6BTE

DNA Polymerase Beta I260Q Binary Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.190 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

I260Q DNA polymerase beta highlights precatalytic conformational rearrangements critical for fidelity.

Liptak, C.Mahmoud, M.M.Eckenroth, B.E.Moreno, M.V.East, K.Alnajjar, K.S.Huang, J.Towle-Weicksel, J.B.Doublie, S.Loria, J.P.Sweasy, J.B.

(2018) Nucleic Acids Res 46: 10740-10756

  • DOI: 10.1093/nar/gky825
  • Primary Citation of Related Structures:  
    6BTE, 6BTF

  • PubMed Abstract: 
  • DNA polymerase β (pol β) fills single nucleotide gaps in DNA during base excision repair and non-homologous end-joining. Pol β must select the correct nucleotide from among a pool of four nucleotides with similar structures and properties in order to maintain genomic stability during DNA repair ...

    DNA polymerase β (pol β) fills single nucleotide gaps in DNA during base excision repair and non-homologous end-joining. Pol β must select the correct nucleotide from among a pool of four nucleotides with similar structures and properties in order to maintain genomic stability during DNA repair. Here, we use a combination of X-ray crystallography, fluorescence resonance energy transfer and nuclear magnetic resonance to show that pol β's ability to access the appropriate conformations both before and upon binding to nucleotide substrates is integral to its fidelity. Importantly, we also demonstrate that the inability of the I260Q mutator variant of pol β to properly navigate this conformational landscape results in error-prone DNA synthesis. Our work reveals that precatalytic conformational rearrangements themselves are an important underlying mechanism of substrate selection by DNA pol β.


    Organizational Affiliation

    Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase betaA335Homo sapiensMutation(s): 1 
Gene Names: POLB
EC: 2.7.7.7 (PDB Primary Data), 4.2.99 (PDB Primary Data)
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: 2
    MoleculeChainsLengthOrganismImage
    DNA Template StrandB [auth T]16Homo sapiens
    Protein Feature View
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    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      DNA Primer StrandC [auth P]10Homo sapiens
      Protein Feature View
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      • Reference Sequence
      • Find similar nucleic acids by:  Sequence   |   Structure
      • Entity ID: 4
        MoleculeChainsLengthOrganismImage
        DNA Downstream StrandD5Homo sapiens
        Protein Feature View
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        • Reference Sequence
        Small Molecules
        Ligands 3 Unique
        IDChainsName / Formula / InChI Key2D Diagram3D Interactions
        IOD
        Query on IOD

        Download Ideal Coordinates CCD File 
        H [auth A], I [auth A]IODIDE ION
        I
        XMBWDFGMSWQBCA-UHFFFAOYSA-M
         Ligand Interaction
        CL
        Query on CL

        Download Ideal Coordinates CCD File 
        G [auth A]CHLORIDE ION
        Cl
        VEXZGXHMUGYJMC-UHFFFAOYSA-M
         Ligand Interaction
        NA
        Query on NA

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

        Experimental Data

        • Method: X-RAY DIFFRACTION
        • Resolution: 2.20 Å
        • R-Value Free: 0.229 
        • R-Value Work: 0.185 
        • R-Value Observed: 0.190 
        • Space Group: P 1 21 1
        Unit Cell:
        Length ( Å )Angle ( ˚ )
        a = 50.942α = 90
        b = 80.568β = 107.92
        c = 55.133γ = 90
        Software Package:
        Software NamePurpose
        SAINTdata reduction
        SAINTdata scaling
        PHENIXrefinement
        PDB_EXTRACTdata extraction
        PHENIXphasing

        Structure Validation

        View Full Validation Report



        Entry History & Funding Information

        Deposition Data


        Funding OrganizationLocationGrant Number
        National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA080830

        Revision History  (Full details and data files)

        • Version 1.0: 2018-09-26
          Type: Initial release
        • Version 1.1: 2018-10-03
          Changes: Data collection, Database references
        • Version 1.2: 2018-11-28
          Changes: Data collection, Database references
        • Version 1.3: 2019-12-04
          Changes: Author supporting evidence