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193d
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(New page: 200px<br /><applet load="193d" size="450" color="white" frame="true" align="right" spinBox="true" caption="193d" /> '''SOLUTION STRUCTURE OF A QUINOMYCIN BISINTERC...)
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Revision as of 20:04, 24 November 2007
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SOLUTION STRUCTURE OF A QUINOMYCIN BISINTERCALATOR-DNA COMPLEX
Overview
The quinomycin antibiotic UK-63052 (designated QN) exhibits a chemical, structure related to the antibiotic echinomycin which is known to, bisintercalate into DNA. Common features among these antibiotics include, two heterocyclic aromatic ring systems propagating from a cross-bridged, cyclic octadepsipeptide scaffold. We report on the solution structure of, the QN-d(A1-C2-A3-C4-G5-T6-G7-T8) complex (one QN molecule per duplex), based on a combined NMR-molecular dynamics study including intensity-based, refinement. The 3-hydroxy quinaldic acid rings bisintercalate into the, duplex at (A3-C4).(G5-T6) steps and stack with flanking Watson-Crick A3.T6, and C4.G5 base-pairs. The intercalation sites at (A3-C4).(G5-T6) steps are, wedge-shaped and unwound, with significant unwinding also observed at the, (C4-C5).(C4-G5) step bracketed between the intercalation sites. The, cross-bridged cyclic octadepsipeptide is positioned in the minor groove, with the methyl groups on its Ala and NMe-MCp residues directed towards, and making van der Waals contacts with the minor groove edge of the, duplex. A pair of adjacent intermolecular hydrogen bonds between the Ala, backbone atoms and the G5 minor groove edge (Ala-NH to G5-N(3) and G5-NH2e, to Ala-CO) account for the sequence specificity associated with complex, formation. The solution structure of the QN-DNA oligomer complex, which, contains only Watson-Crick base-pairs flanking the bisintercalation site, is compared with the crystal structure of the related echinomycin-DNA, oligomer complex, which contains Hoogsteen base-pairs on either side of, the bisintercalation site.
About this Structure
193D is a Protein complex structure of sequences from [1] with CH3 and NBU as ligands. Full crystallographic information is available from OCA.
Reference
Solution structure of a quinomycin bisintercalator-DNA complex., Chen H, Patel DJ, J Mol Biol. 1995 Feb 10;246(1):164-79. PMID:7853395
Page seeded by OCA on Sat Nov 24 22:12:08 2007
Categories: Protein complex | Chen, H. | Patel, D.J. | CH3 | NBU | Dna | Double helix | Nmr | Quinomycin
