4U6P

Structural mechanism of error-free bypass of major benzo[a]pyrene adduct by human polymerase kappa


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.201 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure and mechanism of error-free replication past the major benzo[a]pyrene adduct by human DNA polymerase kappa.

Jha, V.Bian, C.Xing, G.Ling, H.

(2016) Nucleic Acids Res 44: 4957-4967

  • DOI: 10.1093/nar/gkw204
  • Primary Citation of Related Structures:  
    4U6P, 4U7C

  • PubMed Abstract: 
  • Benzo[a]pyrene (BP) is a well-known and frequently encountered carcinogen which generates a bulky DNA adduct (+)-trans-10S-BP-N(2)-dG (BP-dG) in cells. DNA polymerase kappa (polκ) is the only known Y-family polymerase that bypasses BP-dG accurately and t ...

    Benzo[a]pyrene (BP) is a well-known and frequently encountered carcinogen which generates a bulky DNA adduct (+)-trans-10S-BP-N(2)-dG (BP-dG) in cells. DNA polymerase kappa (polκ) is the only known Y-family polymerase that bypasses BP-dG accurately and thus protects cells from genotoxic BP. Here, we report the structures of human polκ in complex with DNA containing either a normal guanine (G) base or a BP-dG adduct at the active site and a correct deoxycytidine. The structures and supporting biochemical data reveal a unique mechanism for accurate replication by translesion synthesis past the major bulky adduct. The active site of polκ opens at the minor groove side of the DNA substrate to accommodate the bulky BP-dG that is attached there. More importantly, polκ stabilizes the lesion DNA substrate in the same active conformation as for regular B-form DNA substrates and the bulky BPDE ring in a 5' end pointing conformation. The BP-dG adducted DNA substrate maintains a Watson-Crick (BP-dG:dC) base pair within the active site, governing correct nucleotide insertion opposite the bulky adduct. In addition, polκ's unique N-clasp domain supports the open conformation of the enzyme and the extended conformation of the single-stranded template to allow bypass of the bulky lesion. This work illustrates the first molecular mechanism for how a bulky major adduct is replicated accurately without strand misalignment and mis-insertion.


    Organizational Affiliation

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



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase kappa AB526Homo sapiensMutation(s): 0 
Gene Names: POLKDINB1
EC: 2.7.7.7
Find proteins for Q9UBT6 (Homo sapiens)
Explore Q9UBT6 
Go to UniProtKB:  Q9UBT6
NIH Common Fund Data Resources
PHAROS:  Q9UBT6
Protein Feature View
Expand
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(P*GP*CP*GP*GP*AP*TP*CP*AP*C)-3')C, P9unidentified
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*TP*AP*TP*GP*GP*TP*GP*AP*TP*CP*CP*GP*C)-3')D, T13unidentified
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.59 Å
      • R-Value Free: 0.239 
      • R-Value Work: 0.200 
      • R-Value Observed: 0.201 
      • Space Group: P 21 21 21
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 66.15α = 90
      b = 129.286β = 90
      c = 167.713γ = 90
      Software Package:
      Software NamePurpose
      PHENIXrefinement
      MOSFLMdata reduction
      SCALAdata scaling
      PHENIXphasing

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      • Deposited Date: 2014-07-29 
      • Released Date: 2016-01-27 
      • Deposition Author(s): Jha, V.K., Ling, H.

      Revision History 

      • Version 1.0: 2016-01-27
        Type: Initial release
      • Version 1.1: 2016-03-23
        Changes: Derived calculations
      • Version 1.2: 2016-04-13
        Changes: Database references
      • Version 1.3: 2016-06-15
        Changes: Database references