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| | ==Solution Structure of DNA Containing Alpha-OH-PdG: the Mutagenic Adduct Produced by Acrolein== | | ==Solution Structure of DNA Containing Alpha-OH-PdG: the Mutagenic Adduct Produced by Acrolein== |
| - | <StructureSection load='2kda' size='340' side='right' caption='[[2kda]], [[NMR_Ensembles_of_Models | 26 NMR models]]' scene=''> | + | <StructureSection load='2kda' size='340' side='right'caption='[[2kda]]' scene=''> |
| | == Structural highlights == | | == 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2KDA FirstGlance]. <br> | + | <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='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><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> | + | </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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2kd9|2kd9]]</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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2kda FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2kda OCA], [http://pdbe.org/2kda PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2kda RCSB], [http://www.ebi.ac.uk/pdbsum/2kda PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2kda ProSAT]</span></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> | | </table> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Attaluri, S]] | + | [[Category: Large Structures]] |
| - | [[Category: Bonala, R]] | + | [[Category: Attaluri S]] |
| - | [[Category: Johnson, F]] | + | [[Category: Bonala R]] |
| - | [[Category: Santos, C de los]] | + | [[Category: Johnson F]] |
| - | [[Category: Zaliznyak, T]] | + | [[Category: Zaliznyak T]] |
| - | [[Category: Acrolein lesion]] | + | [[Category: De los Santos C]] |
| - | [[Category: Dna]]
| + | |
| - | [[Category: Dna damaged]]
| + | |
| - | [[Category: Dna structure]]
| + | |
| - | [[Category: Exocyclic]]
| + | |
| - | [[Category: Propano-dg lesion]]
| + | |
| Structural highlights
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[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Zaliznyak T, Bonala R, Attaluri S, Johnson F, de los Santos C. Solution structure of DNA containing alpha-OH-PdG: the mutagenic adduct produced by acrolein. Nucleic Acids Res. 2009 Apr;37(7):2153-63. Epub 2009 Feb 17. PMID:19223332 doi:10.1093/nar/gkp076
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