5W2C

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.212 

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
  • Structures With Same Primary Citation

  • 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 N 2 -2'-deoxyguanosine (N 2 -dG) and N 6 -2'-deoxyadenosine (N 6 -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-N 2 -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 Chemistry, Indian Institute of Technology Bombay , Mumbai 400076, India.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase kappaA, B551Homo 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
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  • Reference Sequence
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(P*CP*GP*GP*AP*TP*CP*GP*AP*C)-3')C, P9unidentified
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*TP*AP*TP*(LDG)P*TP*CP*GP*AP*TP*CP*CP*G)-3')D, T13unidentified
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DZ4
Query on DZ4

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

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A, B
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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A, B
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

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A
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.212 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.709α = 90
b = 128.923β = 90
c = 167.705γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
REFMACphasing

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2017-06-06 
  • Released Date: 2017-10-18 
  • Deposition Author(s): Jha, V.K., Ling, H.

Revision History 

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