6BRX

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

• PDB DOI:  https://doi.org/10.2210/pdb6BRX/pdb
• NAKB: 6BRX

• Classification: REPLICATION
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-12-01 Released: 2018-08-22 
• Deposition Author(s): Jha, V.K., Ling, H.
• Funding Organization(s): Canadian Institutes of Health Research (CIHR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.269 
• R-Value Work: 0.214 
• R-Value Observed: 0.216 

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

• PubMed: 29715472 
• DOI: https://doi.org/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. 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.

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Organizational Affiliation: 

Department of Biochemistry, Schulich School of Medicine & Dentistry, University of Western Ontario, London, Ontario N6A 5C1, Canada. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 141.88 kDa 
• Atom Count: 7,902 
• Modelled Residue Count: 907 
• Deposited Residue Count: 1,146 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase kappa	A, B	551	Homo sapiens	Mutation(s): 0  Gene Names: POLK, DINB1 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

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*TP*AP*CP*AP*TP*AP*CP*AP*C)-3')	C, E [auth P]	9	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*AP*TP*GP*GP*TP*GP*TP*AP*TP*GP*TP*A)-3')	D, F [auth T]	13	synthetic construct

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0KX	J [auth A], L [auth B]	2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]cytidine C9 H17 N4 O12 P3 STYMTWKSQLVXJN-SHYZEUOFSA-N
CPT	N [auth D], Q [auth T]	Cisplatin Cl2 H6 N2 Pt LXZZYRPGZAFOLE-UHFFFAOYSA-L
PEG	M [auth D], P [auth T]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
MG	G [auth A], H [auth A], I [auth A], K [auth B], O [auth P]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.269 
• R-Value Work: 0.214 
• R-Value Observed: 0.216 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.69	α = 90
b = 129.06	β = 90
c = 168.088	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
SCALA	data scaling
REFMAC	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-08-22 
Deposition Author(s): Jha, V.K., Ling, H.

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Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	MOP-94590

Revision History  

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