View source for 5ytz


==Crystal structure of echinomycin-d(ACGTCGT)2 complex==
<StructureSection load='5ytz' size='340' side='right'caption='[[5ytz]], [[Resolution|resolution]] 1.55&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[5ytz]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_echinatus Streptomyces echinatus] and [https://en.wikipedia.org/wiki/Unidentified Unidentified]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YTZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YTZ FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.55&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BRU:5-BROMO-2-DEOXYURIDINE-5-MONOPHOSPHATE'>BRU</scene>, <scene name='pdbligand=DSN:D-SERINE'>DSN</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=MVA:N-METHYLVALINE'>MVA</scene>, <scene name='pdbligand=N2C:N,S-DIMETHYLCYSTEINE'>N2C</scene>, <scene name='pdbligand=NCY:N-METHYLCYSTEINE'>NCY</scene>, <scene name='pdbligand=QUI:2-CARBOXYQUINOXALINE'>QUI</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=5ytz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ytz OCA], [https://pdbe.org/5ytz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ytz RCSB], [https://www.ebi.ac.uk/pdbsum/5ytz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ytz ProSAT]</span></td></tr>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Small-molecule compounds that target mismatched base pairs in DNA offer a novel prospective for cancer diagnosis and therapy. The potent anticancer antibiotic echinomycin functions by intercalating into DNA at CpG sites. Surprisingly, we found that the drug strongly prefers to bind to consecutive CpG steps separated by a single T:T mismatch. The preference appears to result from enhanced cooperativity associated with the binding of the second echinomycin molecule. Crystallographic studies reveal that this preference originates from the staggered quinoxaline rings of the two neighboring antibiotic molecules that surround the T:T mismatch forming continuous stacking interactions within the duplex. These and other associated changes in DNA conformation allow the formation of a minor groove pocket for tight binding of the second echinomycin molecule. We also show that echinomycin displays enhanced cytotoxicity against mismatch repair-deficient cell lines, raising the possibility of repurposing the drug for detection and treatment of mismatch repair-deficient cancers.

Cooperative recognition of T:T mismatch by echinomycin causes structural distortions in DNA duplex.,Wu PC, Tzeng SL, Chang CK, Kao YF, Waring MJ, Hou MH Nucleic Acids Res. 2018 May 8. pii: 4993785. doi: 10.1093/nar/gky345. PMID:29741655<ref>PMID:29741655</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5ytz" style="background-color:#fffaf0;"></div>

==See Also==
*[[Hypoxia-Inducible Factors|Hypoxia-Inducible Factors]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Streptomyces echinatus]]
[[Category: Unidentified]]
[[Category: Hou MH]]
[[Category: Kao YF]]
[[Category: Wu PC]]