5WNX

DNA polymerase beta substrate complex with incoming 6-TdGTP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.214 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structures of a DNA Polymerase Inserting Therapeutic Nucleotide Analogues.

Schaich, M.A.Smith, M.R.Cloud, A.S.Holloran, S.M.Freudenthal, B.D.

(2017) Chem Res Toxicol 30: 1993-2001

  • DOI: 10.1021/acs.chemrestox.7b00173
  • Primary Citation of Related Structures:  
    5WNX, 5WNY, 5WNZ, 5WO0

  • PubMed Abstract: 
  • Members of the nucleoside analogue class of cancer therapeutics compete with canonical nucleotides to disrupt numerous cellular processes, including nucleotide homeostasis, DNA and RNA synthesis, and nucleotide metabolism. Nucleoside analogues are triphosphorylated and subsequently inserted into genomic DNA, contributing to the efficacy of therapeutic nucleosides in multiple ways ...

    Members of the nucleoside analogue class of cancer therapeutics compete with canonical nucleotides to disrupt numerous cellular processes, including nucleotide homeostasis, DNA and RNA synthesis, and nucleotide metabolism. Nucleoside analogues are triphosphorylated and subsequently inserted into genomic DNA, contributing to the efficacy of therapeutic nucleosides in multiple ways. In some cases, the altered base acts as a mutagen, altering the DNA sequence to promote cellular death; in others, insertion of the altered nucleotide triggers DNA repair pathways, which produce lethal levels of cytotoxic intermediates such as single and double stranded DNA breaks. As a prerequisite to many of these biological outcomes, the modified nucleotide must be accommodated in the DNA polymerase active site during nucleotide insertion. Currently, the molecular contacts that mediate DNA polymerase insertion of modified nucleotides remain unknown for multiple therapeutic compounds, despite decades of clinical use. To determine how modified bases are inserted into duplex DNA, we used mammalian DNA polymerase β (pol β) to visualize the structural conformations of four therapeutically relevant modified nucleotides, 6-thio-2'-deoxyguanosine-5'-triphosphate (6-TdGTP), 5-fluoro-2'-deoxyuridine-5'-triphosphate (5-FdUTP), 5-formyl-deoxycytosine-5'-triphosphate (5-FodCTP), and 5-formyl-deoxyuridine-5'-triphosphate (5-FodUTP). Together, the structures reveal a pattern in which the modified nucleotides utilize Watson-Crick base pairing interactions similar to that of unmodified nucleotides. The nucleotide modifications were consistently positioned in the major groove of duplex DNA, accommodated by an open cavity in pol β. These results provide novel information for the rational design of new therapeutic nucleoside analogues and a greater understanding of how modified nucleotides are tolerated by polymerases.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, University of Kansas Medical Center , Kansas City, Kansas 66160, United States.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase betaD [auth A]335Homo sapiensMutation(s): 0 
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*CP*CP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')A [auth T]16synthetic construct
    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*GP*C)-3')B [auth P]10synthetic construct
      Protein Feature View
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      • Reference Sequence
      • Find similar nucleic acids by:  Sequence   |   Structure
      • Entity ID: 3
        MoleculeChainsLengthOrganismImage
        DNA (5'-D(P*GP*TP*CP*GP*G)-3')C [auth D]5synthetic construct
        Protein Feature View
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        • Reference Sequence
        Small Molecules
        Ligands 4 Unique
        IDChainsName / Formula / InChI Key2D Diagram3D Interactions
        SGT (Subject of Investigation/LOI)
        Query on SGT

        Download Ideal Coordinates CCD File 
        H [auth A]2-amino-9-{2-deoxy-5-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-erythro-pentofuranosyl}-1,9-dihydro-6H-purine-6-thione
        C10 H16 N5 O12 P3 S
        BXZRFHUVVWIHMV-KVQBGUIXSA-N
         Ligand Interaction
        CA
        Query on CA

        Download Ideal Coordinates CCD File 
        I [auth A], J [auth A]CALCIUM ION
        Ca
        BHPQYMZQTOCNFJ-UHFFFAOYSA-N
         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: 2.55 Å
        • R-Value Free: 0.289 
        • R-Value Work: 0.206 
        • R-Value Observed: 0.214 
        • Space Group: P 1 21 1
        Unit Cell:
        Length ( Å )Angle ( ˚ )
        a = 50.243α = 90
        b = 79.203β = 107.36
        c = 55.625γ = 90
        Software Package:
        Software NamePurpose
        PHENIXrefinement
        HKL-3000data reduction
        HKL-3000data scaling
        PHENIXphasing

        Structure Validation

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        Ligand Structure Quality Assessment  



        Entry History & Funding Information

        Deposition Data


        Funding OrganizationLocationGrant Number
        National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)United StatesES024432

        Revision History  (Full details and data files)

        • Version 1.0: 2017-09-13
          Type: Initial release
        • Version 1.1: 2017-11-29
          Changes: Author supporting evidence, Database references
        • Version 1.2: 2019-12-18
          Changes: Author supporting evidence