4NJC

RNA Polymerase interacting protein YkzG from Geobacillus stearothermophilus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.213 

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

  • 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 ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Geobacillus stearothermophilus YkzG
A, B, C, D, E, F, G, H
65N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E, F, G, H
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.213 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 35.650α = 90.00
b = 82.780β = 92.76
c = 83.430γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
MAR345dtbdata collection
SCALAdata scaling
BUCCANEERmodel building
BUCCANEERphasing
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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