Nucleotide insertion opposite a cis-syn thymine dimer by a replicative DNA polymerase from bacteriophage T7

Nat Struct Mol Biol. 2004 Aug;11(8):784-90. doi: 10.1038/nsmb792. Epub 2004 Jul 4.


Ultraviolet-induced DNA damage poses a lethal block to replication. To understand the structural basis for this, we determined crystal structures of a replicative DNA polymerase from bacteriophage T7 in complex with nucleotide substrates and a DNA template containing a cis-syn cyclobutane pyrimidine dimer (CPD). When the 3' thymine is the templating base, the CPD is rotated out of the polymerase active site and the fingers subdomain adopts an open orientation. When the 5' thymine is the templating base, the CPD lies within the polymerase active site where it base-pairs with the incoming nucleotide and the 3' base of the primer, while the fingers are in a closed conformation. These structures reveal the basis for the strong block of DNA replication that is caused by this photolesion.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Bacteriophage T7 / chemistry*
  • Binding Sites
  • Crystallography, X-Ray
  • DNA Damage
  • DNA-Directed DNA Polymerase / chemistry*
  • DNA-Directed DNA Polymerase / metabolism
  • Dimerization
  • Models, Chemical
  • Models, Molecular
  • Mutation
  • Protein Binding
  • Protein Conformation
  • Protein Structure, Tertiary
  • Pyrimidines / chemistry
  • Thymine / chemistry
  • Ultraviolet Rays


  • Pyrimidines
  • bacteriophage T7 induced DNA polymerase
  • DNA-Directed DNA Polymerase
  • Thymine

Associated data

  • PDB/1SKR
  • PDB/1SKS
  • PDB/1SKW
  • PDB/1SL0
  • PDB/1SL1
  • PDB/1SL2