2p7v: Difference between revisions

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<StructureSection load='2p7v' size='340' side='right'caption='[[2p7v]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
<StructureSection load='2p7v' size='340' side='right'caption='[[2p7v]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[2p7v]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2P7V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2P7V FirstGlance]. <br>
<table><tr><td colspan='2'>[[2p7v]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2P7V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2P7V FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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]] 2.6&#8491;</td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">rsd ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), rpoD, alt ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=2p7v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2p7v OCA], [https://pdbe.org/2p7v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2p7v RCSB], [https://www.ebi.ac.uk/pdbsum/2p7v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2p7v ProSAT]</span></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=2p7v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2p7v OCA], [https://pdbe.org/2p7v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2p7v RCSB], [https://www.ebi.ac.uk/pdbsum/2p7v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2p7v ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/RSD_ECOLI RSD_ECOLI]] Binds RpoD and negatively regulates RpoD-mediated transcription activation by preventing the interaction between the primary sigma factor RpoD with the catalytic core of the RNA polymerase and with promoter DNA. May be involved in replacement of the RNA polymerase sigma subunit from RpoD to RpoS during the transition from exponential growth to the stationary phase.<ref>PMID:9560209</ref> <ref>PMID:10368152</ref> [[https://www.uniprot.org/uniprot/RPOD_ECOLI RPOD_ECOLI]] Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released. This is the primary sigma factor of this bacterium.
[https://www.uniprot.org/uniprot/RSD_ECOLI RSD_ECOLI] Binds RpoD and negatively regulates RpoD-mediated transcription activation by preventing the interaction between the primary sigma factor RpoD with the catalytic core of the RNA polymerase and with promoter DNA. May be involved in replacement of the RNA polymerase sigma subunit from RpoD to RpoS during the transition from exponential growth to the stationary phase.<ref>PMID:9560209</ref> <ref>PMID:10368152</ref>  
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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</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=2p7v ConSurf].
</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=2p7v ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The Escherichia coli Rsd protein binds tightly and specifically to the RNA polymerase (RNAP) sigma(70) factor. Rsd plays a role in alternative sigma factor-dependent transcription by biasing the competition between sigma(70) and alternative sigma factors for the available core RNAP. Here, we determined the 2.6 A-resolution X-ray crystal structure of Rsd bound to sigma(70) domain 4 (sigma(70)(4)), the primary determinant for Rsd binding within sigma(70). The structure reveals that Rsd binding interferes with the two primary functions of sigma(70)(4), core RNAP binding and promoter -35 element binding. Interestingly, the most highly conserved Rsd residues form a network of interactions through the middle of the Rsd structure that connect the sigma(70)(4)-binding surface with three cavities exposed on distant surfaces of Rsd, suggesting functional coupling between sigma(70)(4) binding and other binding surfaces of Rsd, either for other proteins or for as yet unknown small molecule effectors. These results provide a structural basis for understanding the role of Rsd, as well as its ortholog, AlgQ, a positive regulator of Pseudomonas aeruginosa virulence, in transcription regulation.
Crystal structure of the Escherichia coli regulator of sigma70, Rsd, in complex with sigma70 domain 4.,Patikoglou GA, Westblade LF, Campbell EA, Lamour V, Lane WJ, Darst SA J Mol Biol. 2007 Sep 21;372(3):649-59. Epub 2007 Jul 3. PMID:17681541<ref>PMID:17681541</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2p7v" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Bacillus coli migula 1895]]
[[Category: Escherichia coli]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Campbell, E A]]
[[Category: Campbell EA]]
[[Category: Darst, S A]]
[[Category: Darst SA]]
[[Category: Lamour, V]]
[[Category: Lamour V]]
[[Category: Lane, W J]]
[[Category: Lane WJ]]
[[Category: Patikoglou, G A]]
[[Category: Patikoglou GA]]
[[Category: Westblade, L F]]
[[Category: Westblade LF]]
[[Category: E. coli rsd-sigma 70 complex]]
[[Category: Escherichia coli rsd-sigma 70 complex]]
[[Category: Helix-turn-helix]]
[[Category: Regulation]]
[[Category: Regulator of sigma 70]]
[[Category: Rsd]]
[[Category: Rsd-sigma 70 complex]]
[[Category: Sigma 70]]
[[Category: Sigma 70 domain 4]]
[[Category: Sigma factor]]
[[Category: Transcription]]

Latest revision as of 09:08, 21 February 2024

Crystal structure of the Escherichia coli regulator of sigma 70, Rsd, in complex with sigma 70 domain 4

2p7v, resolution 2.60Å

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