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'''<br /> | '''SOLUTION NMR STRUCTURE OF A TWO-BASE DNA BULGE COMPLEXED WITH AN ENEDIYNE CLEAVING ANALOG, 11 STRUCTURES'''<br /> | ||
==Overview== | ==Overview== | ||
Nucleic acid bulges have been implicated in a number of biological | 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. | ||
==About this Structure== | ==About this Structure== | ||
2NEO is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with NCS as [http://en.wikipedia.org/wiki/ligand ligand]. This structure | 2NEO is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with <scene name='pdbligand=NCS:'>NCS</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. This structure supersedes the now removed PDB entry 1NEO. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NEO OCA]. | ||
==Reference== | ==Reference== | ||
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[[Category: Protein complex]] | [[Category: Protein complex]] | ||
[[Category: Gao, X.]] | [[Category: Gao, X.]] | ||
[[Category: Goldberg, I | [[Category: Goldberg, I H.]] | ||
[[Category: Ji, J.]] | [[Category: Ji, J.]] | ||
[[Category: Stassinopoulos, A.]] | [[Category: Stassinopoulos, A.]] | ||
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[[Category: enediyne antibiotics antitumor agents]] | [[Category: enediyne antibiotics antitumor agents]] | ||
''Page seeded by [http:// | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 18:08:07 2008'' | ||
Revision as of 16:08, 21 February 2008
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SOLUTION NMR STRUCTURE OF A TWO-BASE DNA BULGE COMPLEXED WITH AN ENEDIYNE CLEAVING ANALOG, 11 STRUCTURES
Overview
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.
About this Structure
2NEO is a Protein complex structure of sequences from [1] with NCS as ligand. This structure supersedes the now removed PDB entry 1NEO. Full crystallographic information is available from OCA.
Reference
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
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