1BPX

DNA POLYMERASE BETA/DNA COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Work: 0.253 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structures of human DNA polymerase beta complexed with gapped and nicked DNA: evidence for an induced fit mechanism.

Sawaya, M.R.Prasad, R.Wilson, S.H.Kraut, J.Pelletier, H.

(1997) Biochemistry 36: 11205-11215

  • DOI: 10.1021/bi9703812
  • Primary Citation of Related Structures:  
    1BPZ, 1BPY, 1BPX

  • PubMed Abstract: 
  • DNA polymerase beta (pol beta) fills single nucleotide (nt) gaps in DNA produced by the base excision repair pathway of mammalian cells. Crystal structures have been determined representing intermediates in the 1 nt gap-filling reaction of pol beta: the binary complex with a gapped DNA substrate (2 ...

    DNA polymerase beta (pol beta) fills single nucleotide (nt) gaps in DNA produced by the base excision repair pathway of mammalian cells. Crystal structures have been determined representing intermediates in the 1 nt gap-filling reaction of pol beta: the binary complex with a gapped DNA substrate (2.4 A resolution), the ternary complex including ddCTP (2.2 A), and the binary product complex containing only nicked DNA (2.6 A). Upon binding ddCTP to the binary gap complex, the thumb subdomain rotates into the closed conformation to contact the otherwise solvent-exposed ddCTP-template base pair. Thumb movement triggers further conformational changes which poise catalytic residue Asp192, dNTP, and template for nucleotidyl transfer, effectively assembling the active site. In the product nicked DNA complex, the thumb returns to the open conformation as in the gapped binary DNA complex, facilitating dissociation of the product. These findings suggest that pol beta may enhance fidelity by an induced fit mechanism in which correct base pairing between template and incoming dNTP induces alignment of catalytic groups for catalysis (via thumb closure), but incorrect base pairing will not. The structures also reveal that pol beta binds both gapped and nicked DNA with a 90 degrees kink occurring precisely at the 5'-phosphodiester linkage of the templating residue. If the DNA were not kinked in this way, contact between the thumb and dNTP-template base pair, presumably important for the checking mechanism, would be impossible, especially when the gap is but a single nucleotide. Such a 90 degrees kink may be a mechanistic feature employed by any polymerase involved in filling gaps to completion.


    Related Citations: 
    • Characterization of the Metal Ion Binding Helix-Hairpin-Helix Motifs in Human DNA Polymerase Beta by X-Ray Structural Analysis
      Pelletier, H., Sawaya, M.R.
      (1996) Biochemistry 35: 12778
    • 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
    • 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
    • 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
    • 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

    Organizational Affiliation

    Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0506, USA. mrs@heckle.med.harvard.edu



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (DNA POLYMERASE BETA)D [auth A]335Homo sapiensMutation(s): 0 
Gene Names: POLB
EC: 2.7.7.7 (PDB Primary Data), 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
Expand
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*CP*CP*GP*AP*CP*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')A [auth T]16N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3')B [auth P]10N/A
      • Find similar nucleic acids by:  Sequence   |   Structure
      • Entity ID: 3
        MoleculeChainsLengthOrganismImage
        DNA (5'-D(*GP*TP*CP*GP*G)-3')C [auth D]5N/A
        Small Molecules
        Ligands 1 Unique
        IDChainsName / Formula / InChI Key2D Diagram3D Interactions
        NA
        Query on NA

        Download Ideal Coordinates CCD File 
        E [auth D], F [auth A]SODIUM ION
        Na
        FKNQFGJONOIPTF-UHFFFAOYSA-N
         Ligand Interaction
        Experimental Data & Validation

        Experimental Data

        • Method: X-RAY DIFFRACTION
        • Resolution: 2.40 Å
        • R-Value Work: 0.253 
        • Space Group: P 1 21 1
        Unit Cell:
        Length ( Å )Angle ( ˚ )
        a = 52.767α = 90
        b = 79.395β = 106.35
        c = 54.622γ = 90
        Software Package:
        Software NamePurpose
        DENZOdata reduction
        SCALEPACKdata scaling
        MERLOTphasing
        TNTrefinement

        Structure Validation

        View Full Validation Report



        Entry History 

        Deposition Data

        Revision History  (Full details and data files)

        • Version 1.0: 1997-06-16
          Type: Initial release
        • Version 1.1: 2008-05-22
          Changes: Version format compliance
        • Version 1.2: 2011-07-13
          Changes: Version format compliance