2EX3

Bacteriophage phi29 DNA polymerase bound to terminal protein

Summary for 2EX3

• Entry DOI: 10.2210/pdb2ex3/pdb
• Related: 1XHX 1XHZ 1XI1
• Descriptor: DNA polymerase, DNA terminal protein, LEAD (II) ION (3 entities in total)
• Functional Keywords: dna polymerase: protein primer complex, transferase-replication complex, transferase/replication
• Biological source: Bacillus phage phi29; More
• Cellular location: Virion : P03681
• Total number of polymer chains: 12
• Total formula weight: 558538.95

Authors

Kamtekar, S.,Berman, A.J.,Wang, J.,de Vega, M.,Blanco, L.,Salas, M.,Steitz, T.A. (deposition date: 2005-11-07, release date: 2006-03-14, Last modification date: 2024-04-03)

Primary citation

Kamtekar, S.,Berman, A.J.,Wang, J.,Lazaro, J.M.,de Vega, M.,Blanco, L.,Salas, M.,Steitz, T.A.
The phi29 DNA polymerase:protein-primer structure suggests a model for the initiation to elongation transition
Embo J., 25:1335-1343, 2006

PubMed Abstract: The absolute requirement for primers in the initiation of DNA synthesis poses a problem for replicating the ends of linear chromosomes. The DNA polymerase of bacteriophage phi29 solves this problem by using a serine hydroxyl of terminal protein to prime replication. The 3.0 A resolution structure shows one domain of terminal protein making no interactions, a second binding the polymerase and a third domain containing the priming serine occupying the same binding cleft in the polymerase as duplex DNA does during elongation. Thus, the progressively elongating DNA duplex product must displace this priming domain. Further, this heterodimer of polymerase and terminal protein cannot accommodate upstream template DNA, thereby explaining its specificity for initiating DNA synthesis only at the ends of the bacteriophage genome. We propose a model for the transition from the initiation to the elongation phases in which the priming domain of terminal protein moves out of the active site as polymerase elongates the primer strand. The model indicates that terminal protein should dissociate from polymerase after the incorporation of approximately six nucleotides.

PubMed: 16511564
DOI: 10.1038/sj.emboj.7601027

Experimental method

X-RAY DIFFRACTION (3 Å)