1BPE | pdb_00001bpe

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

• PDB DOI: https://doi.org/10.2210/pdb1BPE/pdb
• BMRB: 5209
• BMRB: 5208

• Classification: NUCLEOTIDYLTRANSFERASE
• Organism(s): Rattus norvegicus
• Mutation(s): No 


• Deposited: 1994-04-12 Released: 1994-07-31 
• 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: 2.90 Å
• R-Value Observed: 
  0.199 (Depositor) 

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 
• DOI: https://doi.org/10.1126/science.7516581
• Primary Citation Related Structures: 
  1BPB, 1BPD, 1BPE, 2BPC


• 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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Organizational Affiliation: 
• Department of Chemistry, University of California, San Diego 92093-0317.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 38.91 kDa 
• Atom Count: 2,158 
• Modeled Residue Count: 284 
• Deposited Residue Count: 335 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA POLYMERASE BETA	A	335	Rattus norvegicus	Mutation(s): 0  EC: 2.7.7.7 (PDB Primary Data), 4.2.99.18 (UniProt), 4.2.99 (UniProt)
UniProt
Find proteins for P06766 (Rattus norvegicus) Explore P06766  Go to UniProtKB:  P06766

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DTP	B [auth A]	2'-DEOXYADENOSINE 5'-TRIPHOSPHATE C10 H16 N5 O12 P3 SUYVUBYJARFZHO-RRKCRQDMSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Observed: 0.199 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.319	α = 90
b = 68.208	β = 91.77
c = 75.038	γ = 90

Software Package:

Software Name	Purpose
TNT	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1994-07-31 
Deposition Author(s): Sawaya, M.R., Pelletier, H., Kumar, A., Wilson, S.H., Kraut, J.

Revision History  

• Version 1.0: 1994-07-31
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-07
  Changes: Data collection, Database references, Derived calculations, Other