View source for 2kda


==Solution Structure of DNA Containing Alpha-OH-PdG: the Mutagenic Adduct Produced by Acrolein==
<StructureSection load='2kda' size='340' side='right'caption='[[2kda]]' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[2kda]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KDA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2KDA FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=63H:(6R)-3-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)-6-HYDROXY-5,6,7,8-TETRAHYDROPYRIMIDO[1,2-A]PURIN-10(3H)-ONE'>63H</scene></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2kda FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2kda OCA], [https://pdbe.org/2kda PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2kda RCSB], [https://www.ebi.ac.uk/pdbsum/2kda PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2kda ProSAT]</span></td></tr>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Acrolein is a cell metabolic product and a main component of cigarette smoke. Its reaction with DNA produces two guanine lesions gamma-OH-PdG, a major adduct that is nonmutagenic in mammalian cells, and the positional isomer alpha-OH-PdG. We describe here the solution structure of a short DNA duplex containing a single alpha-OH-PdG lesion, as determined by solution NMR spectroscopy and restrained molecular dynamics simulations. The spectroscopic data show a mostly regular right-handed helix, locally perturbed at its center by the presence of the lesion. All undamaged residues of the duplex are in anti orientation, forming standard Watson-Crick base-pair alignments. Duplication of proton signals near the damaged site differentiates two enantiomeric duplexes, thus establishing the exocyclic nature of the lesion. At the lesion site, alpha-OH-PdG rotates to a syn conformation, pairing to its counter cytosine residue that is protonated at pH 5.9. Three-dimensional models produced by restrained molecular dynamics simulations show different hydrogen-bonding patterns between the lesion and its cytosine partner and identify further stabilization of alpha-OH-PdG in a syn conformation by intra-residue hydrogen bonds. We compare the alpha-OH-PdG.dC duplex structure with that of duplexes containing the analogous lesion propano-dG and discuss the implications of our findings for the mutagenic bypass of acrolein lesions.

Solution structure of DNA containing alpha-OH-PdG: the mutagenic adduct produced by acrolein.,Zaliznyak T, Bonala R, Attaluri S, Johnson F, de los Santos C Nucleic Acids Res. 2009 Apr;37(7):2153-63. Epub 2009 Feb 17. PMID:19223332<ref>PMID:19223332</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2kda" style="background-color:#fffaf0;"></div>
== References ==
<references/>
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</StructureSection>
[[Category: Large Structures]]
[[Category: Attaluri S]]
[[Category: Bonala R]]
[[Category: Johnson F]]
[[Category: Zaliznyak T]]
[[Category: De los Santos C]]