6BS1 image
Entry Detail
PDB ID:
6BS1
Keywords:
Title:
Crystal Structure of Human DNA polymerase kappa in complex with DNA containing the major cisplatin lesion
Biological Source:
Host Organism:
PDB Version:
Deposition Date:
2017-12-01
Release Date:
2018-08-22
Method Details:
Experimental Method:
Resolution:
3.15 Å
R-Value Free:
0.29
R-Value Work:
0.24
R-Value Observed:
0.24
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:DNA polymerase kappa
Chain IDs:A, B
Chain Length:551
Number of Molecules:2
Biological Source:Homo sapiens
Polymer Type:polydeoxyribonucleotide
Description:DNA (5'-D(P*AP*TP*AP*CP*AP*TP*AP*CP*C)-3')
Chain IDs:C, E (auth: P)
Chain Length:9
Number of Molecules:2
Biological Source:synthetic construct
Polymer Type:polydeoxyribonucleotide
Description:DNA (5'-D(*TP*AP*CP*TP*GP*GP*TP*AP*TP*GP*TP*AP*T)-3')
Chain IDs:D, F (auth: T)
Chain Length:13
Number of Molecules:2
Biological Source:synthetic construct
Primary Citation
Structural Basis for Human DNA Polymerase Kappa to Bypass Cisplatin Intrastrand Cross-Link (Pt-GG) Lesion as an Efficient and Accurate Extender.
J. Mol. Biol. 430 1577 1589 (2018)
PMID: 29715472 DOI: 10.1016/j.jmb.2018.04.023

Abstact

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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