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2mmq

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Revision as of 22:31, 9 August 2018

Solution structure of AGT FAPY Modified duplex

Structural highlights

2mmq is a 2 chain structure. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
NonStd Res:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Publication Abstract from PubMed

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.

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^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Li L, Brown KL, Ma R, Stone MP. 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. Chem Res Toxicol. 2015 Jan 14. PMID:25587868 doi:http://dx.doi.org/10.1021/tx5003832

1 Structural highlights
2 Publication Abstract from PubMed
3 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2mmq"

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 ==Solution structure of AGT FAPY Modified duplex==
 <StructureSection load='2mmq' size='340' side='right' caption='[[2mmq]], [[NMR_Ensembles_of_Models | 1 NMR models]]' scene=''>
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 <table><tr><td colspan='2'>[[2mmq]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2MMQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2MMQ FirstGlance]. <br>
 </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>
-<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=2mmq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2mmq OCA], [http://pdbe.org/2mmq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2mmq RCSB], [http://www.ebi.ac.uk/pdbsum/2mmq PDBsum]</span></td></tr>
+<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=2mmq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2mmq OCA], [http://pdbe.org/2mmq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2mmq RCSB], [http://www.ebi.ac.uk/pdbsum/2mmq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2mmq ProSAT]</span></td></tr>
 </table>
 <div style="background-color:#fffaf0;">

2mmq

From Proteopedia

Revision as of 22:31, 9 August 2018

Solution structure of AGT FAPY Modified duplex

Structural highlights

Publication Abstract from PubMed

References

Contents

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