5HHI image
Deposition Date 2016-01-11
Release Date 2017-01-18
Last Version Date 2023-09-27
Entry Detail
PDB ID:
5HHI
Title:
Structure of human DNA polymerase beta Host-Guest complexed with CBZ-platinated N7-G
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.52 Å
R-Value Free:
0.27
R-Value Work:
0.22
R-Value Observed:
0.22
Space Group:
P 1 21 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:DNA polymerase beta
Gene (Uniprot):POLB
Chain IDs:A
Chain Length:329
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(P*GP*TP*CP*GP*G)-3')
Chain IDs:D
Chain Length:5
Number of Molecules:1
Biological Source:synthetic construct
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(P*CP*CP*TP*GP*CP*TP*CP*CP*TP*C)-3')
Chain IDs:C (auth: P)
Chain Length:10
Number of Molecules:1
Biological Source:synthetic construct
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(*CP*CP*GP*AP*CP*GP*GP*AP*GP*GP*AP*GP*CP*AP*GP*G)-3')
Chain IDs:B (auth: T)
Chain Length:16
Number of Molecules:1
Biological Source:synthetic construct
Primary Citation
Synthesis, structure, and biological evaluation of a platinum-carbazole conjugate.
Chem Biol Drug Des 91 116 125 (2018)
PMID: 28649747 DOI: 10.1111/cbdd.13062

Abstact

Cisplatin resistance is caused, in part, by the efficient removal of the helix-distorting cisplatin 1,2-intrastrand cross-links by nucleotide excision repair (NER) machinery. To make a platinum-DNA adduct that causes less helical distortion than the cisplatin 1,2-intrastrand adduct, we designed and synthesized a monofunctional platinum-carbazole conjugate (carbazoplatin). The 2.5 Å crystal structure of carbazoplatin-DNA adduct revealed both the monoplatination of the N7 of a guanine (G) base and the intercalation into two G:C base pairs, while causing a minor distortion of the DNA helix. A 50-mer dsDNA containing a single carbazoplatin lesion was poorly processed by UvrABC endonuclease, the prokaryotic NER machinery that detects helical distortion and performs dual incision around the lesion. Our cell viability assay indicated that the cytotoxic pathways of carbazoplatin might be different from those of cisplatin; carbazoplatin was 5-8 times more cytotoxic than cisplatin against PANC-1 and MDA-MB-231 cancer cell lines.

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Primary Citation of related structures