Structures of phi29 DNA polymerase complexed with substrate: the mechanism of translocation in B-family polymerases.
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.
Berman
Andrea J
AJ
Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.
Kamtekar
Satwik
S
Goodman
Jessica L
JL
Lázaro
José M
JM
de Vega
Miguel
M
Blanco
Luis
L
Salas
Margarita
M
Steitz
Thomas A
TA
D020816:Amino Acid Motifs; D017103:Bacillus Phages / Q000201:enzymology*; D018360:Crystallography, X-Ray; D004279:DNA, Viral / Q000378:metabolism; D004259:DNA-Directed DNA Polymerase / Q000737:chemistry*; D005092:Exonucleases / Q000378:metabolism; D008958:Models, Molecular; D021381:Protein Transport; D013379:Substrate Specificity; D013698:Templates, Genetic; D014867:Water / Q000378:metabolism
D004279:DNA, Viral; D014867:Water; D004259:DNA-Directed DNA Polymerase; D005092:Exonucleases