1G5L

CO(III)-BLEOMYCIN-OOH BOUND TO AN OLIGONUCLEOTIDE CONTAINING A PHOSPHOGLYCOLATE LESION

Summary for 1G5L

• Entry DOI: 10.2210/pdb1g5l/pdb
• Related: 1G5D 1G5E 1G5K 1GIZ 1GJ0 1GJ1 1GJ2
• Descriptor: 5'-D(*CP*CP*AP*AP*AP*G)-3', 5'-D(P*AP*CP*TP*GP*GP*G)-3', 5'-D(*CP*CP*CP*AP*GP*TP*AP*CP*TP*TP*TP*GP*G)-3', ... (8 entities in total)
• Functional Keywords: damaged dna, dna-drug complex, intercalation, dna
• Total number of polymer chains: 3
• Total formula weight: 9285.54

Authors

Hoehn, S.T.,Junker, H.-D.,Bunt, R.C.,Turner, C.J.,Stubbe, J. (deposition date: 2000-11-01, release date: 2001-06-06, Last modification date: 2024-05-22)

Primary citation

Hoehn, S.T.,Junker, H.D.,Bunt, R.C.,Turner, C.J.,Stubbe, J.
Solution structure of Co(III)-bleomycin-OOH bound to a phosphoglycolate lesion containing oligonucleotide: implications for bleomycin-induced double-strand DNA cleavage.
Biochemistry, 40:5894-5905, 2001

PubMed Abstract: Bleomycin (BLM) is an antitumor antibiotic that is used clinically. Its major cause of cytotoxicity is thought to be related to BLM's ability to cause double-strand (ds) DNA cleavage. A single molecule of BLM appears to cleave both strands of DNA in the presence of its required cofactors Fe(2+) and oxygen without dissociating from the helix. A mechanism for this process has been proposed based on a model structure of the hydroperoxide of Co(III)-BLM (CoBLM) bound sequence-specifically to an intact duplex containing a GTAC site, a hot spot for ds cleavage [Vanderwall, D. E., Lui, S. M., Wu, W., Turner, C. J., Kozarich, J. W., and Stubbe, J. (1997) Chem. Biol. 4, 373-387]. In this paper, we present a structural model for the second cleavage event. Two-dimensional NMR spectroscopy and molecular modeling were carried out to study CoBLM bound to d(CCAAAGXACTGGG).d(CCCAGTACTTTGG), where X represents a 3'-phosphoglycolate lesion next to a 5'-phosphate. Assignments of 729 NOEs, including 51 between the drug and the DNA and 126 within the BLM molecule, have been made. These NOEs in addition to 96 dihedral angle constraints have been used to obtain a well-defined structural model for this complex. The model reveals that the bithiazole tail is partially intercalated between the T19 and the A20 of the duplex and that the metal binding domain is poised for abstraction of the T19 H4' in the minor groove. The modeling further reveals that the predominant conformation of the bithiazole protons is trans. Two cis conformations of these protons are also observed, and ROESY experiments provide evidence for interconversion of all of these forms. The relationship of these observations to the model for ds cleavage is presented.

PubMed: 11352724
DOI: 10.1021/bi002635g

Experimental method

SOLUTION NMR