3WOE

Crystal structure of P23-45 gp39 (6-109) bound to Thermus thermophilus RNA polymerase beta-flap domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.351 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural basis for promoter specificity switching of RNA polymerase by a phage factor.

Tagami, S.Sekine, S.Minakhin, L.Esyunina, D.Akasaka, R.Shirouzu, M.Kulbachinskiy, A.Severinov, K.Yokoyama, S.

(2014) Genes Dev. 28: 521-531

  • DOI: 10.1101/gad.233916.113
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Transcription of DNA to RNA by DNA-dependent RNA polymerase (RNAP) is the first step of gene expression and a major regulation point. Bacteriophages hijack their host's transcription machinery and direct it to serve their needs. The gp39 protein enco ...

    Transcription of DNA to RNA by DNA-dependent RNA polymerase (RNAP) is the first step of gene expression and a major regulation point. Bacteriophages hijack their host's transcription machinery and direct it to serve their needs. The gp39 protein encoded by Thermus thermophilus phage P23-45 binds the host's RNAP and inhibits transcription initiation from its major "-10/-35" class promoters. Phage promoters belonging to the minor "extended -10" class are minimally inhibited. We report the crystal structure of the T. thermophilus RNAP holoenzyme complexed with gp39, which explains the mechanism for RNAP promoter specificity switching. gp39 simultaneously binds to the RNAP β-flap domain and the C-terminal domain of the σ subunit (region 4 of the σ subunit [σ4]), thus relocating the β-flap tip and σ4. The ~45 Å displacement of σ4 is incompatible with its binding to the -35 promoter consensus element, thus accounting for the inhibition of transcription from -10/-35 class promoters. In contrast, this conformational change is compatible with the recognition of extended -10 class promoters. These results provide the structural bases for the conformational modulation of the host's RNAP promoter specificity to switch gene expression toward supporting phage development for gp39 and, potentially, other phage proteins, such as T4 AsiA.


    Organizational Affiliation

    RIKEN Systems and Structural Biology Center, Tsurumi-ku, Yokohama 230-0045, Japan;




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit beta
A, C
130Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpoB
EC: 2.7.7.6
Find proteins for Q8RQE9 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q8RQE9
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Putative uncharacterized protein
B, D
106Thermus virus P23-45Mutation(s): 0 
Find proteins for A7XX65 (Thermus virus P23-45)
Go to UniProtKB:  A7XX65
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
B, D
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.351 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.181 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 99.232α = 90.00
b = 99.232β = 90.00
c = 117.190γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-03-12
    Type: Initial release
  • Version 1.1: 2015-03-25
    Type: Database references