title: Insights into strand displacement and processivity from the crystal structure of the protein-primed DNA polymerase of bacteriophage phi29.
abstract: The DNA polymerase from phage phi29 is a B family polymerase that initiates replication using a protein as a primer, attaching the first nucleotide of the phage genome to the hydroxyl of a specific serine of the priming protein. The crystal structure of phi29 DNA polymerase determined at 2.2 A resolution provides explanations for its extraordinary processivity and strand displacement activities. Homology modeling suggests that downstream template DNA passes through a tunnel prior to entering the polymerase active site. This tunnel is too small to accommodate double-stranded DNA and requires the separation of template and nontemplate strands. Members of the B family of DNA polymerases that use protein primers contain two sequence insertions: one forms a domain not previously observed in polymerases, while the second resembles the specificity loop of T7 RNA polymerase. The high processivity of phi29 DNA polymerase may be explained by its topological encirclement of both the downstream template and the upstream duplex DNA.
authors.affiliation: Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA.
authors.forename: Satwik
authors.initials: S
authors.lastname: Kamtekar
authors.forename: Andrea J
authors.initials: AJ
authors.lastname: Berman
authors.forename: Jimin
authors.initials: J
authors.lastname: Wang
authors.forename: José M
authors.initials: JM
authors.lastname: Lázaro
authors.forename: Miguel
authors.initials: M
authors.lastname: de Vega
authors.forename: Luis
authors.initials: L
authors.lastname: Blanco
authors.forename: Margarita
authors.initials: M
authors.lastname: Salas
authors.forename: Thomas A
authors.initials: TA
authors.lastname: Steitz
mesh_terms: D000595:Amino Acid Sequence; D017103:Bacillus Phages / Q000201:enzymology*; D017123:Bacteriophage T7 / Q000201:enzymology; D001483:Base Sequence; D001665:Binding Sites; D018360:Crystallography, X-Ray; D004277:DNA, Single-Stranded / Q000378:metabolism; D004259:DNA-Directed DNA Polymerase / Q000737:chemistry* / Q000378:metabolism; D008954:Models, Biological; D008958:Models, Molecular; D009154:Mutation; D017434:Protein Structure, Tertiary; D055672:Static Electricity; D013698:Templates, Genetic
chemical_list: D004277:DNA, Single-Stranded; D004259:DNA-Directed DNA Polymerase