Human DNA polymerase iota incorporates dCTP opposite template G via a G.C + Hoogsteen base pair

Structure. 2005 Oct;13(10):1569-77. doi: 10.1016/j.str.2005.08.010.

Abstract

Human DNA polymerase iota (hPoliota), a member of the Y family of DNA polymerases, differs in remarkable ways from other DNA polymerases, incorporating correct nucleotides opposite template purines with a much higher efficiency and fidelity than opposite template pyrimidines. We present here the crystal structure of hPoliota bound to template G and incoming dCTP, which reveals a G.C + Hoogsteen base pair in a DNA polymerase active site. We show that the hPoliota active site has evolved to favor Hoogsteen base pairing, wherein the template sugar is fixed in a cavity that reduces the C1'-C1' distance across the nascent base pair from approximately 10.5 A in other DNA polymerases to 8.6 A in hPoliota. The rotation of G from anti to syn is then largely in response to this curtailed C1'-C1' distance. A G.C+ Hoogsteen base pair suggests a specific mechanism for hPoliota's ability to bypass N(2)-adducted guanines that obstruct replication.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Base Composition
  • Base Pairing*
  • Binding Sites
  • Catalysis
  • Computer Simulation
  • Crystallography, X-Ray
  • DNA-Directed DNA Polymerase / metabolism*
  • Deoxycytosine Nucleotides / metabolism*
  • Humans
  • Models, Molecular
  • Protein Folding
  • Protein Structure, Tertiary
  • Rotation
  • Spectrum Analysis, Raman
  • Templates, Genetic

Substances

  • Deoxycytosine Nucleotides
  • 2'-deoxycytidine 5'-triphosphate
  • DNA polymerase iota
  • DNA-Directed DNA Polymerase