1w25: Difference between revisions
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== | ==Response regulator PleD in complex with c-diGMP== | ||
[[1w25]] is a 2 chain structure with sequence from [ | <StructureSection load='1w25' size='340' side='right'caption='[[1w25]], [[Resolution|resolution]] 2.70Å' scene=''> | ||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[1w25]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Caulobacter_vibrioides_CB15 Caulobacter vibrioides CB15]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1W25 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1W25 FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.7Å</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>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=1w25 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1w25 OCA], [https://pdbe.org/1w25 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1w25 RCSB], [https://www.ebi.ac.uk/pdbsum/1w25 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1w25 ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/PLED_CAUVN PLED_CAUVN] Response regulator that is part of a signal transduction pathway controlling cell differentiation in the swarmer-to-stalked cell transition.<ref>PMID:12622822</ref> Catalyzes the condensation of two GTP molecules to the cyclic dinucleotide di-GMP (c-di-GMP), which acts as a secondary messenger.<ref>PMID:15075296</ref> | |||
== 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/w2/1w25_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=1w25 ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Recent discoveries suggest that a novel second messenger, bis-(3'-->5')-cyclic di-GMP (c-diGMP), is extensively used by bacteria to control multicellular behavior. Condensation of two GTP to the dinucleotide is catalyzed by the widely distributed diguanylate cyclase (DGC or GGDEF) domain that occurs in various combinations with sensory and/or regulatory modules. The crystal structure of the unorthodox response regulator PleD from Caulobacter crescentus, which consists of two CheY-like receiver domains and a DGC domain, has been solved in complex with the product c-diGMP. PleD forms a dimer with the CheY-like domains (the stem) mediating weak monomer-monomer interactions. The fold of the DGC domain is similar to adenylate cyclase, but the nucleotide-binding mode is substantially different. The guanine base is H-bonded to Asn-335 and Asp-344, whereas the ribosyl and alpha-phosphate moieties extend over the beta2-beta3-hairpin that carries the GGEEF signature motif. In the crystal, c-diGMP molecules are crosslinking active sites of adjacent dimers. It is inferred that, in solution, the two DGC domains of a dimer align in a two-fold symmetric way to catalyze c-diGMP synthesis. Two mutually intercalated c-diGMP molecules are found tightly bound at the stem-DGC interface. This allosteric site explains the observed noncompetitive product inhibition. We propose that product inhibition is due to domain immobilization and sets an upper limit for the concentration of this second messenger in the cell. | |||
Structural basis of activity and allosteric control of diguanylate cyclase.,Chan C, Paul R, Samoray D, Amiot NC, Giese B, Jenal U, Schirmer T Proc Natl Acad Sci U S A. 2004 Dec 7;101(49):17084-9. Epub 2004 Nov 29. PMID:15569936<ref>PMID:15569936</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 1w25" style="background-color:#fffaf0;"></div> | |||
==See Also== | ==See Also== | ||
*[[ | *[[Diguanylate cyclase|Diguanylate cyclase]] | ||
*[[Response regulator 3D structure|Response regulator 3D structure]] | |||
*[[Response regulator|Response regulator]] | == References == | ||
<references/> | |||
__TOC__ | |||
== | </StructureSection> | ||
< | [[Category: Caulobacter vibrioides CB15]] | ||
[[Category: Caulobacter vibrioides]] | [[Category: Large Structures]] | ||
[[Category: | [[Category: Chan C]] | ||
[[Category: | [[Category: Jenal U]] | ||
[[Category: | [[Category: Schirmer T]] | ||
[[Category: | |||
Latest revision as of 12:09, 9 May 2024
Response regulator PleD in complex with c-diGMPResponse regulator PleD in complex with c-diGMP
Structural highlights
FunctionPLED_CAUVN Response regulator that is part of a signal transduction pathway controlling cell differentiation in the swarmer-to-stalked cell transition.[1] Catalyzes the condensation of two GTP molecules to the cyclic dinucleotide di-GMP (c-di-GMP), which acts as a secondary messenger.[2] 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 PubMedRecent discoveries suggest that a novel second messenger, bis-(3'-->5')-cyclic di-GMP (c-diGMP), is extensively used by bacteria to control multicellular behavior. Condensation of two GTP to the dinucleotide is catalyzed by the widely distributed diguanylate cyclase (DGC or GGDEF) domain that occurs in various combinations with sensory and/or regulatory modules. The crystal structure of the unorthodox response regulator PleD from Caulobacter crescentus, which consists of two CheY-like receiver domains and a DGC domain, has been solved in complex with the product c-diGMP. PleD forms a dimer with the CheY-like domains (the stem) mediating weak monomer-monomer interactions. The fold of the DGC domain is similar to adenylate cyclase, but the nucleotide-binding mode is substantially different. The guanine base is H-bonded to Asn-335 and Asp-344, whereas the ribosyl and alpha-phosphate moieties extend over the beta2-beta3-hairpin that carries the GGEEF signature motif. In the crystal, c-diGMP molecules are crosslinking active sites of adjacent dimers. It is inferred that, in solution, the two DGC domains of a dimer align in a two-fold symmetric way to catalyze c-diGMP synthesis. Two mutually intercalated c-diGMP molecules are found tightly bound at the stem-DGC interface. This allosteric site explains the observed noncompetitive product inhibition. We propose that product inhibition is due to domain immobilization and sets an upper limit for the concentration of this second messenger in the cell. Structural basis of activity and allosteric control of diguanylate cyclase.,Chan C, Paul R, Samoray D, Amiot NC, Giese B, Jenal U, Schirmer T Proc Natl Acad Sci U S A. 2004 Dec 7;101(49):17084-9. Epub 2004 Nov 29. PMID:15569936[3] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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