6DT8

Bacteriophage N4 RNA polymerase II elongation complex 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Minimalism and functionality: Structural lessons from the heterodimeric N4 bacteriophage RNA polymerase II.

Molodtsov, V.Murakami, K.S.

(2018) J. Biol. Chem. 293: 13616-13625

  • DOI: 10.1074/jbc.RA118.003447
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Genomes of phages, mitochondria, and chloroplasts are transcribed by a diverse group of transcriptional machineries with structurally related single-subunit RNA polymerases (RNAPs). Our understanding of transcription mechanisms of these enzymes is pr ...

    Genomes of phages, mitochondria, and chloroplasts are transcribed by a diverse group of transcriptional machineries with structurally related single-subunit RNA polymerases (RNAPs). Our understanding of transcription mechanisms of these enzymes is predominantly based on biochemical and structural studies of three most-studied members, transcription factor-independent phage T7 RNAP, transcription factor-dependent phage N4 virion-encapsidated RNAP, and transcription factor-dependent mitochondrial RNAPs (mtRNAP). Although these RNAPs employ completely different mechanisms for promoter recognition and transcription termination, these enzymes are relatively large and formed by single polypeptides. Historically being a model enzyme for studying the mechanisms of transcription by T7-like RNAPs, however, T7 RNAP represents only a small group of RNAPs in this family. The vast majority of T7-like RNAPs are transcription factor-dependent, and several of them are heterodimeric enzymes. Here, we report X-ray crystal structures of transcription complexes of the smallest and heterodimeric form of T7-like RNAP, bacteriophage N4 RNAPII, providing insights into the structural organization of a minimum RNAP in this family. We analyze structural and functional aspects of heterodimeric architecture of N4 RNAPII concerning the mechanisms of transcription initiation and transition to processive RNA elongation. Interestingly, N4 RNAPII maintains the same conformation in promoter-bound and elongation transcription complexes, revealing a novel transcription mechanism for single-subunit RNAPs. This work establishes a structural basis for studying mechanistic aspects of transcription by factor-dependent minimum RNAP.


    Organizational Affiliation

    From the Department of Biochemistry and Molecular Biology, The Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802 vum5@psu.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RNAP1
A
269Enterobacteria phage N4Mutation(s): 0 
Find proteins for Q8LTE4 (Enterobacteria phage N4)
Go to UniProtKB:  Q8LTE4
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
RNAP2
B
404Enterobacteria phage N4Mutation(s): 0 
Find proteins for Q8LTE3 (Enterobacteria phage N4)
Go to UniProtKB:  Q8LTE3
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(P*AP*CP*CP*CP*AP*CP*CP*AP*AP*AP*AP*A)-3')C49synthetic construct
Entity ID: 4
MoleculeChainsLengthOrganism
RNA (5'-R(P*UP*GP*GP*UP*GP*G)-3')D12synthetic construct
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.190 
  • Space Group: I 4
Unit Cell:
Length (Å)Angle (°)
a = 174.760α = 90.00
b = 174.760β = 90.00
c = 76.404γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PHASERphasing
HKL-2000data reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01GM087350

Revision History 

  • Version 1.0: 2018-07-11
    Type: Initial release
  • Version 1.1: 2018-10-03
    Type: Advisory, Data collection, Database references