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CRYSTAL STRUCTURE OF DNA POLYMERASE BETA COMPLEXED WITH DNA AND CR-TMPPCP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.226 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Insight into the catalytic mechanism of DNA polymerase beta: structures of intermediate complexes.

Arndt, J.W.Gong, W.Zhong, X.Showalter, A.K.Liu, J.Dunlap, C.A.Lin, Z.Paxson, C.Tsai, M.D.Chan, M.K.

(2001) Biochemistry 40: 5368-5375

  • DOI: 10.1021/bi002176j
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The catalytic reaction mediated by DNA polymerases is known to require two Mg(II) ions, one associated with dNTP binding and the other involved in metal ion catalysis of the chemical step. Here we report a functional intermediate structure of a DNA p ...

    The catalytic reaction mediated by DNA polymerases is known to require two Mg(II) ions, one associated with dNTP binding and the other involved in metal ion catalysis of the chemical step. Here we report a functional intermediate structure of a DNA polymerase with only one metal ion bound, the DNA polymerase beta-DNA template-primer-chromium(III).2'-deoxythymidine 5'-beta,gamma-methylenetriphosphate [Cr(III).dTMPPCP] complex, at 2.6 A resolution. The complex is distinct from the structures of other polymerase-DNA-ddNTP complexes in that the 3'-terminus of the primer has a free hydroxyl group. Hence, this structure represents a fully functional intermediate state. Support for this contention is provided by the observation of turnover in biochemical assays of crystallized protein as well as from the determination that soaking Pol beta crystals with Mn(II) ions leads to formation of the product complex, Pol beta-DNA-Cr(III).PCP, whose structure is also reported. An important feature of both structures is that the fingers subdomain is closed, similar to structures of other ternary complexes in which both metal ion sites are occupied. These results suggest that closing of the fingers subdomain is induced specifically by binding of the metal-dNTP complex prior to binding of the catalytic Mg(2+) ion. This has led us to reevaluate our previous evidence regarding the existence of a rate-limiting conformational change in Pol beta's reaction pathway. The results of stopped-flow studies suggest that there is no detectable rate-limiting conformational change step.


    Organizational Affiliation

    Departments of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DNA POLYMERASE BETA
A, B
335Rattus norvegicusMutation(s): 0 
Gene Names: Polb
EC: 2.7.7.7 (PDB Primary Data), 4.2.99 (UniProt)
Find proteins for P06766 (Rattus norvegicus)
Go to UniProtKB:  P06766
Protein Feature View
  • Reference Sequence
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*AP*AP*TP*AP*GP*GP*CP*GP*TP*CP*G)-3'C, T11N/A
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(P*CP*GP*AP*CP*GP*CP*C)-3'D, P7N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TTE
Query on TTE

Download CCD File 
A, B
PHOSPHOMETHYL PHOSPHONIC ACID DEOXYTHYMIDYLATE ESTER
C11 H19 N2 O13 P3
HEDAITKJNKXWIZ-DJLDLDEBSA-N
 Ligand Interaction
CR
Query on CR

Download CCD File 
A, B
CHROMIUM ION
Cr
BFGKITSFLPAWGI-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.226 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.911α = 90
b = 56.162β = 107.25
c = 86.055γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SDMSdata scaling
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-04-23
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance