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2mmr

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'''Unreleased structure'''
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==AGC FAPY modified duplex Major isomer==
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<StructureSection load='2mmr' size='340' side='right' caption='[[2mmr]], [[NMR_Ensembles_of_Models | 1 NMR models]]' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2mmr]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2MMR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2MMR FirstGlance]. <br>
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</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAG:[1,2-DIDEOXY[2-AMINO-5-([9-HYDROXY-AFLATOXINB2-8-YL]-FORMYL-AMINO)-6-OXO-1,6-IHYDRO-PYRIMIDIN-4-YLAMINO]-RIBOFURANOSE]-5-MONOPHOSPHATE+GROUP'>FAG</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2mmr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2mmr OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2mmr RCSB], [http://www.ebi.ac.uk/pdbsum/2mmr PDBsum]</span></td></tr>
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</table>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Aflatoxin B1 (AFB1), a mycotoxin produced by Aspergillus flavus, is oxidized by cytochrome P450 enzymes to aflatoxin B1-8,9-epoxide, which alkylates DNA at N7-dG. Under basic conditions, this N7-dG adduct rearranges to yield the trans-8,9-dihydro-8-(2,6-diamino-4-oxo-3,4-dihydropyrimid-5-yl-formamido)-9-hydro xy aflatoxin B1 (AFB1-FAPY) adduct. The AFB1-FAPY adduct exhibits geometrical isomerism involving the formamide moiety. NMR analyses of duplex oligodeoxynucleotides containing the 5'-XA-3', 5'-XC-3', 5'-XT-3', and 5'-XY-3' sequences (X = AFB1-FAPY; Y = 7-deaza-dG) demonstrate that the equilibrium between E and Z isomers is controlled by major groove hydrogen bonding interactions. Structural analysis of the adduct in the 5'-XA-3' sequence indicates the preference of the E isomer of the formamide group, attributed to formation of a hydrogen bond between the formyl oxygen and the N6 exocyclic amino group of the 3'-neighbor adenine. While the 5'-XA-3' sequence exhibits the E isomer, the 5'-XC-3' sequence exhibits a 7:3 E:Z ratio at equilibrium at 283 K. The E isomer is favored by a hydrogen bond between the formyl oxygen and the N4-dC exocyclic amino group of the 3'-neighbor cytosine. The 5'-XT-3' and 5'-XY-3' sequences cannot form such a hydrogen bond between the formyl oxygen and the 3'-neighbor T or Y, respectively, and in these sequence contexts the Z isomer is favored. Additional equilibria between alpha and beta anomers and the potential to exhibit atropisomers about the C5-N5 bond do not depend upon sequence. In each of the four DNA sequences, the AFB1-FAPY adduct maintains the beta deoxyribose configuration. Each of these four sequences feature the atropisomer of the AFB1 moiety that is intercalated above the 5'-face of the damaged guanine. This enforces the Ra axial conformation for the C5-N5 bond.
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The entry 2mmr is ON HOLD until Paper Publication
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DNA Sequence Modulates Geometrical Isomerism of the trans-8,9-Dihydro-8-(2,6-diamino-4-oxo-3,4-dihydropyrimid-5-yl-formamido)-9-hydro xy Aflatoxin B Adduct.,Li L, Brown KL, Ma R, Stone MP Chem Res Toxicol. 2015 Jan 14. PMID:25587868<ref>PMID:25587868</ref>
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Authors: Li, L., Stone, M.
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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Description: AGC FAPY modified duplex Major isomer
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== References ==
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[[Category: Unreleased Structures]]
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Li, L]]
[[Category: Stone, M]]
[[Category: Stone, M]]
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[[Category: Li, L]]
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[[Category: Aflatoxin b1]]
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[[Category: Agc]]
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[[Category: Deoxyribonucleic acid]]
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[[Category: Dna]]
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[[Category: Dna adduct]]
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[[Category: Fapy]]
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[[Category: Formamidopyrimidine]]
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[[Category: Hydrogen bond]]
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[[Category: Intercalation]]
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[[Category: Major isomer]]
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[[Category: Sequence dependence]]

Revision as of 13:52, 25 February 2015

AGC FAPY modified duplex Major isomer

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