3ISC

Binary complex of human DNA polymerase beta with an abasic site (THF) in the gapped DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

DNA polymerase beta substrate specificity: side chain modulation of the "A-rule".

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

(2009) J Biol Chem 284: 31680-31689

  • DOI: 10.1074/jbc.M109.029843
  • Primary Citation of Related Structures:  
    3ISB, 3ISC, 3ISD

  • PubMed Abstract: 
  • Apurinic/apyrimidinic (AP) sites are continuously generated in genomic DNA. Left unrepaired, AP sites represent noninstructional premutagenic lesions that are impediments to DNA synthesis. When DNA polymerases encounter an AP site, they generally ins ...

    Apurinic/apyrimidinic (AP) sites are continuously generated in genomic DNA. Left unrepaired, AP sites represent noninstructional premutagenic lesions that are impediments to DNA synthesis. When DNA polymerases encounter an AP site, they generally insert dAMP. This preferential insertion is referred to as the A-rule. Crystallographic structures of DNA polymerase (pol) beta, a family X polymerase, with active site mismatched nascent base pairs indicate that the templating (i.e. coding) base is repositioned outside of the template binding pocket thereby diminishing interactions with the incorrect incoming nucleotide. This effectively produces an abasic site because the template pocket is devoid of an instructional base. However, the template pocket is not empty; an arginine residue (Arg-283) occupies the space vacated by the templating nucleotide. In this study, we analyze the kinetics of pol beta insertion opposite an AP site and show that the preferential incorporation of dAMP is lost with the R283A mutant. The crystallographic structures of pol beta bound to gapped DNA with an AP site analog (tertrahydrofuran) in the gap (binary complex) and with an incoming nonhydrolyzable dATP analog (ternary complex) were solved. These structures reveal that binding of the dATP analog induces a closed polymerase conformation, an unstable primer terminus, and an upstream shift of the templating residue even in the absence of a template base. Thus, dATP insertion opposite an abasic site and dATP misinsertions have common features.


    Organizational Affiliation

    Laboratory of Structural Biology, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
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
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    5'-D(P*GP*TP*CP*GP*G)-3'D5synthetic construct
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3'P10synthetic construct
      • Find similar nucleic acids by:  Sequence   |   Structure
      • Entity ID: 4
        MoleculeChainsLengthOrganismImage
        5'-D(*CP*CP*GP*AP*CP*(3DR)P*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'T16synthetic construct
        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: 2.00 Å
        • R-Value Free: 0.227 
        • R-Value Work: 0.186 
        • R-Value Observed: 0.186 
        • Space Group: P 1 21 1
        Unit Cell:
        Length ( Å )Angle ( ˚ )
        a = 54.41α = 90
        b = 79.3β = 105.8
        c = 54.95γ = 90
        Software Package:
        Software NamePurpose
        HKL-2000data collection
        CNSrefinement
        HKL-2000data reduction
        HKL-2000data scaling
        CNSphasing

        Structure Validation

        View Full Validation Report



        Entry History 

        Deposition Data

        Revision History 

        • Version 1.0: 2009-09-15
          Type: Initial release
        • Version 1.1: 2011-07-13
          Changes: Version format compliance
        • Version 1.2: 2019-02-06
          Changes: Data collection, Database references, Refinement description, Source and taxonomy, Structure summary