193d: Difference between revisions

<table><tr><td colspan='2'>[[193d]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces Streptomyces]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=193D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=193D FirstGlance]. <br>

</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR, 4 models</td></tr>

<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CPC:2-METHYL-1-METHYLAMINO-CYCLOPROPANE+CARBOXYLIC+ACID'>CPC</scene>, <scene name='pdbligand=DSN:D-SERINE'>DSN</scene>, <scene name='pdbligand=HQU:3-HYDROXYQUINALDIC+ACID'>HQU</scene>, <scene name='pdbligand=NCY:N-METHYLCYSTEINE'>NCY</scene>, <scene name='pdbligand=NYB:N-METHYL-S-[(1R)-1-METHYLPROPYL]-L-CYSTEINE'>NYB</scene></td></tr>

<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=193d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=193d OCA], [https://pdbe.org/193d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=193d RCSB], [https://www.ebi.ac.uk/pdbsum/193d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=193d ProSAT]</span></td></tr>

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<ref>PMID:7853395</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>

</div>

<div class="pdbe-citations 193d" style="background-color:#fffaf0;"></div>

== References ==

<references/>

[[Category: Large Structures]]

[[Category: Streptomyces]]

[[Category: Chen H]]

[[Category: Patel DJ]]