2PYL

Phi29 DNA polymerase complexed with primer-template DNA and incoming nucleotide substrates (ternary complex)

Summary for 2PYL

• Entry DOI: 10.2210/pdb2pyl/pdb
• Related: 2PY5 2PYJ 2PZS
• Descriptor: 5'-d(GACTGCTTAC(2DA))-3', 5'-d(CTGACGAATGTACA)-3', DNA polymerase, ... (7 entities in total)
• Functional Keywords: protein-dna complex, replication, transferase-dna complex, transferase/dna
• Biological source: Bacillus phage phi29
• Total number of polymer chains: 3
• Total formula weight: 75230.12

Authors

Berman, A.J.,Kamtekar, S.,Goodman, J.L.,Lazaro, J.M.,de Vega, M.,Blanco, L.,Salas, M.,Steitz, T.A. (deposition date: 2007-05-16, release date: 2007-07-17, Last modification date: 2023-08-30)

Primary citation

Berman, A.J.,Kamtekar, S.,Goodman, J.L.,Lazaro, J.M.,de Vega, M.,Blanco, L.,Salas, M.,Steitz, T.A.
Structures of phi29 DNA polymerase complexed with substrate: the mechanism of translocation in B-family polymerases
Embo J., 26:3494-3505, 2007

PubMed 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.

PubMed: 17611604
DOI: 10.1038/sj.emboj.7601780

Experimental method

X-RAY DIFFRACTION (2.2 Å)