Structures of phi29 DNA polymerase complexed with substrate: the mechanism of translocation in B-family polymerases.

Publication Type:

Journal Article

Authors:

Berman, Andrea J; Kamtekar, Satwik; Goodman, Jessica L; Lázaro, José M; de Vega, Miguel; Blanco, Luis; Salas, Margarita; Steitz, Thomas A

Source:

EMBO J, Volume 26, Issue 14, p.3494-505 (2007)

Keywords:

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

Abstract:

<p>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.</p>