3ISD

Ternary complex of human DNA polymerase beta with an abasic site (THF): DAPCPP mismatch


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.195 

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 insert dAMP ...

    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
Expand
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    5'-D(P*GP*TP*CP*GP*G)-3'B [auth D]5synthetic 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'C [auth P]10synthetic 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'D [auth T]16synthetic construct
        Small Molecules
        Ligands 4 Unique
        IDChainsName / Formula / InChI Key2D Diagram3D Interactions
        F2A
        Query on F2A

        Download Ideal Coordinates CCD File 
        N [auth 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 Ideal Coordinates CCD File 
        O [auth A]1,2-ETHANEDIOL
        C2 H6 O2
        LYCAIKOWRPUZTN-UHFFFAOYSA-N
         Ligand Interaction
        MN
        Query on MN

        Download Ideal Coordinates CCD File 
        G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], Q [auth T]MANGANESE (II) ION
        Mn
        WAEMQWOKJMHJLA-UHFFFAOYSA-N
         Ligand Interaction
        NA
        Query on NA

        Download Ideal Coordinates CCD File 
        E [auth A], F [auth A], PSODIUM 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: 2.60 Å
        • R-Value Free: 0.262 
        • R-Value Work: 0.195 
        • R-Value Observed: 0.195 
        • Space Group: P 1 21 1
        Unit Cell:
        Length ( Å )Angle ( ˚ )
        a = 54.7α = 90
        b = 77.64β = 113.67
        c = 55.22γ = 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  (Full details and data files)

        • 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