This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

2k9l

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

Structure of the Core Binding Domain of sigma54

Structural highlights

2k9l is a 1 chain structure with sequence from Aquifex aeolicus. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Solution NMR
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

O66858_AQUAE

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

Transcription initiation by bacterial sigma(54)-RNA polymerase requires a conformational change of the holopolymerase-DNA complex, driven by an enhancer-binding protein. Although structures of the core polymerase and the more common sigma(70) factor have been determined, little is known about the structure of the sigma(54) variant. We report here the structure of an Aquifex aeolicus sigma(54) domain (residues 69-198), which binds core RNA polymerase. The structure is composed of two distinct subdomains held together by a small, conserved hydrophobic interface that appears to act as a fracture point in the structure. The N-terminal, four-helical subdomain has a negative surface and conserved residues that likely contact the core polymerase, while the C-terminal, three-helical bundle has a strongly positive patch that could contact DNA. Sequence conservation indicates that these structural features are conserved and are important for the role of sigma(54) in the polymerase complex.

Structure of the RNA polymerase core-binding domain of sigma(54) reveals a likely conformational fracture point.,Hong E, Doucleff M, Wemmer DE J Mol Biol. 2009 Jul 3;390(1):70-82. Epub 2009 May 5. PMID:19426742^[1]

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

References

↑ Hong E, Doucleff M, Wemmer DE. Structure of the RNA polymerase core-binding domain of sigma(54) reveals a likely conformational fracture point. J Mol Biol. 2009 Jul 3;390(1):70-82. Epub 2009 May 5. PMID:19426742 doi:http://dx.doi.org/10.1016/j.jmb.2009.04.070

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/2k9l"

Categories: Aquifex aeolicus | Large Structures | Hong E | Wemmer D

@@ Line 1: / Line 1: @@
 ==Structure of the Core Binding Domain of sigma54==
-<StructureSection load='2k9l' size='340' side='right'caption='[[2k9l]], [[NMR_Ensembles_of_Models | 20 NMR models]]' scene=''>
+<StructureSection load='2k9l' size='340' side='right'caption='[[2k9l]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2k9l]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"aquifex_aeolicus"_huber_and_stetter_2001 "aquifex aeolicus" huber and stetter 2001]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2K9L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2K9L FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2k9l]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2K9L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2K9L FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2k9m|2k9m]]</div></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">rpoN ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=63363 "Aquifex aeolicus" Huber and Stetter 2001])</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=2k9l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2k9l OCA], [https://pdbe.org/2k9l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2k9l RCSB], [https://www.ebi.ac.uk/pdbsum/2k9l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2k9l ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/O66858_AQUAE O66858_AQUAE]
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 34: / Line 35: @@
 __TOC__
 </StructureSection>
-[[Category: Aquifex aeolicus huber and stetter 2001]]
+[[Category: Aquifex aeolicus]]
 [[Category: Large Structures]]
-[[Category: Hong, E]]
+[[Category: Hong E]]
-[[Category: Wemmer, D]]
+[[Category: Wemmer D]]
-[[Category: Protein]]
-[[Category: Transcription]]

2k9l

From Proteopedia

Current revision

Structure of the Core Binding Domain of sigma54

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox