193d

SOLUTION STRUCTURE OF A QUINOMYCIN BISINTERCALATOR-DNA COMPLEX

spinqualitylabelsall models 193d, 4 NMR models Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 193d is a 3 chain structure. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: HQU NonStd Res: CPC, DSN, NCY, NYB Related: 185d, 1pfe, 1vs2, 1xvk, 1xvn, 1xvr, 2adw, 2da8, 3go3 Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Publication Abstract from PubMed 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. Solution structure of a quinomycin bisintercalator-DNA complex.,Chen H, Patel DJ J Mol Biol. 1995 Feb 10;246(1):164-79. PMID:7853395 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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