3C2J image
Deposition Date 2008-01-25
Release Date 2008-06-03
Last Version Date 2024-03-13
Entry Detail
PDB ID:
3C2J
Keywords:
DNA
Title:
Crystal structure analysis of trioxacarcin A covalently bound to d(AACCGGTT)
Biological Source:
Source Organism:
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
1.78 Å
R-Value Free:
0.26
R-Value Work:
0.22
R-Value Observed:
0.22
Space Group:
P 41 2 2
3C2J validation report
Macromolecular Entities
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(*DAP*DAP*DCP*DCP*DGP*DGP*DTP*DT)-3')
Chain IDs:A, B
Chain Length:8
Number of Molecules:2
Biological Source:
Ligand Molecules
GGT
Primary Citation
Crystal structure of trioxacarcin A covalently bound to DNA
Nucleic Acids Res. 36 3508 3514 (2008)
PMID: 18453630 DOI: 10.1093/nar/gkn245

Abstact

We report a crystal structure that shows an antibiotic that extracts a nucleobase from a DNA molecule 'caught in the act' after forming a covalent bond but before departing with the base. The structure of trioxacarcin A covalently bound to double-stranded d(AACCGGTT) was determined to 1.78 A resolution by MAD phasing employing brominated oligonucleotides. The DNA-drug complex has a unique structure that combines alkylation (at the N7 position of a guanine), intercalation (on the 3'-side of the alkylated guanine), and base flip-out. An antibiotic-induced flipping-out of a single, nonterminal nucleobase from a DNA duplex was observed for the first time in a crystal structure.

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Primary Citation of related structures
3C2J