A unified DNA- and dNTP-binding mode for DNA polymerases

Trends Biochem Sci. 1998 Aug;23(8):277-81. doi: 10.1016/s0968-0004(98)01250-x.


Crystal structures of various DNA polymerases show a common structural topology that resembles a right hand and has distinct finger, palm and thumb subdomains. Early models of the klenow fragment (KF) of Escherichia coli polymerase I showed DNA entering a large cleft that faces the palm subdomain where the catalytic site is situated1,2. However, subsequent resolution of the structures of HIV-1 reverse transcriptase, KF and polymerase beta (pol beta) bound to DNA3-5 yielded conflicting data that suggested a different orientation for DNA bound to pol beta compared with DNA bound to other polymerases. The debate, on the correct orientation of the template-primer DNA, that followed failed to reach a consensus. Using an alternative superposition scheme, we now provide convincing evidence for a common DNA-binding mode that is applicable to all polymerases, including pol beta.

Publication types

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

MeSH terms

  • Binding Sites
  • DNA / metabolism
  • DNA Polymerase I / chemistry
  • DNA Polymerase I / metabolism
  • DNA Polymerase beta / chemistry
  • DNA Polymerase beta / metabolism
  • DNA-Directed DNA Polymerase / chemistry*
  • DNA-Directed DNA Polymerase / metabolism*
  • HIV Reverse Transcriptase / chemistry
  • HIV Reverse Transcriptase / metabolism
  • Models, Molecular*
  • Protein Conformation
  • Taq Polymerase / chemistry
  • Taq Polymerase / metabolism


  • DNA
  • Taq Polymerase
  • HIV Reverse Transcriptase
  • DNA Polymerase I
  • DNA Polymerase beta
  • DNA-Directed DNA Polymerase