4RPZ

Human DNA Polymerase Beta With Gapped DNA Containing an 8-oxo-7,8-dihydro-Guanine (8-oxoG)and dCTP soaked with MgCl2 for 60 s


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.198 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Viewing Human DNA Polymerase beta Faithfully and Unfaithfully Bypass an Oxidative Lesion by Time-Dependent Crystallography.

Vyas, R.Reed, A.J.Tokarsky, E.J.Suo, Z.

(2015) J Am Chem Soc 137: 5225-5230

  • DOI: 10.1021/jacs.5b02109
  • Primary Citation of Related Structures:  
    4RPX, 4RPY, 4RPZ, 4RQ0, 4RQ1, 4RQ2, 4RQ3, 4RQ4, 4RQ5, 4RQ6, 4RQ7, 4RQ8

  • PubMed Abstract: 
  • One common oxidative DNA lesion, 8-oxo-7,8-dihydro-2'-deoxyguanine (8-oxoG), is highly mutagenic in vivo due to its anti-conformation forming a Watson-Crick base pair with correct deoxycytidine 5'-triphosphate (dCTP) and its syn-conformation forming a Hoogsteen base pair with incorrect deoxyadenosine 5'-triphosphate (dATP) ...

    One common oxidative DNA lesion, 8-oxo-7,8-dihydro-2'-deoxyguanine (8-oxoG), is highly mutagenic in vivo due to its anti-conformation forming a Watson-Crick base pair with correct deoxycytidine 5'-triphosphate (dCTP) and its syn-conformation forming a Hoogsteen base pair with incorrect deoxyadenosine 5'-triphosphate (dATP). Here, we utilized time-resolved X-ray crystallography to follow 8-oxoG bypass by human DNA polymerase β (hPolβ). In the 12 solved structures, both Watson-Crick (anti-8-oxoG:anti-dCTP) and Hoogsteen (syn-8-oxoG:anti-dATP) base pairing were clearly visible and were maintained throughout the chemical reaction. Additionally, a third Mg(2+) appeared during the process of phosphodiester bond formation and was located between the reacting α- and β-phosphates of the dNTP, suggesting its role in stabilizing reaction intermediates. After phosphodiester bond formation, hPolβ reopened its conformation, pyrophosphate was released, and the newly incorporated primer 3'-terminal nucleotide stacked, rather than base paired, with 8-oxoG. These structures provide the first real-time pictures, to our knowledge, of how a polymerase correctly and incorrectly bypasses a DNA lesion.


    Organizational Affiliation

    †Department of Chemistry and Biochemistry, ‡The Ohio State Biochemistry and §Biophysics Programs, The Ohio State University, Columbus, Ohio 43210, United States.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase betaA343Homo sapiensMutation(s): 0 
Gene Names: POL BPOLB
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 (5'-D(P*GP*TP*CP*GP*G)-3')B [auth D]5synthetic construct
    Protein Feature View
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    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*CP*C)-3')C [auth P]11synthetic construct
      Protein Feature View
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      • Reference Sequence
      • Find similar nucleic acids by:  Sequence   |   Structure
      • Entity ID: 4
        MoleculeChainsLengthOrganismImage
        DNA (5'-D(*CP*CP*GP*AP*CP*(8OG)P*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')D [auth T]16synthetic construct
        Protein Feature View
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        • Reference Sequence
        Small Molecules
        Ligands 5 Unique
        IDChainsName / Formula / InChI Key2D Diagram3D Interactions
        DCP (Subject of Investigation/LOI)
        Query on DCP

        Download Ideal Coordinates CCD File 
        N [auth A], O [auth D]2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE
        C9 H16 N3 O13 P3
        RGWHQCVHVJXOKC-SHYZEUOFSA-N
         Ligand Interaction
        PPV
        Query on PPV

        Download Ideal Coordinates CCD File 
        M [auth A]PYROPHOSPHATE
        H4 O7 P2
        XPPKVPWEQAFLFU-UHFFFAOYSA-N
         Ligand Interaction
        CL
        Query on CL

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

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

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

        Experimental Data

        • Method: X-RAY DIFFRACTION
        • Resolution: 2.19 Å
        • R-Value Free: 0.251 
        • R-Value Work: 0.195 
        • R-Value Observed: 0.198 
        • Space Group: P 1 21 1
        Unit Cell:
        Length ( Å )Angle ( ˚ )
        a = 49.41α = 90
        b = 79.32β = 106.2
        c = 55.41γ = 90
        Software Package:
        Software NamePurpose
        PHASERphasing
        REFMACrefinement
        MOSFLMdata reduction
        SCALEPACKdata scaling

        Structure Validation

        View Full Validation Report



        Ligand Structure Quality Assessment  



        Entry History 

        Deposition Data

        Revision History  (Full details and data files)

        • Version 1.0: 2015-04-15
          Type: Initial release
        • Version 1.1: 2015-05-06
          Changes: Database references