6waf: Difference between revisions
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==Crystal Structure of SmcR N55I from Vibrio vulnificus== | ==Crystal Structure of SmcR N55I from Vibrio vulnificus== | ||
<StructureSection load='6waf' size='340' side='right'caption='[[6waf]]' scene=''> | <StructureSection load='6waf' size='340' side='right'caption='[[6waf]], [[Resolution|resolution]] 3.38Å' 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=6WAF OCA]. For a <b>guided tour on the structure components</b> use [ | <table><tr><td colspan='2'>[[6waf]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_27562 Atcc 27562]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6WAF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6WAF FirstGlance]. <br> | ||
</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> | ||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">smcR, vvpR, CRN32_08135, CRN52_17705, D8T54_02235, D8T65_23975, JS86_16400 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=672 ATCC 27562])</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=6waf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6waf OCA], [https://pdbe.org/6waf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6waf RCSB], [https://www.ebi.ac.uk/pdbsum/6waf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6waf ProSAT]</span></td></tr> | |||
</table> | </table> | ||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Quorum sensing gene expression in vibrios is regulated by the LuxR/HapR family of transcriptional factors, which includes Vibrio vulnificus SmcR. The consensus binding site of Vibrio LuxR/HapR/SmcR proteins is palindromic but highly degenerate with sequence variations at each promoter. To examine the mechanism by which SmcR recognizes diverse DNA sites, we generated SmcR separation-of-function mutants that either repress or activate transcription but not both. SmcR N55I is restricted in recognition of single base-pair variations in DNA binding site sequences and thus is defective at transcription activation but retains interaction with RNA polymerase (RNAP) alpha. SmcR S76A, L139R and N142D substitutions disrupt the interaction with RNAP alpha but retain functional DNA binding activity. X-ray crystallography and small angle X-ray scattering data show that the SmcR DNA binding domain exists in two conformations (wide and narrow), and the protein complex forms a mixture of dimers and tetramers in solution. The three RNAP interaction-deficient variants also have two DNA binding domain conformations, whereas SmcR N55I exhibits only the wide conformation. These data support a model in which two mechanisms drive SmcR transcriptional activation: interaction with RNAP and a multi-conformational DNA binding domain that permits recognition of variable DNA sites. | |||
The DNA binding domain of the Vibrio vulnificus SmcR transcription factor is flexible and binds diverse DNA sequences.,Newman JD, Russell MM, Fan L, Wang YX, Gonzalez-Gutierrez G, van Kessel JC Nucleic Acids Res. 2021 Jun 4;49(10):5967-5984. doi: 10.1093/nar/gkab387. PMID:34023896<ref>PMID:34023896</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 6waf" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Transcriptional activator 3D structures|Transcriptional activator 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Atcc 27562]] | |||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Gonzalez-Gutierrez G]] | [[Category: Gonzalez-Gutierrez, G]] | ||
[[Category: Newman | [[Category: Kessel, J C.van]] | ||
[[Category: Russell | [[Category: Newman, J D]] | ||
[[Category: | [[Category: Russell, M M]] | ||
[[Category: Dna-binding protein]] | |||
[[Category: Quorum-sensing]] | |||
[[Category: Transcription]] | |||
[[Category: Transcription factor]] | |||
Revision as of 06:45, 2 July 2021
Crystal Structure of SmcR N55I from Vibrio vulnificusCrystal Structure of SmcR N55I from Vibrio vulnificus
Structural highlights
Publication Abstract from PubMedQuorum sensing gene expression in vibrios is regulated by the LuxR/HapR family of transcriptional factors, which includes Vibrio vulnificus SmcR. The consensus binding site of Vibrio LuxR/HapR/SmcR proteins is palindromic but highly degenerate with sequence variations at each promoter. To examine the mechanism by which SmcR recognizes diverse DNA sites, we generated SmcR separation-of-function mutants that either repress or activate transcription but not both. SmcR N55I is restricted in recognition of single base-pair variations in DNA binding site sequences and thus is defective at transcription activation but retains interaction with RNA polymerase (RNAP) alpha. SmcR S76A, L139R and N142D substitutions disrupt the interaction with RNAP alpha but retain functional DNA binding activity. X-ray crystallography and small angle X-ray scattering data show that the SmcR DNA binding domain exists in two conformations (wide and narrow), and the protein complex forms a mixture of dimers and tetramers in solution. The three RNAP interaction-deficient variants also have two DNA binding domain conformations, whereas SmcR N55I exhibits only the wide conformation. These data support a model in which two mechanisms drive SmcR transcriptional activation: interaction with RNAP and a multi-conformational DNA binding domain that permits recognition of variable DNA sites. The DNA binding domain of the Vibrio vulnificus SmcR transcription factor is flexible and binds diverse DNA sequences.,Newman JD, Russell MM, Fan L, Wang YX, Gonzalez-Gutierrez G, van Kessel JC Nucleic Acids Res. 2021 Jun 4;49(10):5967-5984. doi: 10.1093/nar/gkab387. PMID:34023896[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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