1TVA

HUMAN DNA POLYMERASE BETA COMPLEXED WITH NICKED DNA CONTAINING A MISMATCHED TEMPLATE THYMIDINE AND INCOMING CYTIDINE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.212 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural insights into DNA polymerase Beta deterrents for misincorporation support an induced-fit mechanism for fidelity

Krahn, J.M.Beard, W.A.Wilson, S.H.

(2004) Structure 12: 1823-1832

  • DOI: 10.1016/j.str.2004.08.001
  • Primary Citation of Related Structures:  
    1TV9, 1TVA

  • PubMed Abstract: 
  • DNA polymerases generally select the correct nucleotide from a pool of structurally similar molecules to preserve Watson-Crick base-pairing rules. We report the structure of DNA polymerase beta with DNA mismatches situated in the polymerase active site. This was achieved by using nicked product DNA that traps the mispair (template-primer, A-C or T-C) in the nascent base pair binding pocket ...

    DNA polymerases generally select the correct nucleotide from a pool of structurally similar molecules to preserve Watson-Crick base-pairing rules. We report the structure of DNA polymerase beta with DNA mismatches situated in the polymerase active site. This was achieved by using nicked product DNA that traps the mispair (template-primer, A-C or T-C) in the nascent base pair binding pocket. The structure of each mispair complex indicates that the bases do not form hydrogen bonds with one another, but form a staggered arrangement where the bases of the mispair partially overlap. This prevents closure/opening of the N subdomain that is believed to be required for catalytic cycling. The partially open conformation of the N subdomain results in distinct hydrogen bonding networks that are unique for each mispair. These structures define diverse molecular aspects of misinsertion that are consistent with the induced-fit model for substrate specificity.


    Organizational Affiliation

    Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, P.O. Box 12233, Research Triangle Park, NC 27709, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase betaD [auth A]335Homo sapiensMutation(s): 0 
Gene Names: POLB
EC: 2.7.7.7 (PDB Primary Data), 4.2.99 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P06746 (Homo sapiens)
Explore P06746 
Go to UniProtKB:  P06746
PHAROS:  P06746
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    5'-D(*CP*CP*GP*AP*CP*TP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'A [auth T]16N/A
    Protein Feature View
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    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*CP*C)-3'B [auth P]11N/A
      Protein Feature View
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      • Reference Sequence
      • Find similar nucleic acids by:  Sequence   |   Structure
      • Entity ID: 3
        MoleculeChainsLengthOrganismImage
        5'-D(P*GP*TP*CP*GP*G)-3'C [auth D]5N/A
        Protein Feature View
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        • Reference Sequence
        Small Molecules
        Ligands 3 Unique
        IDChainsName / Formula / InChI Key2D Diagram3D Interactions
        PO4
        Query on PO4

        Download Ideal Coordinates CCD File 
        H [auth A]PHOSPHATE ION
        O4 P
        NBIIXXVUZAFLBC-UHFFFAOYSA-K
         Ligand Interaction
        MG
        Query on MG

        Download Ideal Coordinates CCD File 
        E [auth P], I [auth A]MAGNESIUM ION
        Mg
        JLVVSXFLKOJNIY-UHFFFAOYSA-N
         Ligand Interaction
        NA
        Query on NA

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

        Experimental Data

        • Method: X-RAY DIFFRACTION
        • Resolution: 2.60 Å
        • R-Value Free: 0.282 
        • R-Value Work: 0.212 
        • R-Value Observed: 0.212 
        • Space Group: P 1 21 1
        Unit Cell:
        Length ( Å )Angle ( ˚ )
        a = 54.6α = 90
        b = 79.7β = 106.4
        c = 54.6γ = 90
        Software Package:
        Software NamePurpose
        DENZOdata reduction
        SCALEPACKdata scaling
        CNSrefinement
        CNSphasing

        Structure Validation

        View Full Validation Report




        Entry History 

        Deposition Data

        Revision History  (Full details and data files)

        • Version 1.0: 2004-11-23
          Type: Initial release
        • Version 1.1: 2008-04-30
          Changes: Version format compliance
        • Version 1.2: 2011-07-13
          Changes: Version format compliance