3kyg: Difference between revisions

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{{Seed}}
[[Image:3kyg.jpg|left|200px]]


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==Crystal structure of VCA0042 (L135R) complexed with c-di-GMP==
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<StructureSection load='3kyg' size='340' side='right'caption='[[3kyg]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
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== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<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>
or leave the SCENE parameter empty for the default display.
</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>
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<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>
{{STRUCTURE_3kyg|  PDB=3kyg  |  SCENE=  }}
<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 ==
[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>
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    <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/initialview03.spt</scriptWhenUnchecked>
    <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/main_output.php?pdb_ID=3kyg ConSurf].
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== 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.


===Crystal structure of VCA0042 (L135R) complexed with c-di-GMP===
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<ref>PMID:20226196</ref>


 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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(as it appears on PubMed at http://www.pubmed.gov), where 20226196 is the PubMed ID number.
== References ==
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<references/>
{{ABSTRACT_PUBMED_20226196}}
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</StructureSection>
==About this Structure==
[[Category: Large Structures]]
3KYG is a 2 chains structure with sequences from [http://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].
 
==Reference==
<ref group="xtra">PMID:20226196</ref><references group="xtra"/>
[[Category: Vibrio cholerae]]
[[Category: Vibrio cholerae]]
[[Category: Choi, B S.]]
[[Category: Choi BS]]
[[Category: Kim, H.]]
[[Category: Kim H]]
[[Category: Ko, J.]]
[[Category: Ko J]]
[[Category: Ryu, K S.]]
[[Category: Ryu KS]]
[[Category: C-di-gmp]]
[[Category: Pilz domain]]
[[Category: Pp4397]]
[[Category: Unknown function]]
[[Category: Vca0042]]
 
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Retrieved from "https://proteopedia.org/3kyg"