1CKT image
Deposition Date 1999-04-23
Release Date 1999-06-30
Last Version Date 2023-12-27
Entry Detail
PDB ID:
1CKT
Title:
CRYSTAL STRUCTURE OF HMG1 DOMAIN A BOUND TO A CISPLATIN-MODIFIED DNA DUPLEX
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
2.50 Å
R-Value Free:
0.23
R-Value Work:
0.23
R-Value Observed:
0.23
Space Group:
C 1 2 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:HIGH MOBILITY GROUP 1 PROTEIN
Gene (Uniprot):Hmgb1
Chain IDs:C (auth: A)
Chain Length:71
Number of Molecules:1
Biological Source:Rattus norvegicus
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
5IU A DU 5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
Ligand Molecules
Primary Citation
Basis for recognition of cisplatin-modified DNA by high-mobility-group proteins.
Nature 399 708 712 (1999)
PMID: 10385126 DOI: 10.1038/21460

Abstact

The anticancer activity of cis-diamminedichloroplatinum(II) (cisplatin) arises from its ability to damage DNA, with the major adducts formed being intrastrand d(GpG) and d(ApG) crosslinks. These crosslinks bend and unwind the duplex, and the altered structure attracts high-mobility-group domain (HMG) and other proteins. This binding of HMG-domain proteins to cisplatin-modified DNA has been postulated to mediate the antitumour properties of the drug. Many HMG-domain proteins recognize altered DNA structures such as four-way junctions and cisplatin-modified DNA, but until now the molecular basis for this recognition was unknown. Here we describe mutagenesis, hydroxyl-radical footprinting and X-ray studies that elucidate the structure of a 1:1 cisplatin-modified DNA/HMG-domain complex. Domain A of the structure-specific HMG-domain protein HMG1 binds to the widened minor groove of a 16-base-pair DNA duplex containing a site-specific cis-[Pt(NH3)2[d(GpG)-N7(1),-N7(2)]] adduct. The DNA is strongly kinked at a hydrophobic notch created at the platinum-DNA crosslink and protein binding extends exclusively to the 3' side of the platinated strand. A phenylalanine residue at position 37 intercalates into a hydrophobic notch created at the platinum crosslinked d(GpG) site and binding of the domain is dramatically reduced in a mutant in which alanine is substituted for phenylalanine at this position.

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Primary Citation of related structures