3OWG

Crystal structure of vaccinia virus Polyadenylate polymerase(vp55)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.86 Å
  • R-Value Free: 0.316 
  • R-Value Work: 0.253 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Domain-level rocking motion within a polymerase that translocates on single-stranded nucleic acid.

Li, H.Li, C.Zhou, S.Poulos, T.L.Gershon, P.D.

(2013) Acta Crystallogr.,Sect.D 69: 617-624

  • DOI: 10.1107/S0907444913000346

  • PubMed Abstract: 
  • Vaccinia virus poly(A) polymerase (VP55) is the only known polymerase that can translocate independently with respect to single-stranded nucleic acid (ssNA). Previously, its structure has only been solved in the context of the VP39 processivity facto ...

    Vaccinia virus poly(A) polymerase (VP55) is the only known polymerase that can translocate independently with respect to single-stranded nucleic acid (ssNA). Previously, its structure has only been solved in the context of the VP39 processivity factor. Here, a crystal structure of unliganded monomeric VP55 has been solved to 2.86 Å resolution, showing the first backbone structural isoforms among either VP55 or its processivity factor (VP39). Backbone differences between the two molecules of VP55 in the asymmetric unit indicated that unliganded monomeric VP55 can undergo a `rocking' motion of the N-terminal domain with respect to the other two domains, which may be `rigidified' upon VP39 docking. This observation is consistent with previously demonstrated experimental molecular dynamics of the monomer during translocation with respect to nucleic acid and with different mechanisms of translocation in the presence and absence of processivity factor VP39. Side-chain conformational changes in the absence of ligand were observed at a key primer contact site and at the catalytic center of VP55. The current structure completes the trio of possible structural forms for VP55 and VP39, namely the VP39 monomer, the VP39-VP55 heterodimer and the VP55 monomer.


    Related Citations: 
    • 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
    • Polymerase translocation with respect to single-stranded nucleic acid: looping or wrapping of primer around a poly(A) polymerase.
      Li, C.,Li, H.,Zhou, S.,Sun, E.,Yoshizawa, J.,Poulos, T.L.,Gershon, P.D.
      (2009) Structure 17: 680


    Organizational Affiliation

    Department of Molecular Biology and Biochemistry, Xinxiang Medical University, Xinxiang, Henan 453003, People's Republic of China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Poly(A) polymerase catalytic subunit
A, B
485Vaccinia virus (strain Western Reserve)Mutation(s): 1 
Gene Names: PAPL
EC: 2.7.7.19
Find proteins for P23371 (Vaccinia virus (strain Western Reserve))
Go to UniProtKB:  P23371
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.86 Å
  • R-Value Free: 0.316 
  • R-Value Work: 0.253 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 80.128α = 90.00
b = 161.290β = 90.00
c = 97.672γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
HKL-2000data reduction
CNSrefinement
Blu-Icedata collection
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-09-21
    Type: Initial release
  • Version 1.1: 2013-04-03
    Type: Database references
  • Version 1.2: 2017-11-08
    Type: Refinement description