Biological Assembly 1  

 3D View: Structure

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 28774.53 
• Atom Count: 1934 
• Residue Count: 248 
• Unique protein chains: 1

1BPB

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

• DOI: 10.2210/pdb1BPB/pdb

• Classification: NUCLEOTIDYLTRANSFERASE
• Organism(s): Rattus norvegicus


• Deposited: 1994-04-12 Released: 1994-06-22 
• Deposition Author(s): Sawaya, M.R., Pelletier, H., Kumar, A., Wilson, S.H., Kraut, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.3 Å

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

• PubMed: 7516581 
• Primary Citation of Related Structures:  
  2BPC, 1BPE, 1BPD


• 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 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.

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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




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Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
DNA POLYMERASE BETA	A	248	Rattus norvegicus	Mutation(s): 0  Gene Names: Polb EC: 2.7.7.7, 4.2.99.-
Find proteins for P06766 (Rattus norvegicus) Go to UniProtKB:  P06766

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.3 Å
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length (Å)	Angle (°)
a = 120.576	α = 90.00
b = 63.520	β = 90.00
c = 38.215	γ = 90.00

Software Package:

Software Name	Purpose
TNT	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1994-04-12 
• Released Date: 1994-06-22 
• Deposition Author(s): Sawaya, M.R., Pelletier, H., Kumar, A., Wilson, S.H., Kraut, J.

Revision History 

• Version 1.0: 1994-06-22
  Type: Initial release
• Version 1.1: 2008-03-24
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance
• Version 1.3: 2011-11-16
  Type: Atomic model