5T14

DNA polymerase kappa extending beyond a bulky major benzo[a]pyrene adduct


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 

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Literature

Structural basis of accurate replication beyond a bulky major benzo[a]pyrene adduct by human DNA polymerase kappa.

Jha, V.Ling, H.

(2017) DNA Repair (Amst) 49: 43-50

  • DOI: 10.1016/j.dnarep.2016.11.001
  • Primary Citation of Related Structures:  
    5T14

  • PubMed Abstract: 
  • Human Y-family DNA polymerase kappa (polκ) is specialized to bypass bulky lesions in DNA in an error-free way, thus protecting cells from carcinogenic bulky DNA adducts. Benzo[a]pyrene (BP) is one of the most ubiquitous polycyclic aromatic hydrocarbons and an environmental carcinogen ...

    Human Y-family DNA polymerase kappa (polκ) is specialized to bypass bulky lesions in DNA in an error-free way, thus protecting cells from carcinogenic bulky DNA adducts. Benzo[a]pyrene (BP) is one of the most ubiquitous polycyclic aromatic hydrocarbons and an environmental carcinogen. BP covalently modifies DNA and generates mutagenic, bulky adducts. The major BP adduct formed in cells is 10S (+)-trans-anti-BP-N 2 -dG adduct (BP-dG), which is associated with cancer. The molecular mechanism of how polκ replicates BP-dG accurately is not clear. Here we report the structure of polκ captured at the lesion-extension stage: the enzyme is extending the primer strand after the base pair containing the BP-dG adduct in the template strand at the -1 position. Polκ accommodates the BP adduct in the nascent DNA's minor groove and keeps the adducted DNA helix in a B-form. Two water molecules cover the edge of the minor groove of the replicating base pair (0 position), which is secured by the BP ring in the -1 position in a 5' orientation. The 5' oriented BP adduct keeps correct Watson-Crick base pairing in the active site and promotes high fidelity replication. Our structural and biochemical data reveal a unique molecular basis for accurate DNA replication right after the bulky lesion BP-dG.


    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

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase kappaA, B527Homo 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

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Entity ID: 2
MoleculeChainsLengthOrganismImage
DNAC, E [auth P]9unidentified
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsLengthOrganismImage
DNAD, F [auth T]13unidentified
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DZ4 (Subject of Investigation/LOI)
Query on DZ4

Download Ideal Coordinates CCD File 
I [auth A], M [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
PGE
Query on PGE

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J [auth B]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.25α = 90
b = 128.82β = 90
c = 167.46γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Deposited Date: 2016-08-17 
  • Released Date: 2016-12-21 
  • Deposition Author(s): Jha, V.K., Ling, H.

Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)CanadaMOP-67128

Revision History  (Full details and data files)

  • Version 1.0: 2016-12-21
    Type: Initial release
  • Version 1.1: 2017-01-18
    Changes: Database references
  • Version 1.2: 2020-01-08
    Changes: Author supporting evidence