4UB3

DNA polymerase beta closed product complex with a templating cytosine and 8-oxodGMP, 60 s


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.217 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Uncovering the polymerase-induced cytotoxicity of an oxidized nucleotide.

Freudenthal, B.D.Beard, W.A.Perera, L.Shock, D.D.Kim, T.Schlick, T.Wilson, S.H.

(2015) Nature 517: 635-639

  • DOI: 10.1038/nature13886
  • Primary Citation of Related Structures:  
    4UAY, 4UAZ, 4UB1, 4UB2, 4UB3, 4UB4, 4UB5, 4UAW, 4UBB, 4UBC

  • PubMed Abstract: 
  • Oxidative stress promotes genomic instability and human diseases. A common oxidized nucleoside is 8-oxo-7,8-dihydro-2'-deoxyguanosine, which is found both in DNA (8-oxo-G) and as a free nucleotide (8-oxo-dGTP). Nucleotide pools are especially vulnera ...

    Oxidative stress promotes genomic instability and human diseases. A common oxidized nucleoside is 8-oxo-7,8-dihydro-2'-deoxyguanosine, which is found both in DNA (8-oxo-G) and as a free nucleotide (8-oxo-dGTP). Nucleotide pools are especially vulnerable to oxidative damage. Therefore cells encode an enzyme (MutT/MTH1) that removes free oxidized nucleotides. This cleansing function is required for cancer cell survival and to modulate Escherichia coli antibiotic sensitivity in a DNA polymerase (pol)-dependent manner. How polymerases discriminate between damaged and non-damaged nucleotides is not well understood. This analysis is essential given the role of oxidized nucleotides in mutagenesis, cancer therapeutics, and bacterial antibiotics. Even with cellular sanitizing activities, nucleotide pools contain enough 8-oxo-dGTP to promote mutagenesis. This arises from the dual coding potential where 8-oxo-dGTP(anti) base pairs with cytosine and 8-oxo-dGTP(syn) uses its Hoogsteen edge to base pair with adenine. Here we use time-lapse crystallography to follow 8-oxo-dGTP insertion opposite adenine or cytosine with human pol β, to reveal that insertion is accommodated in either the syn- or anti-conformation, respectively. For 8-oxo-dGTP(anti) insertion, a novel divalent metal relieves repulsive interactions between the adducted guanine base and the triphosphate of the oxidized nucleotide. With either templating base, hydrogen-bonding interactions between the bases are lost as the enzyme reopens after catalysis, leading to a cytotoxic nicked DNA repair intermediate. Combining structural snapshots with kinetic and computational analysis reveals how 8-oxo-dGTP uses charge modulation during insertion that can lead to a blocked DNA repair intermediate.


    Organizational Affiliation

    Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, PO Box 12233, Research Triangle Park, North Carolina 27709-2233, 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
Protein Feature View
Expand
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    5'-D(*CP*CP*GP*AP*CP*CP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'T16synthetic construct
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*CP*(8OG))-3'P11synthetic construct
      • Find similar nucleic acids by:  Sequence   |   Structure
      • Entity ID: 3
        MoleculeChainsLengthOrganismImage
        5'-D(P*GP*TP*CP*GP*G)-3'D5synthetic construct
        Small Molecules
        Ligands 3 Unique
        IDChainsName / Formula / InChI Key2D Diagram3D Interactions
        PPV
        Query on PPV

        Download Ideal Coordinates CCD File 
        A
        PYROPHOSPHATE
        H4 O7 P2
        XPPKVPWEQAFLFU-UHFFFAOYSA-N
         Ligand Interaction
        MG
        Query on MG

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

        Download Ideal Coordinates CCD File 
        A
        SODIUM ION
        Na
        FKNQFGJONOIPTF-UHFFFAOYSA-N
         Ligand Interaction
        Experimental Data & Validation

        Experimental Data

        • Method: X-RAY DIFFRACTION
        • Resolution: 2.06 Å
        • R-Value Free: 0.274 
        • R-Value Work: 0.214 
        • R-Value Observed: 0.217 
        • Space Group: P 1 21 1
        Unit Cell:
        Length ( Å )Angle ( ˚ )
        a = 50.698α = 90
        b = 80.094β = 107.8
        c = 55.358γ = 90
        Software Package:
        Software NamePurpose
        PHENIXrefinement

        Structure Validation

        View Full Validation Report



        Entry History & Funding Information

        Deposition Data


        Funding OrganizationLocationGrant Number
        National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)United StatesES050158
        National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)United StatesES050161
        National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)United StatesES043010

        Revision History 

        • Version 1.0: 2014-11-12
          Type: Initial release
        • Version 1.1: 2014-12-03
          Changes: Database references
        • Version 1.2: 2015-02-04
          Changes: Database references
        • Version 1.3: 2019-11-27
          Changes: Author supporting evidence, Database references, Derived calculations, Other, Source and taxonomy