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

J Am Chem Soc. 2014 Apr 2;136(13):4927-37. doi: 10.1021/ja4102375. Epub 2014 Mar 21.

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • African Swine Fever / virology
  • African Swine Fever Virus / chemistry
  • African Swine Fever Virus / enzymology*
  • African Swine Fever Virus / metabolism
  • Animals
  • Base Pairing
  • DNA / chemistry
  • DNA / metabolism*
  • DNA Polymerase beta / chemistry
  • DNA Polymerase beta / metabolism
  • DNA-Directed DNA Polymerase / chemistry*
  • DNA-Directed DNA Polymerase / metabolism*
  • Deoxycytosine Nucleotides / metabolism
  • Deoxyguanine Nucleotides / metabolism
  • Guanosine Triphosphate / metabolism
  • Models, Molecular
  • Nuclear Magnetic Resonance, Biomolecular
  • Protein Conformation
  • Swine / virology

Substances

  • Deoxycytosine Nucleotides
  • Deoxyguanine Nucleotides
  • 2'-deoxycytidine 5'-triphosphate
  • Guanosine Triphosphate
  • deoxyguanosine triphosphate
  • DNA
  • DNA polymerase X
  • DNA Polymerase beta
  • DNA-Directed DNA Polymerase