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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==
<StructureSection load='1kvh' size='340' side='right'caption='[[1kvh]]' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1kvh]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KVH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KVH FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NCS:SPIRO[[7-METHOXY-5-METHYL-1,2-DIHYDRO-NAPHTHALENE]-3,1-[5-HYDROXY-9-[2-METHYLAMINO-2,6-DIDEOXYGALACTOPYRANOSYL-OXY]-5-(2-OXO-[1,3]DIOXOLAN-4-YL)-3A,5,9,9A-TETRAHYDRO-3H-1-OXA-CYCLOPENTA[A]-S-INDACEN-2-ONE]]'>NCS</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=1kvh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kvh OCA], [https://pdbe.org/1kvh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kvh RCSB], [https://www.ebi.ac.uk/pdbsum/1kvh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kvh ProSAT]</span></td></tr>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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.

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<ref>PMID:11955061</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1kvh" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Bare S]]
[[Category: Gao X]]
[[Category: Goldberg IH]]
[[Category: Ji J]]
[[Category: Kwon Y]]
[[Category: Stassinopoulos A]]