2M2T

ASFV Pol X structure


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 2000 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

How a low-fidelity DNA polymerase chooses non-Watson-Crick from Watson-Crick incorporation.

Wu, W.J.Su, M.I.Wu, J.L.Kumar, S.Lim, L.H.Wang, C.W.Nelissen, F.H.Chen, M.C.Doreleijers, J.F.Wijmenga, S.S.Tsai, M.D.

(2014) J.Am.Chem.Soc. 136: 4927-4937

  • DOI: 10.1021/ja4102375
  • Primary Citation of Related Structures:  2M2U, 2M2V, 2M2W

  • PubMed Abstract: 
  • A dogma for DNA polymerase catalysis is that the enzyme binds DNA first, followed by MgdNTP. This mechanism contributes to the selection of correct dNTP by Watson-Crick base pairing, but it cannot explain how low-fidelity DNA polymerases overcome Wat ...

    A dogma for DNA polymerase catalysis is that the enzyme binds DNA first, followed by MgdNTP. This mechanism contributes to the selection of correct dNTP by Watson-Crick base pairing, but it cannot explain how low-fidelity DNA polymerases overcome Watson-Crick base pairing to catalyze non-Watson-Crick dNTP incorporation. DNA polymerase X from the deadly African swine fever virus (Pol X) is a half-sized repair polymerase that catalyzes efficient dG:dGTP incorporation in addition to correct repair. Here we report the use of solution structures of Pol X in the free, binary (Pol X:MgdGTP), and ternary (Pol X:DNA:MgdGTP with dG:dGTP non-Watson-Crick pairing) forms, along with functional analyses, to show that Pol X uses multiple unprecedented strategies to achieve the mutagenic dG:dGTP incorporation. Unlike high fidelity polymerases, Pol X can prebind purine MgdNTP tightly and undergo a specific conformational change in the absence of DNA. The prebound MgdGTP assumes an unusual syn conformation stabilized by partial ring stacking with His115. Upon binding of a gapped DNA, also with a unique mechanism involving primarily helix αE, the prebound syn-dGTP forms a Hoogsteen base pair with the template anti-dG. Interestingly, while Pol X prebinds MgdCTP weakly, the correct dG:dCTP ternary complex is readily formed in the presence of DNA. H115A mutation disrupted MgdGTP binding and dG:dGTP ternary complex formation but not dG:dCTP ternary complex formation. The results demonstrate the first solution structural view of DNA polymerase catalysis, a unique DNA binding mode, and a novel mechanism for non-Watson-Crick incorporation by a low-fidelity DNA polymerase.


    Organizational Affiliation

    Institute of Biological Chemistry, and ‡Genomics Research Center, Academia Sinica , 128 Academia Road Sec. 2, Nankang, Taipei 115, Taiwan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Repair DNA polymerase X
A
174African swine fever virus (strain Badajoz 1971 Vero-adapted)EC: 2.7.7.7
Find proteins for P42494 (African swine fever virus (strain Badajoz 1971 Vero-adapted))
Go to UniProtKB:  P42494
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 2000 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2013-01-03 
  • Released Date: 2014-04-02 
  • Deposition Author(s): Wu, W., Su, M., Tsai, M.

Revision History 

  • Version 1.0: 2014-04-02
    Type: Initial release
  • Version 1.1: 2014-11-12
    Type: Database references