2PO4

X-ray crystal structure of polymerase domain of the bacteriophage N4 virion RNA polymerase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.219 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

X-ray crystal structure of polymerase domain of the bacteriophage N4 virion RNA polymerase

Murakami, K.S.Davydova, E.K.Rothman-Denes, L.B.

(2008) Proc.Natl.Acad.Sci.USA 15: 5046-5051

  • DOI: 10.1073/pnas.0712325105

  • PubMed Abstract: 
  • Coliphage N4 virion RNA polymerase (vRNAP), which is injected into the host upon infection, transcribes the phage early genes from promoters that have a 5-bp stem-3 nt loop hairpin structure. Here, we describe the 2.0-A resolution x-ray crystal struc ...

    Coliphage N4 virion RNA polymerase (vRNAP), which is injected into the host upon infection, transcribes the phage early genes from promoters that have a 5-bp stem-3 nt loop hairpin structure. Here, we describe the 2.0-A resolution x-ray crystal structure of N4 mini-vRNAP, a member of the T7-like, single-unit RNAP family and the minimal component having all RNAP functions of the full-length vRNAP. The structure resembles a "fisted right hand" with Fingers, Palm and Thumb subdomains connected to an N-terminal domain. We established that the specificity loop extending from the Fingers along with W129 of the N-terminal domain play critical roles in hairpin-promoter recognition. A comparison with the structure of the T7 RNAP initiation complex reveals that the pathway of the DNA to the active site is blocked in the apo-form vRNAP, indicating that vRNAP must undergo a large-scale conformational change upon promoter DNA binding and explaining the highly restricted promoter specificity of vRNAP that is essential for phage early transcription.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA. kum14@psu.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Virion RNA polymerase
A
1104Enterobacteria phage N4Mutation(s): 0 
Gene Names: 50
EC: 2.7.7.6
Find proteins for Q859P9 (Enterobacteria phage N4)
Go to UniProtKB:  Q859P9
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.219 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 83.047α = 90.00
b = 103.258β = 90.00
c = 159.430γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-2000data reduction
DENZOdata reduction
CNSrefinement
HKL-2000data scaling
MLPHAREphasing
RESOLVEphasing
SCALEPACKdata scaling
CBASSdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-04-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-10-18
    Type: Refinement description