1WAF

DNA POLYMERASE FROM BACTERIOPHAGE RB69


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of a pol alpha family replication DNA polymerase from bacteriophage RB69.

Wang, J.Sattar, A.K.Wang, C.C.Karam, J.D.Konigsberg, W.H.Steitz, T.A.

(1997) Cell 89: 1087-1099

  • Primary Citation of Related Structures:  1WAJ
  • Also Cited By: 3CFP, 3CFR

  • PubMed Abstract: 
  • The 2.8 A resolution crystal structure of the bacteriophage RB69 gp43, a member of the eukaryotic pol alpha family of replicative DNA polymerases, shares some similarities with other polymerases but shows many differences. Although its palm domain ha ...

    The 2.8 A resolution crystal structure of the bacteriophage RB69 gp43, a member of the eukaryotic pol alpha family of replicative DNA polymerases, shares some similarities with other polymerases but shows many differences. Although its palm domain has the same topology as other polymerases, except rat DNA polymerase beta, one of the three carboxylates required for nucleotidyl transfer is located on a different beta strand. The structures of the fingers and thumb domains are unrelated to all other known polymerase structures. The editing 3'-5' exonuclease domain of gp43 is homologous to that of E. coli DNA polymerase I but lies on the opposite side of the polymerase active site. An extended structure-based alignment of eukaryotic DNA polymerase sequences provides structural insights that should be applicable to most eukaryotic DNA polymerases.


    Related Citations: 
    • Modular Organization of T4 DNA Polymerase. Evidence from Phylogenetics
      Wang, C.C.,Yeh, L.S.,Karam, J.D.
      (1995) J.Biol.Chem. 270: 26558
    • Structural Basis for Phenotypes of Mutant Pol Alpha Family DNA Polymerases
      Wang, J.,Steitz, T.
      () TO BE PUBLISHED --: --
    • Crystal Structures of an NH2-Terminal Fragment of T4 DNA Polymerase and its Complexes with Single-Stranded DNA and with Divalent Metal Ions
      Wang, J.,Yu, P.,Lin, T.C.,Konigsberg, W.H.,Steitz, T.A.
      (1996) Biochemistry 35: 8110
    • Primary Structure of T4 DNA Polymerase. Evolutionary Relatedness to Eucaryotic and Other Procaryotic DNA Polymerases
      Spicer, E.K.,Rush, J.,Fung, C.,Reha-Krantz, L.J.,Karam, J.D.,Konigsberg, W.H.
      (1988) J.Biol.Chem. 263: 7478


    Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8114, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA POLYMERASE
A, B
903Enterobacteria phage RB69Gene Names: 43
EC: 2.7.7.7, 3.1.11.-
Find proteins for Q38087 (Enterobacteria phage RB69)
Go to UniProtKB:  Q38087
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GMP
Query on GMP

Download SDF File 
Download CCD File 
A, B
GUANOSINE
C10 H13 N5 O5
NYHBQMYGNKIUIF-UUOKFMHZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.198 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 88.320α = 90.00
b = 196.860β = 92.57
c = 118.310γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
X-PLORphasing
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-01-14
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance