4NJC

RNA Polymerase interacting protein YkzG from Geobacillus stearothermophilus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.216 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

epsilon, a New Subunit of RNA Polymerase Found in Gram-Positive Bacteria

Keller, A.N.Yang, X.Wiedermannova, J.Delumeau, O.Krasny, L.Lewis, P.J.

(2014) J Bacteriol 196: 3622-3632

  • DOI: 10.1128/JB.02020-14
  • Primary Citation of Related Structures:  
    4NJC

  • PubMed Abstract: 
  • RNA polymerase in bacteria is a multisubunit protein complex that is essential for gene expression. We have identified a new subunit of RNA polymerase present in the high-A+T Firmicutes phylum of Gram-positive bacteria and have named it ε. Previously ε had been identified as a small protein (ω1) that copurified with RNA polymerase ...

    RNA polymerase in bacteria is a multisubunit protein complex that is essential for gene expression. We have identified a new subunit of RNA polymerase present in the high-A+T Firmicutes phylum of Gram-positive bacteria and have named it ε. Previously ε had been identified as a small protein (ω1) that copurified with RNA polymerase. We have solved the structure of ε by X-ray crystallography and show that it is not an ω subunit. Rather, ε bears remarkable similarity to the Gp2 family of phage proteins involved in the inhibition of host cell transcription following infection. Deletion of ε shows no phenotype and has no effect on the transcriptional profile of the cell. Determination of the location of ε within the assembly of RNA polymerase core by single-particle analysis suggests that it binds toward the downstream side of the DNA binding cleft. Due to the structural similarity of ε with Gp2 and the fact they bind similar regions of RNA polymerase, we hypothesize that ε may serve a role in protection from phage infection.


    Organizational Affiliation

    School of Environmental and Life Sciences, University of Newcastle, Callghan, New South Wales, Australia Peter.Lewis@newcastle.edu.au.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Geobacillus stearothermophilus YkzGA, B, C, D, E, F, G, H65Geobacillus stearothermophilusMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for A0A0K2H5X8 (Geobacillus stearothermophilus (strain DSM 13240 / CIP 106956 / 10))
Explore A0A0K2H5X8 
Go to UniProtKB:  A0A0K2H5X8
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E, F, G, HL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.216 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.65α = 90
b = 82.78β = 92.76
c = 83.43γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
BUCCANEERmodel building
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
BUCCANEERphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-08-20
    Type: Initial release
  • Version 1.1: 2014-10-22
    Changes: Database references