1kvh

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NCSi-gb-bulge-DNA complex induced formation of a DNA bulge structure by a molecular wedge ligand-post-activated neocarzinostatin chromophore

Overview

Our previous structure elucidation of the complexes of DNA and, postactivated neocarzinostatin chromophore (NCS-chrom) compounds revealed, two distinctly different binding modes of this antitumor molecule. A, thorough understanding of these results will provide the molecular basis, for the binding and DNA chain cleavage properties of NCS-chrom. NCSi-gb is, one of the postactivated mimics of NCS-chrom which is formed under, thiol-free conditions and is able to bind to DNA. This report describes, the structure refinement of the NCSi-gb-bulge-DNA complex [Stassinopoulos, A., Jie, J., Gao, X., and Goldberg, I. H. (1996) Science 272, 1943-1946], and the NMR characterization of the free bulge-DNA and free NCSi-gb. These, results reveal that the formation of the complex involves conformational, changes in both the DNA and the ligand molecule. Of mechanistic importance, for the NCS-chrom-DNA interaction, the two ring systems of the drug are, brought closer to each other in the complex. This conformation correlates, well with the previously observed marked enhancement of the formation of a, DNA bulge cleaving species in the presence of bulge-DNA sequences, due to, the promotion of the intramolecular radical quenching of the activated, NCS-chrom. Interestingly, the binding of NCSi-gb promotes the formation of, a bulge binding pocket; this was not found in the unbound DNA. NCS-chrom, is unique among the enediyne antibiotics in its ability to undergo two, different mechanisms of activation to form two different DNA binding and, cleaving species. The two corresponding DNA complexes are compared. One, the bulge-DNA binder NCSi-gb, involves the major groove, and the second, the duplex binder NCSi-glu which is generated by glutathione-induced, activation, involves the minor groove. Since the two NCS-chrom-related, ligand molecules contain some common chemical structural elements, such as, the carbohydrate ring, the striking differences in their DNA recognition, and chain cleavage specificity provide insights into the fundamental, principles of DNA recognition and ligand design.

About this Structure

1KVH is a Protein complex structure of sequences from [1] with NCS as ligand. Full crystallographic information is available from OCA.

Reference

Induced formation of a DNA bulge structure by a molecular wedge ligand-postactivated neocarzinostatin chromophore., Gao X, Stassinopoulos A, Ji J, Kwon Y, Bare S, Goldberg IH, Biochemistry. 2002 Apr 23;41(16):5131-43. PMID:11955061

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