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3kyg

From Proteopedia

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Crystal structure of VCA0042 (L135R) complexed with c-di-GMP

Structural highlights

3kyg is a 2 chain structure with sequence from Vibrio cholerae. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.1Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

YCGRL_VIBCH May act 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 (Potential). Binds bis-(3'-5') cyclic diguanylic acid (c-di-GMP) with a dissociation constant of 170 nM in the presence of 10 mM KCl and with 100 nM in its absence. Binds 1 to 2 c-di-GMP per subunit. Only 1 c-di-GMP is seen in the wild-type crystal, while 2 are seen in the mutant. Depending on the concentration of K(+) stoichiometries of 1:1, 1.43:1 and 2:1 are determined by isothermal titration calorimetry.

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/3kyg"

@@ Line 1: / Line 1: @@
 ==Crystal structure of VCA0042 (L135R) complexed with c-di-GMP==
-<StructureSection load='3kyg' size='340' side='right' caption='[[3kyg]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
+<StructureSection load='3kyg' size='340' side='right'caption='[[3kyg]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3kyg]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillo_virgola_del_koch"_trevisan_1884 "bacillo virgola del koch" trevisan 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KYG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3KYG FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3kyg]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Vibrio_cholerae Vibrio cholerae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KYG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3KYG 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>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">VC_A0042 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=666 "Bacillo virgola del Koch" Trevisan 1884])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5GP:GUANOSINE-5-MONOPHOSPHATE'>5GP</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=3kyg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kyg OCA], [http://pdbe.org/3kyg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3kyg RCSB], [http://www.ebi.ac.uk/pdbsum/3kyg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3kyg ProSAT]</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=3kyg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kyg OCA], [https://pdbe.org/3kyg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3kyg RCSB], [https://www.ebi.ac.uk/pdbsum/3kyg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3kyg ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/YCGRL_VIBCH YCGRL_VIBCH]] May act 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 (Potential). Binds bis-(3'-5') cyclic diguanylic acid (c-di-GMP) with a dissociation constant of 170 nM in the presence of 10 mM KCl and with 100 nM in its absence. Binds 1 to 2 c-di-GMP per subunit. Only 1 c-di-GMP is seen in the wild-type crystal, while 2 are seen in the mutant. Depending on the concentration of K(+) stoichiometries of 1:1, 1.43:1 and 2:1 are determined by isothermal titration calorimetry.
+[https://www.uniprot.org/uniprot/YCGRL_VIBCH YCGRL_VIBCH] May act 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 (Potential). Binds bis-(3'-5') cyclic diguanylic acid (c-di-GMP) with a dissociation constant of 170 nM in the presence of 10 mM KCl and with 100 nM in its absence. Binds 1 to 2 c-di-GMP per subunit. Only 1 c-di-GMP is seen in the wild-type crystal, while 2 are seen in the mutant. Depending on the concentration of K(+) stoichiometries of 1:1, 1.43:1 and 2:1 are determined by isothermal titration calorimetry.
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ky/3kyg_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ky/3kyg_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 33: / Line 33: @@
 __TOC__
 </StructureSection>
-[[Category: Bacillo virgola del koch trevisan 1884]]
+[[Category: Large Structures]]
-[[Category: Choi, B S]]
+[[Category: Vibrio cholerae]]
-[[Category: Kim, H]]
+[[Category: Choi BS]]
-[[Category: Ko, J]]
+[[Category: Kim H]]
-[[Category: Ryu, K S]]
+[[Category: Ko J]]
-[[Category: C-di-gmp]]
+[[Category: Ryu KS]]
-[[Category: Pilz domain]]
-[[Category: Pp4397]]
-[[Category: Unknown function]]
-[[Category: Vca0042]]

3kyg

From Proteopedia

Current revision

Crystal structure of VCA0042 (L135R) 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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