PDBsum entry 2m2t

Transferase

PDB id: 2m2t

Contents

Protein chain

174 a.a.

PDB id:

2m2t

Name:

Transferase

Title:

Asfv pol x structure

Structure:

Repair DNA polymerase x. Chain: a. Synonym: pol x. Engineered: yes

Source:

African swine fever virus. Organism_taxid: 10497. Expressed in: escherichia coli. Expression_system_taxid: 562.

NMR struc:

20 models

Authors:

W.Wu,M.Su,M.Tsai

Key ref:

W.J.Wu et al. (2014). How a low-fidelity DNA polymerase chooses non-Watson-Crick from Watson-Crick incorporation. J Am Chem Soc, 136, 4927-4937. PubMed id: 24617852 DOI: 10.1021/ja4102375

Date:

03-Jan-13 Release date: 02-Apr-14

Protein chain

P42494  (DPOLX_ASFB7) -  Repair DNA polymerase X from African swine fever virus (strain Badajoz 1971 Vero-adapted)

Seq: 174 a.a.

Struc: 174 a.a.

Enzyme reactions

• Enzyme class: E.C.2.7.7.7 - DNA-directed Dna polymerase.
• Reaction: DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1021/ja4102375

J Am Chem Soc 136:4927-4937 (2014)

PubMed id: 24617852

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

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

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 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.