2rde: Difference between revisions

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[[Image:2rde.png|left|200px]]


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==Crystal structure of VCA0042 complexed with c-di-GMP==
The line below this paragraph, containing "STRUCTURE_2rde", creates the "Structure Box" on the page.
<StructureSection load='2rde' size='340' side='right'caption='[[2rde]], [[Resolution|resolution]] 1.92&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[2rde]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Vibrio_cholerae_O395 Vibrio cholerae O395]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RDE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RDE 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]] 1.92&#8491;</td></tr>
-->
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=C2E:9,9-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d 3,2-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one)'>C2E</scene></td></tr>
{{STRUCTURE_2rde|  PDB=2rde  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2rde FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rde OCA], [https://pdbe.org/2rde PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rde RCSB], [https://www.ebi.ac.uk/pdbsum/2rde PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rde ProSAT], [https://www.topsan.org/Proteins/NESGC/2rde TOPSAN]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/A0A0H3ADR8_VIBC3 A0A0H3ADR8_VIBC3]
== 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/rd/2rde_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=2rde ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The second messenger cyclic diguanylate (c-di-GMP) controls the transition between motile and sessile growth in eubacteria, but little is known about the proteins that sense its concentration. Bioinformatics analyses suggested that PilZ domains bind c-di-GMP and allosterically modulate effector pathways. We have determined a 1.9 A crystal structure of c-di-GMP bound to VCA0042/PlzD, a PilZ domain-containing protein from Vibrio cholerae. Either this protein or another specific PilZ domain-containing protein is required for V. cholerae to efficiently infect mice. VCA0042/PlzD comprises a C-terminal PilZ domain plus an N-terminal domain with a similar beta-barrel fold. C-di-GMP contacts seven of the nine strongly conserved residues in the PilZ domain, including three in a seven-residue long N-terminal loop that undergoes a conformational switch as it wraps around c-di-GMP. This switch brings the PilZ domain into close apposition with the N-terminal domain, forming a new allosteric interaction surface that spans these domains and the c-di-GMP at their interface. The very small size of the N-terminal conformational switch is likely to explain the facile evolutionary diversification of the PilZ domain.


===Crystal structure of VCA0042 complexed with c-di-GMP===
The structural basis of cyclic diguanylate signal transduction by PilZ domains.,Benach J, Swaminathan SS, Tamayo R, Handelman SK, Folta-Stogniew E, Ramos JE, Forouhar F, Neely H, Seetharaman J, Camilli A, Hunt JF EMBO J. 2007 Dec 12;26(24):5153-66. Epub 2007 Nov 22. PMID:18034161<ref>PMID:18034161</ref>


 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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The line below this paragraph, {{ABSTRACT_PUBMED_18034161}}, adds the Publication Abstract to the page
<div class="pdbe-citations 2rde" style="background-color:#fffaf0;"></div>
(as it appears on PubMed at http://www.pubmed.gov), where 18034161 is the PubMed ID number.
== References ==
-->
<references/>
{{ABSTRACT_PUBMED_18034161}}
__TOC__
 
</StructureSection>
==About this Structure==
[[Category: Large Structures]]
[[2rde]] is a 2 chain structure with sequence 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=2RDE OCA].
[[Category: Vibrio cholerae O395]]
 
[[Category: Benach J]]
==See Also==
[[Category: Camilli A]]
*[[C-di-GMP receptors with PilZ domain|C-di-GMP receptors with PilZ domain]]
[[Category: Forouhar F]]
*[[PilZ domain|PilZ domain]]
[[Category: Handelman S]]
*[[VCA0042 complexed with c-di-GMP|VCA0042 complexed with c-di-GMP]]
[[Category: Hunt JF]]
 
[[Category: Neely H]]
==Reference==
[[Category: Seetharaman J]]
<ref group="xtra">PMID:018034161</ref><references group="xtra"/>
[[Category: Swaminathan SS]]
[[Category: Vibrio cholerae]]
[[Category: Tamayo R]]
[[Category: Benach, J.]]
[[Category: Camilli, A.]]
[[Category: Forouhar, F.]]
[[Category: Handelman, S.]]
[[Category: Hunt, J F.]]
[[Category: NESG, Northeast Structural Genomics Consortium.]]
[[Category: Neely, H.]]
[[Category: Seetharaman, J.]]
[[Category: Swaminathan, S S.]]
[[Category: Tamayo, R.]]
[[Category: C-di-gmp]]
[[Category: Nesg]]
[[Category: Northeast structural genomics consortium]]
[[Category: Protein structure initiative]]
[[Category: Psi-2]]
[[Category: Structural genomic]]
[[Category: Unknown function]]
[[Category: Vca0042]]
[[Category: Vibrio cholerae]]

Latest revision as of 11:54, 30 August 2023

Crystal structure of VCA0042 complexed with c-di-GMP

2rde, resolution 1.92Å

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