This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

1u6c

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 01:14, 12 September 2015

The NMR-derived solution structure of the (2S,3S)-N6-(2,3,4-trihydroxybutyl)-2'-deoxyadenosyl DNA adduct of butadiene diol epoxide

Structural highlights

1u6c 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

Publication Abstract from PubMed

The solution structure of the (2S,3S)-N(6)-(2,3,4-trihydroxybutyl)-2'-deoxyadenosyl adduct arising from the alkylation of adenine N(6) at position X(6) in d(CGGACXAGAAG).d(CTTCTTGTCCG), by butadiene diol epoxide, was determined. This oligodeoxynucleotide contains codon 61 (underlined) of the human N-ras protooncogene. This oligodeoxynucleotide, containing the adenine N(6) adduct butadiene triol (BDT) adduct at the second position of codon 61, was named the ras61 S,S-BDT-(61,2) adduct. NMR spectroscopy revealed modest structural perturbations localized to the site of adduction at X(6).T(17), and its nearest-neighbor base pairs C(5).G(18) and A(7).T(16). All sequential NOE connectivities arising from DNA protons were observed. Torsion angle analysis from COSY data suggested that the deoxyribose sugar at X(6) remained in the C2'-endo conformation. Molecular dynamics calculations using a simulated annealing protocol restrained by a total of 442 NOE-derived distances and J coupling-derived torsion angles refined structures in which the BDT moiety oriented in the major groove. Relaxation matrix analysis suggested hydrogen bonding between the hydroxyl group located at the beta-carbon of the BDT moiety and the T(17) O(4) of the modified base pair X(6).T(17). The minimal perturbation of DNA induced by this major groove adduct correlated with its facile bypass by three Escherichia coli DNA polymerases in vitro and its weak mutagenicity [Carmical, J. R., Nechev, L. V., Harris, C. M., Harris, T. M., and Lloyd, R. S. (2000) Environ. Mol. Mutagen. 35, 48-56]. Overall, the structure of this adduct is consistent with an emerging pattern in which major groove adenine N(6) alkylation products of styrene and butadiene oxides that do not strongly perturb DNA structure are not strongly mutagenic.

Structure of a site specific major groove (2S,3S)-N6-(2,3,4-trihydroxybutyl)-2'-deoxyadenosyl DNA adduct of butadiene diol epoxide.,Scholdberg TA, Nechev LV, Merritt WK, Harris TM, Harris CM, Lloyd RS, Stone MP Chem Res Toxicol. 2004 Jun;17(6):717-30. PMID:15206893^[1]

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

References

↑ Scholdberg TA, Nechev LV, Merritt WK, Harris TM, Harris CM, Lloyd RS, Stone MP. Structure of a site specific major groove (2S,3S)-N6-(2,3,4-trihydroxybutyl)-2'-deoxyadenosyl DNA adduct of butadiene diol epoxide. Chem Res Toxicol. 2004 Jun;17(6):717-30. PMID:15206893 doi:http://dx.doi.org/10.1021/tx034271+

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/1u6c"

@@ Line 4: / Line 4: @@
 <table><tr><td colspan='2'>[[1u6c]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1U6C OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1U6C FirstGlance]. <br>
 </td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=2BU:(2S,3S)-N6-(2,3,4-TRIHYDROXYBUTYL)-2-DEOXYADENOSINE+MONO+PHOSPHORIC+ACID'>2BU</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=1u6c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u6c OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1u6c RCSB], [http://www.ebi.ac.uk/pdbsum/1u6c 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=1u6c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u6c OCA], [http://pdbe.org/1u6c PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1u6c RCSB], [http://www.ebi.ac.uk/pdbsum/1u6c PDBsum]</span></td></tr>
 </table>
 <div style="background-color:#fffaf0;">
@@ Line 14: / Line 14: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 1u6c" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>

1u6c

From Proteopedia

Revision as of 01:14, 12 September 2015

The NMR-derived solution structure of the (2S,3S)-N6-(2,3,4-trihydroxybutyl)-2'-deoxyadenosyl DNA adduct of butadiene diol epoxide

Structural highlights

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox