2neo: Difference between revisions
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== | ==SOLUTION NMR STRUCTURE OF A TWO-BASE DNA BULGE COMPLEXED WITH AN ENEDIYNE CLEAVING ANALOG, 11 STRUCTURES== | ||
<StructureSection load='2neo' size='340' side='right'caption='[[2neo]]' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[2neo]] is a 1 chain structure. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1neo 1neo]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NEO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2NEO 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>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</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=2neo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2neo OCA], [https://pdbe.org/2neo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2neo RCSB], [https://www.ebi.ac.uk/pdbsum/2neo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2neo ProSAT]</span></td></tr> | |||
</table> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Nucleic acid bulges have been implicated in a number of biological processes and are specific cleavage targets for the enediyne antitumor antibiotic neocarzinostatin chromophore in a base-catalyzed, radical-mediated reaction. The solution structure of the complex between an analog of the bulge-specific cleaving species and an oligodeoxynucleotide containing a two-base bulge was elucidated by nuclear magnetic resonance. An unusual binding mode involves major groove recognition by the drug carbohydrate unit and tight fitting of the wedge-shaped drug in the triangular prism pocket formed by the two looped-out bulge bases and the neighboring base pairs. The two drug rings mimic helical DNA bases, complementing the bent DNA structure. The putative abstracting drug radical is 2.2 +/- 0.1 angstroms from the pro-S H5' of the target bulge nucleotide. This structure clarifies the mechanism of bulge recognition and cleavage by a drug and provides insight into the design of bulge-specific nucleic acid binding molecules. | Nucleic acid bulges have been implicated in a number of biological processes and are specific cleavage targets for the enediyne antitumor antibiotic neocarzinostatin chromophore in a base-catalyzed, radical-mediated reaction. The solution structure of the complex between an analog of the bulge-specific cleaving species and an oligodeoxynucleotide containing a two-base bulge was elucidated by nuclear magnetic resonance. An unusual binding mode involves major groove recognition by the drug carbohydrate unit and tight fitting of the wedge-shaped drug in the triangular prism pocket formed by the two looped-out bulge bases and the neighboring base pairs. The two drug rings mimic helical DNA bases, complementing the bent DNA structure. The putative abstracting drug radical is 2.2 +/- 0.1 angstroms from the pro-S H5' of the target bulge nucleotide. This structure clarifies the mechanism of bulge recognition and cleavage by a drug and provides insight into the design of bulge-specific nucleic acid binding molecules. | ||
Solution structure of a two-base DNA bulge complexed with an enediyne cleaving analog.,Stassinopoulos A, Ji J, Gao X, Goldberg IH Science. 1996 Jun 28;272(5270):1943-6. PMID:8658168<ref>PMID:8658168</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
[[Category: | <div class="pdbe-citations 2neo" style="background-color:#fffaf0;"></div> | ||
[[Category: Gao | == References == | ||
[[Category: Goldberg | <references/> | ||
[[Category: Ji | __TOC__ | ||
[[Category: Stassinopoulos | </StructureSection> | ||
[[Category: Large Structures]] | |||
[[Category: Gao X]] | |||
[[Category: Goldberg IH]] | |||
[[Category: Ji J]] | |||
[[Category: Stassinopoulos A]] | |||
Latest revision as of 12:52, 20 December 2023
SOLUTION NMR STRUCTURE OF A TWO-BASE DNA BULGE COMPLEXED WITH AN ENEDIYNE CLEAVING ANALOG, 11 STRUCTURES
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