Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 145.76 kDa 
• Atom Count: 11400 
• Residue Count: 1154 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

2PY5

Phi29 DNA polymerase complexed with single-stranded DNA

• DOI: 10.2210/pdb2PY5/pdb
• NDB: PD1010

• Classification: REPLICATION, TRANSFERASE/DNA
• Organism(s): Bacillus virus phi29
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2007-05-15 Released: 2007-07-17 
• Deposition Author(s): Berman, A.J., Kamtekar, S., Goodman, J.L., Lazaro, J.M., de Vega, M., Blanco, L., Salas, M., Steitz, T.A.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.194 
• R-Value Work: 0.164 
• R-Value Observed: 0.165 

Literature

Structures of phi29 DNA polymerase complexed with substrate: the mechanism of translocation in B-family polymerases

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

(2007) EMBO J 26: 3494-3505

• PubMed: 17611604 
• DOI: 10.1038/sj.emboj.7601780
• Structures With Same Primary Citation


• 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.

---

Organizational Affiliation: 

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

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
DNA polymerase	A, B	575	Bacillus virus phi29	Mutation(s): 2  Gene Names: 2, gp2 EC: 2.7.7.7 (PDB Primary Data), 3.1.11 (UniProt)
Find proteins for P03680 (Bacillus phage phi29) Go to UniProtKB:  P03680

Entity ID: 1
Molecule	Chains	Length	Organism
5'-d(GGACTTT)-3'	D, E,J,L,Y	7	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	A, B	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.194 
• R-Value Work: 0.164 
• R-Value Observed: 0.165 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.195	α = 90
b = 200.178	β = 109.4
c = 66.989	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-05-15 
• Released Date: 2007-07-17 
Deposition Author(s): Berman, A.J., Kamtekar, S., Goodman, J.L., Lazaro, J.M., de Vega, M., Blanco, L., Salas, M., Steitz, T.A.

Revision History 

• Version 1.0: 2007-07-17
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance