9ICO

DNA POLYMERASE BETA (E.C.2.7.7.7)/DNA COMPLEX, SOAKED IN THE PRESENCE OF DTTP AND MGCL2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Observed: 0.152 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A structural basis for metal ion mutagenicity and nucleotide selectivity in human DNA polymerase beta

Pelletier, H.Sawaya, M.R.Wolfle, W.Wilson, S.H.Kraut, J.

(1996) Biochemistry 35: 12762-12777

  • DOI: 10.1021/bi9529566
  • Primary Citation of Related Structures:  
    7ICK, 7ICL, 7ICI, 7ICJ, 7ICO, 7ICP, 7ICM, 7ICN, 7ICG, 7ICH

  • PubMed Abstract: 
  • When crystals of human DNA polymerase beta (pol beta) complexed with DNA [Pelletier, H., Sawaya, M. R., Wolfle, W., Wilson, S. H., & Kraut, J. (1996) Biochemistry 35, 12742-12761] are soaked in the presence of dATP and Mn2+, X-ray structural analysis ...

    When crystals of human DNA polymerase beta (pol beta) complexed with DNA [Pelletier, H., Sawaya, M. R., Wolfle, W., Wilson, S. H., & Kraut, J. (1996) Biochemistry 35, 12742-12761] are soaked in the presence of dATP and Mn2+, X-ray structural analysis shows that nucleotidyl transfer to the primer 3'-OH takes place directly in the crystals, even though the DNA is blunt-ended at the active site. Under similar crystal-soaking conditions, there is no evidence for a reaction when Mn2+ is replaced by Mg2+, which is thought to be the divalent metal ion utilized by most polymerases in vivo. These results suggest that one way Mn2+ may manifest its mutagenic effect on polymerases is by promoting greater reactivity than Mg2+ at the catalytic site, thereby allowing the nucleotidyl transfer reaction to take place with little or no regard to instructions from a template. Non-template-directed nucleotidyl transfer is also observed when pol beta-DNA cocrystals are soaked in the presence of dATP and Zn2+, but the reaction products differ in that the sugar moiety of the incorporated nucleotide appears distorted or otherwise cleaved, in agreement with reports that Zn2+ may act as a polymerase inhibitor rather than as a mutagen [Sirover, M. A., & Loeb, L. A. (1976) Science 194, 1434-1436]. Although no reaction is observed when crystals are soaked in the presence of dATP and other metal ions such as Ca2+, Co2+, Cr3+, or Ni2+, X-ray structural analyses show that these metal ions coordinate the triphosphate moiety of the nucleotide in a manner that differs from that observed with Mg2+. In addition, all metal ions tested, with the exception of Mg2+, promote a change in the side-chain position of aspartic acid 192, which is one of three highly conserved active-site carboxylate residues. Soaking experiments with nucleotides other than dATP (namely, dCTP, dGTP, dTTP, ATP, ddATP, ddCTP, AZT-TP, and dATP alpha S) reveal a non-base-specific binding site on pol beta for the triphosphate and sugar moieties of a nucleotide, suggesting a possible mechanism for nucleotide selectivity whereby triphosphate-sugar binding precedes a check for correct base pairing with the template.


    Related Citations: 
    • Crystal Structures of Human DNA Polymerase Beta Complexed with Nicked and Gapped DNA Substrates
      Sawaya, M.R., Rawson, T., Wilson, S.H., Kraut, J., Pelletier, H.
      () To be published --: --
    • The Role of Thumb Movement and Template Bending in Polymerase Fidelity
      Pelletier, H.
      () To be published --: --
    • Crystal Structures of Human DNA Polymerase Beta Complexed with DNA; Implications for Catalytic Mechanism, Processivity, and Fidelity
      Pelletier, H., Sawaya, M.R., Wolfle, W., Wilson, S.H., Kraut, J.
      (1996) Biochemistry 35: 12742
    • Characterization of the Metal Ion-Binding HHH Motifs in Human DNA Polymerase Beta by X-Ray Structural Analysis
      Pelletier, H., Sawaya, M.R.
      (1996) Biochemistry 35: 12778
    • Polymerase Structures and Mechanism
      Pelletier, H.
      (1994) Science 266: 2025
    • Structures of Ternary Complexes of Rat DNA Polymerase Beta, a DNA Template- Primer, and ddCTP
      Pelletier, H., Sawaya, M.R., Kumar, A., Wilson, S.H., Kraut, J.
      (1994) Science 264: 1891
    • 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

    Organizational Affiliation

    Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla 92093-0506, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (DNA POLYMERASE BETA (E.C.2.7.7.7))A335Homo sapiensMutation(s): 0 
Gene Names: POLB
EC: 2.7.7.7 (UniProt), 4.2.99 (UniProt)
Find proteins for P06746 (Homo sapiens)
Explore P06746 
Go to UniProtKB:  P06746
NIH Common Fund Data Resources
PHAROS  P06746
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*CP*AP*TP*CP*TP*GP*T)-3')T7N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*CP*AP*GP*AP*TP*G)-3')P6N/A
      Small Molecules
      Ligands 1 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      NA
      Query on NA

      Download CCD File 
      A
      SODIUM ION
      Na
      FKNQFGJONOIPTF-UHFFFAOYSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.90 Å
      • R-Value Observed: 0.152 
      • Space Group: P 21 21 2
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 178.631α = 90
      b = 57.708β = 90
      c = 48.502γ = 90
      Software Package:
      Software NamePurpose
      TNTrefinement
      SDMSdata reduction
      SDMSdata scaling
      TNTphasing

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      Revision History 

      • Version 1.0: 1995-12-16
        Type: Initial release
      • Version 1.1: 2008-05-22
        Changes: Version format compliance
      • Version 1.2: 2011-07-13
        Changes: Version format compliance