2p7v

From Proteopedia

(Difference between revisions)

Revision as of 15:18, 17 June 2021

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

Structural highlights

2p7v is a 2 chain structure with sequence from "bacillus_coli"_migula_1895 "bacillus coli" migula 1895. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Gene:	rsd ("Bacillus coli" Migula 1895), rpoD, alt ("Bacillus coli" Migula 1895)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[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.^[1] ^[2] [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.

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 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^[3]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Jishage M, Ishihama A. A stationary phase protein in Escherichia coli with binding activity to the major sigma subunit of RNA polymerase. Proc Natl Acad Sci U S A. 1998 Apr 28;95(9):4953-8. PMID:9560209
↑ Jishage M, Ishihama A. Transcriptional organization and in vivo role of the Escherichia coli rsd gene, encoding the regulator of RNA polymerase sigma D. J Bacteriol. 1999 Jun;181(12):3768-76. PMID:10368152
↑ Patikoglou GA, Westblade LF, Campbell EA, Lamour V, Lane WJ, Darst SA. Crystal structure of the Escherichia coli regulator of sigma70, Rsd, in complex with sigma70 domain 4. J Mol Biol. 2007 Sep 21;372(3):649-59. Epub 2007 Jul 3. PMID:17681541 doi:10.1016/j.jmb.2007.06.081

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2p7v"

@@ Line 1: / Line 1: @@
 ==Crystal structure of the Escherichia coli regulator of sigma 70, Rsd, in complex with sigma 70 domain 4==
-<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 ==
-<table><tr><td colspan='2'>[[2p7v]] is a 2 chain structure with sequence from [http://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 [http://oca.weizmann.ac.il/oca-docs/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/"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>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
+</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='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">rsd ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), rpoD, alt ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2p7v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2p7v OCA], [http://pdbe.org/2p7v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2p7v RCSB], [http://www.ebi.ac.uk/pdbsum/2p7v PDBsum], [http://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>
 == Function ==
-[[http://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>  [[http://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>  [[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.
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 31: / Line 31: @@
 ==See Also==
-*[[Sigma factor|Sigma factor]]
+*[[Sigma factor 3D structures|Sigma factor 3D structures]]
 == References ==
 <references/>
@@ Line 37: / Line 37: @@
 </StructureSection>
 [[Category: Bacillus coli migula 1895]]
+[[Category: Large Structures]]
 [[Category: Campbell, E A]]
 [[Category: Darst, S A]]

2p7v

From Proteopedia

Revision as of 15:18, 17 June 2021

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

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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