1b5k: Difference between revisions
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==3,N4-ETHENO-2'-DEOXYCYTIDINE OPPOSITE THYMIDINE IN AN 11-MER DUPLEX, SOLUTION STRUCTURE FROM NMR AND MOLECULAR DYNAMICS== | ==3,N4-ETHENO-2'-DEOXYCYTIDINE OPPOSITE THYMIDINE IN AN 11-MER DUPLEX, SOLUTION STRUCTURE FROM NMR AND MOLECULAR DYNAMICS== | ||
<StructureSection load='1b5k' size='340' side='right' caption='[[1b5k]], [[NMR_Ensembles_of_Models | 2 NMR models]]' scene=''> | <StructureSection load='1b5k' size='340' side='right'caption='[[1b5k]], [[NMR_Ensembles_of_Models | 2 NMR models]]' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[1b5k]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B5K OCA]. For a <b>guided tour on the structure components</b> use [http:// | <table><tr><td colspan='2'>[[1b5k]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B5K OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1B5K FirstGlance]. <br> | ||
</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDC:N3,N4-ETHENO-2-DEOXYCYTIDINE-5-MONOPHOSPHATE'>EDC</scene></td></tr> | </td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDC:N3,N4-ETHENO-2-DEOXYCYTIDINE-5-MONOPHOSPHATE'>EDC</scene></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http:// | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1b5k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1b5k OCA], [http://pdbe.org/1b5k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1b5k RCSB], [http://www.ebi.ac.uk/pdbsum/1b5k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1b5k ProSAT]</span></td></tr> | ||
</table> | </table> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
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__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | |||
[[Category: Cullinan, D]] | [[Category: Cullinan, D]] | ||
[[Category: Eisenberg, M]] | [[Category: Eisenberg, M]] | ||
Revision as of 13:31, 16 September 2020
3,N4-ETHENO-2'-DEOXYCYTIDINE OPPOSITE THYMIDINE IN AN 11-MER DUPLEX, SOLUTION STRUCTURE FROM NMR AND MOLECULAR DYNAMICS3,N4-ETHENO-2'-DEOXYCYTIDINE OPPOSITE THYMIDINE IN AN 11-MER DUPLEX, SOLUTION STRUCTURE FROM NMR AND MOLECULAR DYNAMICS
Structural highlights
Publication Abstract from PubMedThe exocyclic 3,N4-etheno-2'-deoxycytidine adduct was incorporated at the center of the oligodeoxynucleotide duplex d(C-G-T-A-C-epsilon C-C-A-T-G-C).d (G-C-A-T-G-T-G-T-A-C-G), and its solution structure was analyzed using high-resolution proton NMR spectroscopy and molecular dynamics simulations. The experimental data indicate that the oligodeoxynucleotide duplex adopts a right-handed helical structure with sugar puckers in the C2'-endo/C3'-exo range and Watson-Crick hydrogen bond alignments for all base pairs. NOE connectivities established a syn orientation for the glycosidic torsion angle of the exocyclic adduct. Restrained molecular dynamics simulations, using the full relaxation matrix approach, produced a three-dimensional model in agreement with the experimental data. The structure shows only minor perturbations in the sugar-phosphate backbone and a 27 degrees bend of the helical axis at the lesion site. On the refined model a well-formed hydrogen bond between T (N3H) and epsilon C(N4) stabilizes the epsilon C(syn).T(anti) base pair alignment, reflecting the preference of the adduct for the syn orientation. Furthermore, the epsilon C(syn).T(anti) base pair stacks with flanking base pairs. We discuss a correlation between the mutagenic properties of the adduct and the three-dimensional structure of the epsilon C.dA and epsilon C.T duplexes. NMR solution structure of an oligodeoxynucleotide duplex containing the exocyclic lesion 3,N4-etheno-2'-deoxycytidine opposite thymidine: comparison with the duplex containing deoxyadenosine opposite the adduct.,Cullinan D, Korobka A, Grollman AP, Patel DJ, Eisenberg M, de los Santos C Biochemistry. 1996 Oct 15;35(41):13319-27. PMID:8873598[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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