3C2M

Ternary complex of DNA POLYMERASE BETA with a G:dAPCPP mismatch in the active site

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.214 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Structures of DNA polymerase beta with active-site mismatches suggest a transient abasic site intermediate during misincorporation.

Batra, V.K., Beard, W.A., Shock, D.D., Pedersen, L.C., Wilson, S.H.

(2008) Mol Cell 30: 315-324

  • DOI: 10.1016/j.molcel.2008.02.025
  • Primary Citation of Related Structures:  
    3C2K, 3C2L, 3C2M

  • PubMed Abstract: 

    • We report the crystallographic structures of DNA polymerase beta with dG-dAMPCPP and dC-dAMPCPP mismatches in the active site. These premutagenic structures were obtained with a nonhydrolyzable incoming nucleotide analog, dAMPCPP, and Mn(2+). Substit ...

    We report the crystallographic structures of DNA polymerase beta with dG-dAMPCPP and dC-dAMPCPP mismatches in the active site. These premutagenic structures were obtained with a nonhydrolyzable incoming nucleotide analog, dAMPCPP, and Mn(2+). Substituting Mn(2+) for Mg(2+) significantly decreases the fidelity of DNA synthesis. The structures reveal that the enzyme is in a closed conformation like that observed with a matched Watson-Crick base pair. The incorrect dAMPCPP binds in a conformation identical to that observed with the correct nucleotide. To accommodate the incorrect nucleotide and closed protein conformation, the template strand in the vicinity of the active site has shifted upstream over 3 A, removing the coding base from the active site and generating an abasic templating pocket. The primer terminus rotates as its complementary template base is repositioned. This rotation moves O3' of the primer terminus away from the alpha-phosphate of the incoming nucleotide, thereby deterring misincorporation.

    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 betaA335Homo sapiensMutation(s): 0 
Gene Names: POLB
EC: 2.7.7.7 (PDB Primary Data), 4.2.99 (PDB Primary Data)
Find proteins for P06746 (Homo sapiens)
Explore P06746 
Go to UniProtKB:  P06746
NIH Common Fund Data Resources
PHAROS  P06746
GTEx  ENSG00000070501
Protein Feature View
Expand
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*DCP*DCP*DGP*DAP*DCP*DGP*DGP*DCP*DGP*DCP*DAP*DTP*DCP*DAP*DGP*DC)-3')T16N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
      • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*DGP*DCP*DTP*DGP*DAP*DTP*DGP*DCP*DGP*DC)-3')P10N/A
      • Find similar nucleic acids by:  Sequence   |   Structure
        • Entity ID: 3
        MoleculeChainsLengthOrganismImage
        DNA (5'-D(P*DGP*DTP*DCP*DGP*DG)-3')D5N/A
        Small Molecules
        Ligands 4 Unique
        IDChainsName / Formula / InChI Key2D Diagram3D Interactions
        F2A
        Query on F2A
        Download CCD File 
        A
        		2'-deoxy-5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]adenosine
        C11 H18 N5 O11 P3
        XETARULVTCYJAN-XLPZGREQSA-N        		 Ligand Interaction
        EDO
        Query on EDO
        Download CCD File 
        A, D
        		1,2-ETHANEDIOL
        C2 H6 O2
        LYCAIKOWRPUZTN-UHFFFAOYSA-N        		 Ligand Interaction
        MN
        Query on MN
        Download CCD File 
        A, T
        		MANGANESE (II) ION
        Mn
        WAEMQWOKJMHJLA-UHFFFAOYSA-N        		 Ligand Interaction
        NA
        Query on NA
        Download CCD File 
        A, P, T
        		SODIUM ION
        Na
        FKNQFGJONOIPTF-UHFFFAOYSA-N        		 Ligand Interaction
        External Ligand Annotations 
        IDBinding Affinity (Sequence Identity %)
        F2AKi:  5000   nM  BindingDB
        Experimental Data & Validation

        Experimental Data

        • Method: X-RAY DIFFRACTION
        • Resolution: 2.15 Å
        • R-Value Free: 0.270 
        • R-Value Work: 0.214 
        • R-Value Observed: 0.214 
        • Space Group: P 1 21 1
        Unit Cell:
        Length ( Å )Angle ( ˚ )
        a = 54.75α = 90
        b = 78.37β = 113.36
        c = 55.17γ = 90
        Software Package:
        Software NamePurpose
        CNSrefinement
        HKL-2000data collection
        HKL-2000data reduction
        HKL-2000data scaling
        CNSphasing

        Structure Validation

        View Full Validation Report


        View more in-depth experimental data

        Entry History 

        Deposition Data

        Revision History 

        • Version 1.0: 2008-05-20
          Type: Initial release
        • Version 1.1: 2011-07-13
          Changes: Version format compliance