4M9N

DNA Polymerase Beta E295K Soaked with dATP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.195 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

The E295K Cancer Variant of Human Polymerase beta Favors the Mismatch Conformational Pathway during Nucleotide Selection.

Eckenroth, B.E.Towle-Weicksel, J.B.Sweasy, J.B.Doublie, S.

(2013) J Biol Chem 288: 34850-34860

  • DOI: 10.1074/jbc.M113.510891
  • Primary Citation of Related Structures:  
    4M9G, 4M9H, 4M9J, 4M9L, 4M9N

  • PubMed Abstract: 
  • DNA polymerase β (pol β) is responsible for gap filling synthesis during repair of damaged DNA as part of the base excision repair pathway. Human pol β mutations were recently identified in a high percentage (∼30%) of tumors. Characterization of specific cancer variants is particularly useful to further the understanding of the general mechanism of pol β while providing context to disease contribution ...

    DNA polymerase β (pol β) is responsible for gap filling synthesis during repair of damaged DNA as part of the base excision repair pathway. Human pol β mutations were recently identified in a high percentage (∼30%) of tumors. Characterization of specific cancer variants is particularly useful to further the understanding of the general mechanism of pol β while providing context to disease contribution. We showed that expression of the carcinoma variant E295K induces cellular transformation. The poor polymerase activity exhibited by the variant was hypothesized to be caused by the destabilization of proper active site assembly by the glutamate to lysine mutation. Here, we show that this variant exhibits an unusual preference for binding dCTP opposite a templating adenine over the cognate dTTP. Biochemical studies indicate that the noncognate competes with the cognate nucleotide for binding to the polymerase active site with the noncognate incorporation a function of higher affinity and not increased activity. In the crystal structure of the variant bound to dA:dCTP, the fingers domain closes around the mismatched base pair. Nucleotide incorporation is hindered because key residues in the polymerase active site are not properly positioned for nucleotidyl transfer. In contrast to the noncognate dCTP, neither the cognate dTTP nor its nonhydrolyzable analog induced fingers closure, as isomorphous difference Fourier maps show that the cognate nucleotides are bound to the open state of the polymerase. Comparison with published structures provides insight into the structural rearrangements within pol β that occur during the process of nucleotide discrimination.


    Organizational Affiliation

    From the Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont 05405 and.



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
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  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA Template StrandB [auth T]16N/A
    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]10N/A
      Protein Feature View
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      • Reference Sequence
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      • Entity ID: 4
        MoleculeChainsLengthOrganismImage
        DNA Downstream StrandD5N/A
        Protein Feature View
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        • Reference Sequence
        Small Molecules
        Ligands 3 Unique
        IDChainsName / Formula / InChI Key2D Diagram3D Interactions
        DTP (Subject of Investigation/LOI)
        Query on DTP

        Download Ideal Coordinates CCD File 
        H [auth A]2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
        C10 H16 N5 O12 P3
        SUYVUBYJARFZHO-RRKCRQDMSA-N
         Ligand Interaction
        MG
        Query on MG

        Download Ideal Coordinates CCD File 
        G [auth A]MAGNESIUM ION
        Mg
        JLVVSXFLKOJNIY-UHFFFAOYSA-N
         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: 2.27 Å
        • R-Value Free: 0.227 
        • R-Value Work: 0.192 
        • R-Value Observed: 0.195 
        • Space Group: P 1 21 1
        Unit Cell:
        Length ( Å )Angle ( ˚ )
        a = 54.523α = 90
        b = 79.215β = 106.24
        c = 54.685γ = 90
        Software Package:
        Software NamePurpose
        DENZOdata reduction
        SCALEPACKdata scaling
        PHENIXrefinement
        PDB_EXTRACTdata extraction

        Structure Validation

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        Ligand Structure Quality Assessment  



        Entry History 

        Deposition Data

        Revision History  (Full details and data files)

        • Version 1.0: 2013-10-16
          Type: Initial release
        • Version 1.1: 2013-10-30
          Changes: Database references
        • Version 1.2: 2013-12-18
          Changes: Database references