3C2J

Crystal structure analysis of trioxacarcin A covalently bound to d(AACCGGTT)

Summary for 3C2J

• Entry DOI: 10.2210/pdb3c2j/pdb
• Descriptor: DNA (5'-D(*DAP*DAP*DCP*DCP*DGP*DGP*DTP*DT)-3'), Trioxacarcin A (3 entities in total)
• Functional Keywords: dna-drug complex, base flipping, b-dna, dna
• Total number of polymer chains: 2
• Total formula weight: 6606.93

Authors

Pfoh, R.,Sheldrick, G.M. (deposition date: 2008-01-25, release date: 2008-06-03, Last modification date: 2024-03-13)

Primary citation

Pfoh, R.,Laatsch, H.,Sheldrick, G.M.
Crystal structure of trioxacarcin A covalently bound to DNA
Nucleic Acids Res., 36:3508-3514, 2008

PubMed Abstract: 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.

PubMed: 18453630
DOI: 10.1093/nar/gkn245

Experimental method

X-RAY DIFFRACTION (1.78 Å)