Structures of phi29 DNA Polymerase Complexed With Substrate: The Mechanism of Translocation in B-family Polymerases

EMBO J. 2007 Jul 25;26(14):3494-505. doi: 10.1038/sj.emboj.7601780. Epub 2007 Jul 5.

Abstract

Replicative DNA polymerases (DNAPs) move along template DNA in a processive manner. The structural basis of the mechanism of translocation has been better studied in the A-family of polymerases than in the B-family of replicative polymerases. To address this issue, we have determined the X-ray crystal structures of phi29 DNAP, a member of the protein-primed subgroup of the B-family of polymerases, complexed with primer-template DNA in the presence or absence of the incoming nucleoside triphosphate, the pre- and post-translocated states, respectively. Comparison of these structures reveals a mechanism of translocation that appears to be facilitated by the coordinated movement of two conserved tyrosine residues into the insertion site. This differs from the mechanism employed by the A-family polymerases, in which a conserved tyrosine moves into the templating and insertion sites during the translocation step. Polymerases from the two families also interact with downstream single-stranded template DNA in very different ways.

Publication types

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

MeSH terms

  • Amino Acid Motifs
  • Bacillus Phages / enzymology*
  • Crystallography, X-Ray
  • DNA, Viral / metabolism
  • DNA-Directed DNA Polymerase / chemistry*
  • Exonucleases / metabolism
  • Models, Molecular
  • Protein Transport
  • Substrate Specificity
  • Templates, Genetic
  • Water / metabolism

Substances

  • DNA, Viral
  • Water
  • DNA-Directed DNA Polymerase
  • Exonucleases