2K9M

Structure of the Core Binding Domain of sigma54


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the least restraint violations 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure of the RNA polymerase core-binding domain of sigma(54) reveals a likely conformational fracture point

Hong, E.Doucleff, M.Wemmer, D.E.

(2009) J Mol Biol 390: 70-82

  • DOI: 10.1016/j.jmb.2009.04.070
  • Primary Citation of Related Structures:  
    2K9M, 2K9L

  • PubMed Abstract: 
  • 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 ...

    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.


    Organizational Affiliation

    Department of Chemistry, University of California, Berkeley, 94720-1460, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RNA polymerase sigma factor RpoNA130Aquifex aeolicusMutation(s): 0 
Gene Names: rpoN
UniProt
Find proteins for O66858 (Aquifex aeolicus (strain VF5))
Explore O66858 
Go to UniProtKB:  O66858
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the least restraint violations 
  • OLDERADO: 2K9M Olderado

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2008-10-19 
  • Released Date: 2009-05-26 
  • Deposition Author(s): Hong, E., Wemmer, D.

Revision History  (Full details and data files)

  • Version 1.0: 2009-05-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance