 2 intercalated (c-di-GMP) dimers per subunit.
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 18: / Line 19: @@
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
-</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3kyf ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 28: / Line 29: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 3kyf" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Pseudomonas putida]]
+[[Category: Psepk]]
 [[Category: Choi, B S]]
 [[Category: Kim, H]]

3kyf

From Proteopedia

Revision as of 15:17, 5 August 2016

Crystal structure of P4397 complexed with c-di-GMP

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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