1XHZ

Phi29 DNA polymerase, orthorhombic crystal form, ssDNA complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.219 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

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

  • DOI: 10.1016/j.molcel.2004.10.019
  • Primary Citation of Related Structures:  

  • 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 ...

    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.

    Related Citations: 
    • Correction of X-ray intensities from single crystals containing lattice translocation defects
      Wang, J.,Kamtekar, S.,Berman, A.J.,Steitz, T.A.
      () TO BE PUBLISHED --: --

    Organizational Affiliation: 

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




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase
A, B, C, D
575Bacillus phage phi29Mutation(s): 2 
Gene Names: 2
EC: 2.7.7.7, 3.1.11.-
Find proteins for P03680 (Bacillus phage phi29)
Go to UniProtKB:  P03680
Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*TP*TP*TP*TP*T)-3'E,F,G,H5N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.219 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 96.662α = 90.00
b = 150.397β = 90.00
c = 198.325γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
HKL-2000data reduction
MOLREPphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-12-07
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance