2BPC

CRYSTAL STRUCTURE OF RAT DNA POLYMERASE BETA: EVIDENCE FOR A COMMON POLYMERASE MECHANISM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of rat DNA polymerase beta: evidence for a common polymerase mechanism.

Sawaya, M.R.Pelletier, H.Kumar, A.Wilson, S.H.Kraut, J.

(1994) Science 264: 1930-1935

  • Primary Citation of Related Structures:  1BPB, 1BPD, 1BPE

  • PubMed Abstract: 
  • Structures of the 31-kilodalton catalytic domain of rat DNA polymerase beta (pol beta) and the whole 39-kilodalton enzyme were determined at 2.3 and 3.6 angstrom resolution, respectively. The 31-kilodalton domain is composed of fingers, palm, and thu ...

    Structures of the 31-kilodalton catalytic domain of rat DNA polymerase beta (pol beta) and the whole 39-kilodalton enzyme were determined at 2.3 and 3.6 angstrom resolution, respectively. The 31-kilodalton domain is composed of fingers, palm, and thumb subdomains arranged to form a DNA binding channel reminiscent of the polymerase domains of the Klenow fragment of Escherichia coli DNA polymerase I, HIV-1 reverse transcriptase, and bacteriophage T7 RNA polymerase. The amino-terminal 8-kilodalton domain is attached to the fingers subdomain by a flexible hinge. The two invariant aspartates found in all polymerase sequences and implicated in catalytic activity have the same geometric arrangement within structurally similar but topologically distinct palms, indicating that the polymerases have maintained, or possibly re-evolved, a common nucleotidyl transfer mechanism. The location of Mn2+ and deoxyadenosine triphosphate in pol beta confirms the role of the invariant aspartates in metal ion and deoxynucleoside triphosphate binding.


    Related Citations: 
    • Structures of Ternary Complexes of Rat DNA Polymerase Beta, a DNA Template-Primer, and ddCTP
      Pelletier, H.,Sawaya, M.R.,Wilson, S.H.,Kraut, J.
      (1994) Science 264: 1891
    • Studies of the Domain Structure of Mammalian DNA Polymerase Beta. Identification of a Discrete Template Binding Domain
      Kumar, A.,Widen, S.G.,Williams, K.R.,Kedar, P.,Karpel, R.L.,Wilson, S.H.
      (1990) J.Biol.Chem. 265: 2124


    Organizational Affiliation

    Department of Chemistry, University of California, San Diego 92093-0317.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA POLYMERASE BETA
A
248Rattus norvegicusGene Names: Polb
EC: 2.7.7.7, 4.2.99.-
Find proteins for P06766 (Rattus norvegicus)
Go to UniProtKB:  P06766
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 119.807α = 90.00
b = 62.633β = 90.00
c = 37.085γ = 90.00
Software Package:
Software NamePurpose
TNTrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-08-31
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance