4TUP

Structure of human DNA polymerase beta complexed with GG as the template (GG0b) in a 1-nucleotide gapped DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.204 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structural Basis for the Inefficient Nucleotide Incorporation Opposite Cisplatin-DNA Lesion by Human DNA Polymerase beta.

Koag, M.C.Lai, L.Lee, S.

(2014) J Biol Chem 289: 31341-31348

  • DOI: 10.1074/jbc.M114.605451
  • Primary Citation of Related Structures:  
    4TUP, 4TUQ, 4TUR, 4TUS

  • PubMed Abstract: 
  • Human DNA polymerase β (polβ) has been suggested to play a role in cisplatin resistance, especially in polβ-overexpressing cancer cells. Polβ has been shown to accurately albeit slowly bypass the cisplatin-1,2-d(GpG) (Pt-GG) intramolecular cross-link in vitro ...

    Human DNA polymerase β (polβ) has been suggested to play a role in cisplatin resistance, especially in polβ-overexpressing cancer cells. Polβ has been shown to accurately albeit slowly bypass the cisplatin-1,2-d(GpG) (Pt-GG) intramolecular cross-link in vitro. Currently, the structural basis for the inefficient Pt-GG bypass mechanism of polβ is unknown. To gain structural insights into the mechanism, we determined two ternary structures of polβ incorporating dCTP opposite the templating Pt-GG lesion in the presence of the active site Mg(2+) or Mn(2+). The Mg(2+)-bound structure shows that the bulky Pt-GG adduct is accommodated in the polβ active site without any steric hindrance. In addition, both guanines of the Pt-GG lesion form Watson-Crick base pairing with the primer terminus dC and the incoming dCTP, providing the structural basis for the accurate bypass of the Pt-GG adduct by polβ. The Mn(2+)-bound structure shows that polβ adopts a catalytically suboptimal semiclosed conformation during the insertion of dCTP opposite the templating Pt-GG, explaining the inefficient replication across the Pt-GG lesion by polβ. Overall, our studies provide the first structural insights into the mechanism of the potential polβ-mediated cisplatin resistance.


    Organizational Affiliation

    From the Division of Medicinal Chemistry, College of Pharmacy, The University of Texas, Austin, Texas 78712 SeongminLee@austin.utexas.edu.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase betaA329Homo 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: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*CP*CP*CP*AP*CP*GP*GP*CP*CP*CP*AP*TP*CP*AP*CP*C)-3')B [auth T]16Homo sapiens
    Protein Feature View
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    • Reference Sequence
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    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*GP*GP*TP*GP*AP*TP*GP*GP*GP*C)-3')C [auth P]10Homo sapiens
      Protein Feature View
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      • Reference Sequence
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      • Entity ID: 4
        MoleculeChainsLengthOrganismImage
        DNA (5'-D(P*GP*TP*GP*GP*G)-3')D5Homo sapiens
        Protein Feature View
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        • Reference Sequence
        Small Molecules
        Ligands 1 Unique
        IDChainsName / Formula / InChI Key2D Diagram3D Interactions
        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: 1.80 Å
        • R-Value Free: 0.236 
        • R-Value Work: 0.203 
        • R-Value Observed: 0.204 
        • Space Group: P 1 21 1
        Unit Cell:
        Length ( Å )Angle ( ˚ )
        a = 54.354α = 90
        b = 79.257β = 105.42
        c = 54.927γ = 90
        Software Package:
        Software NamePurpose
        PHENIXrefinement

        Structure Validation

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        Entry History & Funding Information

        Deposition Data

        • Deposited Date: 2014-06-24 
        • Released Date: 2014-10-01 
        • Deposition Author(s): Koag, M.C., Lee, S.

        Funding OrganizationLocationGrant Number
        National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)United StatesES23101

        Revision History  (Full details and data files)

        • Version 1.0: 2014-10-01
          Type: Initial release
        • Version 1.1: 2014-10-15
          Changes: Database references
        • Version 1.2: 2014-11-19
          Changes: Database references
        • Version 1.3: 2017-09-20
          Changes: Author supporting evidence, Database references, Derived calculations, Other, Source and taxonomy
        • Version 1.4: 2019-12-18
          Changes: Author supporting evidence