5W2A

Structure of human DNA polymerase kappa in complex with Lucidin-derived DNA adduct and incoming dCMPNPP

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.231 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

Mechanism of Error-Free DNA Replication Past Lucidin-Derived DNA Damage by Human DNA Polymerase kappa.

Yockey, O.P., Jha, V., Ghodke, P.P., Xu, T., Xu, W., Ling, H., Pradeepkumar, P.I., Zhao, L.

(2017) Chem. Res. Toxicol. 30: 2023-2032

  • DOI: 10.1021/acs.chemrestox.7b00227
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • DNA damage impinges on genetic information flow and has significant implications in human disease and aging. Lucidin-3-O-primeveroside (LuP) is an anthraquinone derivative present in madder root, which has been used as a coloring agent and food addit ...

    DNA damage impinges on genetic information flow and has significant implications in human disease and aging. Lucidin-3-O-primeveroside (LuP) is an anthraquinone derivative present in madder root, which has been used as a coloring agent and food additive. LuP can be metabolically converted to genotoxic compound lucidin, which subsequently forms lucidin-specific N2-2'-deoxyguanosine (N2-dG) and N6-2'-deoxyadenosine (N6-dA) DNA adducts. Lucidin is mutagenic and carcinogenic in rodents but has low carcinogenic risks in humans. To understand the molecular mechanism of low carcinogenicity of lucidin in humans, we performed DNA replication assays using site-specifically modified oligodeoxynucleotides containing a structural analogue (LdG) of lucidin-N2-dG DNA adduct and determined the crystal structures of DNA polymerase (pol) κ in complex with LdG-bearing DNA and an incoming nucleotide. We examined four human pols (pol η, pol ι, pol κ, and Rev1) in their efficiency and accuracy during DNA replication with LdG; these pols are key players in translesion DNA synthesis. Our results demonstrate that pol κ efficiently and accurately replicates past the LdG adduct, whereas DNA replication by pol η, pol ι is compromised to different extents. Rev1 retains its ability to incorporate dCTP opposite the lesion albeit with decreased efficiency. Two ternary crystal structures of pol κ illustrate that the LdG adduct is accommodated by pol κ at the enzyme active site during insertion and postlesion-extension steps. The unique open active site of pol κ allows the adducted DNA to adopt a standard B-form for accurate DNA replication. Collectively, these biochemical and structural data provide mechanistic insights into the low carcinogenic risk of lucidin in humans.

    Organizational Affiliation: 

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




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase kappa
A, B
551Homo sapiensMutation(s): 0 
Gene Names: POLK (DINB1)
EC: 2.7.7.7
Find proteins for Q9UBT6 (Homo sapiens)
Go to Gene View: POLK
Go to UniProtKB:  Q9UBT6
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(P*GP*CP*GP*GP*AP*TP*CP*AP*G)-3')C,P9unidentified
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*TP*GP*(LDG)P*CP*TP*GP*AP*TP*CP*CP*GP*C)-3')D,T13unidentified
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0KX
Query on 0KX
Download SDF File 
Download CCD File 
A, B
2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]cytidine
C9 H17 N4 O12 P3
STYMTWKSQLVXJN-SHYZEUOFSA-N
 Ligand Interaction
GOL
Query on GOL
Download SDF File 
Download CCD File 
A, B, P
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG
Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
PGE
Query on PGE
Download SDF File 
Download CCD File 
A, B
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
LDG
Query on LDG
D, T
NON-POLYMERC27 H26 N5 O11 PDG
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.231 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 63.891α = 90.00
b = 129.014β = 90.00
c = 167.346γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
REFMACphasing
SCALAdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-06-06 
  • Released Date: 2017-10-18 
  • Deposition Author(s): Jha, V.K., Ling, H.
Funding OrganizationLocationGrant Number
Canadian Institutes of Health (CIHR)CanadaMOP-94590

Revision History 

  • Version 1.0: 2017-10-18
    Type: Initial release
  • Version 1.1: 2017-11-29
    Type: Database references