2O8K

NMR Structure of the Sigma-54 RpoN Domain Bound to the-24 Promoter Element

• PDB DOI: https://doi.org/10.2210/pdb2O8K/pdb
• NAKB: 2O8K
• BMRB: 15083

• Classification: TRANSCRIPTION/DNA
• Organism(s): Aquifex aeolicus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-12-12 Released: 2007-07-17 
• Deposition Author(s): Doucleff, M., Pelton, J.G., Lee, P.S., Wemmer, D.E.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 50 
• Conformers Submitted: 20 
• Selection Criteria: 20 structures with lowest energy and no restraint violations greater than 0.5 A and 5 degrees for distance and dihedral restraints, respectively 

Literature

Structural basis of DNA recognition by the alternative sigma-factor, sigma54.

Doucleff, M., Pelton, J.G., Lee, P.S., Nixon, B.T., Wemmer, D.E.

(2007) J Mol Biol 369: 1070-1078

• PubMed: 17481658 
• DOI: https://doi.org/10.1016/j.jmb.2007.04.019
• Primary Citation of Related Structures:  
  2O8K, 2O9L


• PubMed Abstract: 
  

  The sigma subunit of bacterial RNA polymerase (RNAP) regulates gene expression by directing RNAP to specific promoters. Unlike sigma(70)-type proteins, the alternative sigma factor, sigma(54), requires interaction with an ATPase to open DNA. We present the solution structure of the C-terminal domain of sigma(54) bound to the -24 promoter element, in which the conserved RpoN box motif inserts into the major groove of the DNA. This structure elucidates the basis for sequence specific recognition of the -24 element, orients sigma(54) on the promoter, and suggests how the C-terminal domain of sigma(54) interacts with RNAP.

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Organizational Affiliation: 

Physical Biosciences Division, Lawrence Berkeley National Laboratory and the Department of Chemistry, University of California, Berkeley, CA 94720, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 16.05 kDa 
• Atom Count: 1,091 
• Modelled Residue Count: 91 
• Deposited Residue Count: 91 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA polymerase sigma factor RpoN	C [auth A]	63	Aquifex aeolicus	Mutation(s): 0  Gene Names: rpoN
UniProt
Find proteins for O66858 (Aquifex aeolicus (strain VF5)) Explore O66858  Go to UniProtKB:  O66858

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*TP*TP*TP*TP*GP*GP*CP*AP*CP*GP*TP*TP*TP*C)-3'	A [auth B]	14	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*GP*AP*AP*AP*CP*GP*TP*GP*CP*CP*AP*AP*AP*A)-3'	B [auth C]	14	N/A

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 50 
• Conformers Submitted: 20 
• Selection Criteria: 20 structures with lowest energy and no restraint violations greater than 0.5 A and 5 degrees for distance and dihedral restraints, respectively 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-07-17 
Deposition Author(s): Doucleff, M., Pelton, J.G., Lee, P.S., Wemmer, D.E.

Revision History  

• Version 1.0: 2007-07-17
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2022-03-16
  Changes: Data collection, Database references, Derived calculations
• Version 1.4: 2023-12-27
  Changes: Data collection