1XHZ: Phi29 DNA Polymerase, Orthorhombic Crystal ... - RCSB PDB

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247,287Structures from the PDB archive

1,068,577Computed Structure Models (CSM)

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Display Files Download Files Data API 1XHZ | pdb_00001xhz

Phi29 DNA polymerase, orthorhombic crystal form, ssDNA complex

PDB DOI: https://doi.org/10.2210/pdb1XHZ/pdb
NAKB: 1XHZ

Classification: TRANSFERASE/DNA
Organism(s): Salasvirus phi29
Expression System: Escherichia coli
Mutation(s): Yes
Deposited: 2004-09-21 Released: 2004-12-07
Deposition Author(s): Kamtekar, S., Berman, A.J., Wang, J., Lazaro, J.M., de Vega, M., Blanco, L., Salas, M., Steitz, T.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.268 (Depositor), 0.440 (DCC)
R-Value Work: 0.219 (Depositor), 0.300 (DCC)
R-Value Observed: 0.219 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history. LiteratureDownload Primary Citation

Insights into Strand Displacement and Processivity from the Crystal Structure of the Protein-Primed DNA Polymerase of Bacteriophage phi29

Kamtekar, S., Berman, A.J., Wang, J., Lazaro, J.M., de Vega, M., Blanco, L., Salas, M., Steitz, T.A.

(2004) Mol Cell 16: 609-618

PubMed: 15546620 Search on PubMed
DOI: https://doi.org/10.1016/j.molcel.2004.10.019
Primary Citation of Related Structures: 1XHX, 1XHZ
PubMed 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.
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Organizational Affiliation

Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA.

Asymmetric Unit