6BS1

Crystal Structure of Human DNA polymerase kappa in complex with DNA containing the major cisplatin lesion


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.247 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural Basis for Human DNA Polymerase Kappa to Bypass Cisplatin Intrastrand Cross-Link (Pt-GG) Lesion as an Efficient and Accurate Extender.

Jha, V.Ling, H.

(2018) J Mol Biol 430: 1577-1589

  • DOI: 10.1016/j.jmb.2018.04.023
  • Primary Citation of Related Structures:  
    6BRX, 6BS1

  • PubMed Abstract: 
  • Cisplatin (cis-diamminedichloroplatinum) is a common chemotherapeutic drug that reacts with the N7 atoms of adjacent guanines in DNA to form the Pt-1,2-d(GpG) intrastrand cross-link (Pt-GG), a major product to block DNA replication. Translesion DNA synthesis has been implicated in chemoresistance during cisplatin treatment of cancer due to Pt-GG lesion bypass ...

    Cisplatin (cis-diamminedichloroplatinum) is a common chemotherapeutic drug that reacts with the N7 atoms of adjacent guanines in DNA to form the Pt-1,2-d(GpG) intrastrand cross-link (Pt-GG), a major product to block DNA replication. Translesion DNA synthesis has been implicated in chemoresistance during cisplatin treatment of cancer due to Pt-GG lesion bypass. Gene knockdown studies in human cells have indicated a role for polκ during translesion synthesis of the Pt-GG lesion. However, the bypass activity of polκ with cisplatin lesions has not been well characterized. In this study, we investigated polκ's ability to bypass Pt-GG lesion in vitro and determined two crystal structures of polκ in complex with Pt-GG DNA. The ternary complex structures represent two consecutive stages of lesion bypass: nucleotide insertion opposite the 5'G (Pt-GG2) and primer extension immediately after the lesion (Pt-GG3). Our biochemical data showed that polκ is very efficient and accurate in extending DNA primers after the first G of the Pt-GG lesion. The structures demonstrate that the efficiency and accuracy is achieved by stably accommodating the bases with the cisplatin adduct in the active site for proper Watson-Crick base pairing with the incoming nucleotide in both the second insertion and post-insertion complexes. Our studies suggest that polκ works as an extender for efficient replication of the Pt-GG lesion in cells. This work holds promise for considering polκ, along with polη, as potential targets for drug design, which together could improve the efficacy of cisplatin treatment for cancer therapy.


    Organizational Affiliation

    Department of Biochemistry, Schulich School of Medicine & Dentistry, University of Western Ontario, London, Ontario N6A 5C1, Canada. Electronic address: hling4@uwo.ca.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase kappaA, B551Homo sapiensMutation(s): 0 
Gene Names: POLKDINB1
EC: 2.7.7.7
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UBT6 (Homo sapiens)
Explore Q9UBT6 
Go to UniProtKB:  Q9UBT6
PHAROS:  Q9UBT6
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(P*AP*TP*AP*CP*AP*TP*AP*CP*C)-3')C, E [auth P]9synthetic construct
    Protein Feature View
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    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*TP*AP*CP*TP*GP*GP*TP*AP*TP*GP*TP*AP*T)-3')D, F [auth T]13synthetic construct
      Protein Feature View
      Expand
      • Reference Sequence
      Small Molecules
      Ligands 4 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      DZ4
      Query on DZ4

      Download Ideal Coordinates CCD File 
      O [auth A], V [auth B]2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine
      C10 H17 N6 O11 P3
      WKIPJDSLGCBQCU-RRKCRQDMSA-N
       Ligand Interaction
      CPT
      Query on CPT

      Download Ideal Coordinates CCD File 
      X [auth D], Y [auth T]Cisplatin
      Cl2 H6 N2 Pt
      LXZZYRPGZAFOLE-UHFFFAOYSA-L
       Ligand Interaction
      IOD
      Query on IOD

      Download Ideal Coordinates CCD File 
      J [auth A] , K [auth A] , L [auth A] , M [auth A] , N [auth A] , R [auth B] , S [auth B] , T [auth B] , 
      J [auth A],  K [auth A],  L [auth A],  M [auth A],  N [auth A],  R [auth B],  S [auth B],  T [auth B],  U [auth B]
      IODIDE ION
      I
      XMBWDFGMSWQBCA-UHFFFAOYSA-M
       Ligand Interaction
      MG
      Query on MG

      Download Ideal Coordinates CCD File 
      G [auth A], H [auth A], I [auth A], P [auth B], Q [auth B], W [auth B]MAGNESIUM ION
      Mg
      JLVVSXFLKOJNIY-UHFFFAOYSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 3.15 Å
      • R-Value Free: 0.299 
      • R-Value Work: 0.244 
      • R-Value Observed: 0.247 
      • Space Group: P 21 21 21
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 63.8α = 90
      b = 127.72β = 90
      c = 168.14γ = 90
      Software Package:
      Software NamePurpose
      REFMACrefinement
      iMOSFLMdata reduction
      SCALAdata scaling
      REFMACphasing

      Structure Validation

      View Full Validation Report



      Entry History & Funding Information

      Deposition Data

      • Deposited Date: 2017-12-01 
      • Released Date: 2018-08-22 
      • Deposition Author(s): Jha, V.K., Ling, H.
      • This entry supersedes: 6BRX

      Funding OrganizationLocationGrant Number
      Canadian Institutes of Health Research (CIHR)CanadaMOP-94590

      Revision History  (Full details and data files)

      • Version 1.0: 2018-08-22
        Type: Initial release
      • Version 1.1: 2020-01-08
        Changes: Advisory, Author supporting evidence