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==Crystal Structure of VpsR display novel dimeric architecture and c-di-GMP binding: mechanistic implications in oligomerization, ATPase activity and DNA binding.==
==Crystal Structure of VpsR display novel dimeric architecture and c-di-GMP binding: mechanistic implications in oligomerization, ATPase activity and DNA binding.==
<StructureSection load='7v4e' size='340' side='right'caption='[[7v4e]]' scene=''>
<StructureSection load='7v4e' size='340' side='right'caption='[[7v4e]], [[Resolution|resolution]] 4.00&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7V4E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7V4E FirstGlance]. <br>
<table><tr><td colspan='2'>[[7v4e]] 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=7V4E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7V4E FirstGlance]. <br>
</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=7v4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7v4e OCA], [https://pdbe.org/7v4e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7v4e RCSB], [https://www.ebi.ac.uk/pdbsum/7v4e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7v4e ProSAT]</span></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]] 4&#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>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=7v4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7v4e OCA], [https://pdbe.org/7v4e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7v4e RCSB], [https://www.ebi.ac.uk/pdbsum/7v4e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7v4e ProSAT]</span></td></tr>
</table>
</table>
== Function ==
[https://www.uniprot.org/uniprot/Q9KU59_VIBCH Q9KU59_VIBCH]
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
VpsR, the master regulator of biofilm formation in Vibrio cholerae, is an atypical NtrC1 type bEBP lacking residues essential for sigma(54)-RNAP binding and REC domain phosphorylation. Moreover, transcription from PvpsL, a promoter of biofilm biosynthesis, has been documented in presence of sigma(70)-RNAP/VpsR/c-di-GMP complex. It was proposed that c-di-GMP and VpsR together form an active transcription complex with sigma(70)-RNAP. However, the impact of c-di-GMP imparted on VpsR that leads to transcription activation with sigma(70)-RNAP remained elusive, largely due to the lack of the structure of VpsR and knowledge about c-di-GMP:VpsR interactions. In this direction we have solved the crystal structure of VpsR(RA), containing REC and AAA(+) domains, in apo, AMPPNP/GMPPNP and c-di-GMP bound states. Structures of VpsR(RA) unveiled distinctive REC domain orientation that leads to a novel dimeric association and noncanonical ATP/GTP binding. Moreover, we have demonstrated that at physiological pH VpsR remains as monomer having no ATPase activity but c-di-GMP imparted cooperativity to convert it to dimer with potent activity. Crystal structure of c-di-GMP:VpsR(RA) complex reveals that c-di-GMP binds near the C-terminal end of AAA(+) domain. Trp quenching studies on VpsR(R), VpsR(A), VpsR(RA), VpsR(AD) with c-di-GMP additionally demonstrated that c-di-GMP could potentially bind VpsR(D). We propose that c-di-GMP mediated tethering of VpsR(D) with VpsR(A) could likely favor generating the specific protein-DNA architecture for transcription activation.
Crystal Structure of VpsR Revealed Novel Dimeric Architecture and c-di-GMP Binding Site: Mechanistic Implications in Oligomerization, ATPase Activity and DNA Binding.,Chakrabortty T, Roy Chowdhury S, Ghosh B, Sen U J Mol Biol. 2022 Jan 30;434(2):167354. doi: 10.1016/j.jmb.2021.167354. Epub 2021 , Nov 10. PMID:34774564<ref>PMID:34774564</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 7v4e" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Vibrio cholerae]]
[[Category: Chakrabortty T]]
[[Category: Chakrabortty T]]
[[Category: Sen U]]
[[Category: Sen U]]
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