2kd9: Difference between revisions

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{{Seed}}
[[Image:2kd9.png|left|200px]]


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==Solution Structure of DNA Containing Alpha-OH-PdG: the Mutagenic Adduct Produced by Acrolein==
The line below this paragraph, containing "STRUCTURE_2kd9", creates the "Structure Box" on the page.
<StructureSection load='2kd9' size='340' side='right'caption='[[2kd9]]' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[2kd9]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KD9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2KD9 FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=63G:(6S)-3-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)-6-HYDROXY-5,6,7,8-TETRAHYDROPYRIMIDO[1,2-A]PURIN-10(3H)-ONE'>63G</scene></td></tr>
{{STRUCTURE_2kd9|  PDB=2kd9  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2kd9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2kd9 OCA], [https://pdbe.org/2kd9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2kd9 RCSB], [https://www.ebi.ac.uk/pdbsum/2kd9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2kd9 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===
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>
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The line below this paragraph, {{ABSTRACT_PUBMED_19223332}}, adds the Publication Abstract to the page
<div class="pdbe-citations 2kd9" style="background-color:#fffaf0;"></div>
(as it appears on PubMed at http://www.pubmed.gov), where 19223332 is the PubMed ID number.
== References ==
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<references/>
{{ABSTRACT_PUBMED_19223332}}
__TOC__
 
</StructureSection>
==About this Structure==
[[Category: Large Structures]]
2KD9 is a 2 chains structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KD9 OCA].
[[Category: Attaluri S]]
 
[[Category: Bonala R]]
==Reference==
[[Category: Johnson F]]
<ref group="xtra">PMID:19223332</ref><references group="xtra"/>
[[Category: Zaliznyak T]]
[[Category: Attaluri, S.]]
[[Category: De los Santos C]]
[[Category: Bonala, R.]]
[[Category: Johnson, F.]]
[[Category: Santos, C de los.]]
[[Category: Zaliznyak, T.]]
[[Category: Acrolein lesion]]
[[Category: Dna damaged]]
[[Category: Dna structure]]
[[Category: Exocyclic]]
[[Category: Propano-dg lesion]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed May  6 10:09:17 2009''

Latest revision as of 12:50, 20 December 2023

Solution Structure of DNA Containing Alpha-OH-PdG: the Mutagenic Adduct Produced by Acrolein

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