2GAF

Crystal Structure of the Vaccinia Polyadenylate Polymerase Heterodimer (apo form)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.243 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structures of the vaccinia virus polyadenylate polymerase heterodimer: insights into ATP selectivity and processivity.

Moure, C.M.Bowman, B.R.Gershon, P.D.Quiocho, F.A.

(2006) Mol.Cell 22: 339-349

  • DOI: 10.1016/j.molcel.2006.03.015
  • Primary Citation of Related Structures:  
  • Also Cited By: 3OWG

  • PubMed Abstract: 
  • Polyadenylation of mRNAs in poxviruses, crucial for virion maturation, is carried out by a poly(A) polymerase heterodimer composed of a catalytic component, VP55, and a processivity factor, VP39. The ATP-gamma-S bound and unbound crystal structures o ...

    Polyadenylation of mRNAs in poxviruses, crucial for virion maturation, is carried out by a poly(A) polymerase heterodimer composed of a catalytic component, VP55, and a processivity factor, VP39. The ATP-gamma-S bound and unbound crystal structures of the vaccinia polymerase reveal an unusual architecture for VP55 that comprises of N-terminal, central or catalytic, and C-terminal domains with different topologies and that differs from many polymerases, including the eukaryotic poly(A) polymerases. Residues in the active site of VP55, located between the catalytic and C-terminal domains, make specific interactions with the adenine of the ATP analog, establishing the molecular basis of ATP recognition. VP55's concave surface docks the globular VP39. A model for RNA primer binding that involves all three VP55 domains and VP39 is proposed. The model supports biochemical evidence that VP39 functions as a processivity factor by partially enclosing the RNA primer at the heterodimer interface.


    Organizational Affiliation

    Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase
A
297Vaccinia virusMutation(s): 3 
EC: 2.1.1.57
Find proteins for Q1PIV4 (Vaccinia virus)
Go to UniProtKB:  Q1PIV4
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Poly(A) polymerase catalytic subunit
D
469Vaccinia virus (strain Western Reserve)Mutation(s): 0 
Gene Names: PAPL
EC: 2.7.7.19
Find proteins for P23371 (Vaccinia virus (strain Western Reserve))
Go to UniProtKB:  P23371
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.243 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 69.085α = 90.00
b = 91.260β = 90.00
c = 133.460γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
CNSrefinement
SCALEPACKdata scaling
HKL-2000data reduction
SHARPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-05-16
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance