6NL0

Ternary complex crystal structure of K289M variant of DNA polymerase Beta with "hot-spot sequence" with beta-gamma CF2 analogue of dGTP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.196 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Revealing an Internal Stabilization Deficiency in the DNA Polymerase beta K289M Cancer Variant through the Combined Use of Chemical Biology and X-ray Crystallography.

Batra, V.K.Alnajjar, K.S.Sweasy, J.B.McKenna, C.E.Goodman, M.F.Wilson, S.H.

(2020) Biochemistry 59: 955-963

  • DOI: 10.1021/acs.biochem.9b01072
  • Primary Citation of Related Structures:  
    6NKR, 6NKS, 6NKT, 6NKU, 6NKV, 6NKW, 6NKX, 6NKY, 6NKZ, 6NL0

  • PubMed Abstract: 
  • The human DNA polymerase (pol) β cancer variant K289M has altered polymerase activity in vitro , and the structure of wild-type pol β reveals that the K289 side chain contributes to a network of stabilizing interactions in a C-terminal region of the enzyme distal to the active site ...

    The human DNA polymerase (pol) β cancer variant K289M has altered polymerase activity in vitro , and the structure of wild-type pol β reveals that the K289 side chain contributes to a network of stabilizing interactions in a C-terminal region of the enzyme distal to the active site. Here, we probed the capacity of the K289M variant to tolerate strain introduced within the C-terminal region and active site. Strain was imposed by making use of a dGTP analogue containing a CF 2 group substitution for the β-γ bridging oxygen atom. The ternary complex structure of the K289M variant displays an alteration in the C-terminal region, whereas the structure of wild-type pol β is not altered in the presence of the dGTP CF 2 analogue. The alteration in the K289M variant impacts the active site, because the enzyme in the ternary complex fails to adopt the normal open to closed conformational change and assembly of the catalytically competent active site. These results reveal the importance of the K289-mediated stabilizing network in the C-terminal region of pol β and suggest an explanation for why the K289M cancer variant is deficient in polymerase activity even though the position 289 side chain is distal to the active site.


    Organizational Affiliation

    Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, 111 T. W. Alexander Drive, Research Triangle Park, North Carolina 27709, United States.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase betaD [auth A]335Homo 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: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*CP*CP*GP*AP*AP*CP*AP*AP*GP*CP*AP*TP*CP*AP*GP*C)-3')A [auth T]16Homo sapiens
    Protein Feature View
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    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*TP*(2DT))-3')B [auth P]10Homo sapiens
      Protein Feature View
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      • Reference Sequence
      • Find similar nucleic acids by:  Sequence   |   Structure
      • Entity ID: 3
        MoleculeChainsLengthOrganismImage
        DNA (5'-D(P*TP*TP*CP*GP*G)-3')C [auth D]5Homo sapiens
        Protein Feature View
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        • Reference Sequence
        Small Molecules
        Ligands 4 Unique
        IDChainsName / Formula / InChI Key2D Diagram3D Interactions
        GFF (Subject of Investigation/LOI)
        Query on GFF

        Download Ideal Coordinates CCD File 
        I [auth A]2'-DEOXY-5'-O-[({[DIFLUORO(PHOSPHONO)METHYL](HYDROXY)PHOSPHORYL}OXY)(HYDROXY)PHOSPHORYL]GUANOSINE
        C11 H16 F2 N5 O12 P3
        BLHFKUNEUAHYSE-KVQBGUIXSA-N
         Ligand Interaction
        CL
        Query on CL

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

        Download Ideal Coordinates CCD File 
        E [auth A]MAGNESIUM ION
        Mg
        JLVVSXFLKOJNIY-UHFFFAOYSA-N
         Ligand Interaction
        NA
        Query on NA

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

        Experimental Data

        • Method: X-RAY DIFFRACTION
        • Resolution: 1.97 Å
        • R-Value Free: 0.237 
        • R-Value Work: 0.193 
        • R-Value Observed: 0.196 
        • Space Group: P 1 21 1
        Unit Cell:
        Length ( Å )Angle ( ˚ )
        a = 50.317α = 90
        b = 79.933β = 107.97
        c = 55.119γ = 90
        Software Package:
        Software NamePurpose
        HKL-2000data reduction
        HKL-2000data scaling
        PHENIXrefinement
        PDB_EXTRACTdata extraction
        PHENIXphasing

        Structure Validation

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        Ligand Structure Quality Assessment  



        Entry History 

        Deposition Data

        Revision History  (Full details and data files)

        • Version 1.0: 2020-01-08
          Type: Initial release
        • Version 1.1: 2020-07-22
          Changes: Database references