2PY5

Phi29 DNA polymerase complexed with single-stranded DNA


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 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


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

  • DOI: 10.1038/sj.emboj.7601780
  • Primary Citation of Related Structures:  
    2PY5, 2PYL, 2PYJ, 2PZS

  • 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 ...

    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

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymeraseF [auth A], G [auth B]575Bacillus virus phi29Mutation(s): 2 
Gene Names: 2gp2
EC: 2.7.7.7 (PDB Primary Data), 3.1.11 (UniProt)
Find proteins for P03680 (Bacillus phage phi29)
Explore P03680 
Go to UniProtKB:  P03680
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    5'-d(GGACTTT)-3'A [auth J], B [auth Y], C [auth D], D [auth E], E [auth L]7N/A
    Small Molecules
    Ligands 1 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    EDO
    Query on EDO

    Download Ideal Coordinates CCD File 
    AA [auth B] , BA [auth B] , CA [auth B] , DA [auth B] , EA [auth B] , FA [auth B] , GA [auth B] , H [auth A] , 
    AA [auth B],  BA [auth B],  CA [auth B],  DA [auth B],  EA [auth B],  FA [auth B],  GA [auth B],  H [auth A],  HA [auth B],  I [auth A],  J [auth A],  K [auth A],  L [auth A],  M [auth A],  N [auth A],  O [auth A],  P [auth A],  Q [auth A],  R [auth A],  S [auth A],  T [auth A],  U [auth A],  V [auth A],  W [auth A],  X [auth A],  Y [auth A],  Z [auth B]
    1,2-ETHANEDIOL
    C2 H6 O2
    LYCAIKOWRPUZTN-UHFFFAOYSA-N
     Ligand Interaction
    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 = 54.195α = 90
    b = 200.178β = 109.4
    c = 66.989γ = 90
    Software Package:
    Software NamePurpose
    ADSCdata collection
    PHASERphasing
    REFMACrefinement
    HKL-2000data reduction
    HKL-2000data scaling

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • 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