1JHI image
Deposition Date 2001-06-27
Release Date 2003-07-08
Last Version Date 2024-05-22
Entry Detail
PDB ID:
1JHI
Keywords:
Title:
Solution Structure of a Hedamycin-DNA complex
Biological Source:
Source Organism:
(Taxon ID: ) (Taxon ID: )
Method Details:
Experimental Method:
Conformers Calculated:
100
Conformers Submitted:
10
Selection Criteria:
The 10 structures submitted are those with the lowest energy,and agree best with the NMR data.
Macromolecular Entities
Polymer Type:polydeoxyribonucleotide
Molecule:5'-D(*AP*CP*CP*(HEH)GP*GP*T)-3'
Chain IDs:A, B
Chain Length:6
Number of Molecules:2
Biological Source:
Ligand Molecules
Primary Citation
Structural investigation of the hedamycin:d(ACCGGT)2 complex by NMR and restrained molecular dynamics.
Biochem.Biophys.Res.Commun. 290 1602 1608 (2002)
PMID: 11820806 DOI: 10.1006/bbrc.2002.6369

Abstact

Hedamycin, a member of the pluramycin family of drugs, displays a range of biological responses including antitumor and antimicrobial activity. The mechanism of action is via direct interaction with DNA through intercalation between the bases of the oligonucleotide and alkylation of a guanine residue at 5'-PyG-3' sites. There appears to be some minor structural differences between two earlier studies on the interaction of hedamycin with 5'-PyG-3' sites. In this study, a high-resolution NMR analysis of the hedamycin:d(ACCGGT)2 complex was undertaken in order to investigate the effect of replacing the thymine with a guanine at the preferred 5'-CGT-3' site. The resultant structure was compared with earlier work, with particular emphasis placed on the drug conformation. The structure of the hedamycin:d(ACCGGT)2 complex has many features in common with the two previous NMR structures of hedamycin:DNA complexes but differed in the conformation and orientation of the N,N-dimethylvancosamine saccharide of hedamycin in one of these structures. The preferential binding of hedamycin to 5'-CG-3' over 5'-TG-3' binding sites is explained in terms of the orientation and location of the N,N-dimethylvancosamine saccharide in the minor groove.

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