1b60

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{{STRUCTURE_1b60| PDB=1b60 | SCENE= }}
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==3,N4-ETHENO-2'-DEOXYCYTIDINE OPPOSITE CYTIDINE IN AN 11-MER DUPLEX, SOLUTION STRUCTURE FROM NMR AND MOLECULAR DYNAMICS==
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===3,N4-ETHENO-2'-DEOXYCYTIDINE OPPOSITE CYTIDINE IN AN 11-MER DUPLEX, SOLUTION STRUCTURE FROM NMR AND MOLECULAR DYNAMICS===
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<StructureSection load='1b60' size='340' side='right' caption='[[1b60]], [[NMR_Ensembles_of_Models | 1 NMR models]]' scene=''>
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{{ABSTRACT_PUBMED_10677286}}
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1b60]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B60 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1B60 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=EDC:N3,N4-ETHENO-2-DEOXYCYTIDINE-5-MONOPHOSPHATE'>EDC</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=1b60 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1b60 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1b60 RCSB], [http://www.ebi.ac.uk/pdbsum/1b60 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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Lipid peroxidation products, as well as the metabolic products of vinyl chloride, react with cellular DNA producing the mutagenic adduct 3,N(4)-etheno-2'-deoxycytidine (epsilondC), along with several other exocyclic derivatives. High-resolution NMR spectroscopy and restrained molecular dynamics simulations were used to establish the solution structure of an 11-mer duplex containing an epsilondC.dC base-pair at its center. The NMR data suggested a regular right-handed helical structure having all residues in the anti orientation around the glycosydic torsion angle and Watson-Crick alignments for all canonical base-pairs of the duplex. Restrained molecular dynamics generated a three-dimensional model in excellent agreement with the spectroscopic data. The (epsilondC. dC)-duplex structure is a regular right-handed helix with a slight bend at the lesion site and no severe distortions of the sugar-phosphate backbone. The epsilondC adduct and its partner dC were displaced towards opposite grooves of the helix, resulting in a lesion-containing base-pair that was highly sheared but stabilized to some degree by the formation of a single hydrogen bond. Such a sheared base-pair alignment at the lesion site was previously observed for epsilondC.dG and epsilondC.T duplexes, and was also present in the crystal structures of duplexes containing dG.T and dG. U mismatches. These observations suggest the existence of a substrate structural motif that may be recognized by specific DNA glycosylases during the process of base excision repair.
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==About this Structure==
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Solution structure of an 11-mer duplex containing the 3, N(4)-ethenocytosine adduct opposite 2'-deoxycytidine: implications for the recognition of exocyclic lesions by DNA glycosylases.,Cullinan D, Johnson F, de los Santos C J Mol Biol. 2000 Feb 25;296(3):851-61. PMID:10677286<ref>PMID:10677286</ref>
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[[1b60]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B60 OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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<ref group="xtra">PMID:010677286</ref><references group="xtra"/><references/>
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</div>
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[[Category: Cullinan, D.]]
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== References ==
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[[Category: Johnson, F.]]
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<references/>
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[[Category: Santos, C De Los.]]
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__TOC__
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</StructureSection>
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[[Category: Cullinan, D]]
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[[Category: Johnson, F]]
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[[Category: Santos, C De Los]]
[[Category: Dna]]
[[Category: Dna]]
[[Category: Edc]]
[[Category: Edc]]
[[Category: Ethenodc]]
[[Category: Ethenodc]]
[[Category: Exocyclic lesion]]
[[Category: Exocyclic lesion]]

Revision as of 06:45, 22 December 2014

3,N4-ETHENO-2'-DEOXYCYTIDINE OPPOSITE CYTIDINE IN AN 11-MER DUPLEX, SOLUTION STRUCTURE FROM NMR AND MOLECULAR DYNAMICS

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