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2lt0

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==NMR structure of duplex DNA containing the beta-OH-PdG dA base pair: A mutagenic intermediate of acrolein==
==NMR structure of duplex DNA containing the beta-OH-PdG dA base pair: A mutagenic intermediate of acrolein==
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<StructureSection load='2lt0' size='340' side='right' caption='[[2lt0]], [[NMR_Ensembles_of_Models | 26 NMR models]]' scene=''>
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<StructureSection load='2lt0' size='340' side='right'caption='[[2lt0]]' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[2lt0]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LT0 OCA]. <br>
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<table><tr><td colspan='2'>[[2lt0]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LT0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2LT0 FirstGlance]. <br>
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</td></tr><tr><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><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>
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</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><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2lsz|2lsz]]</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>
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<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </span></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2lt0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lt0 OCA], [https://pdbe.org/2lt0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2lt0 RCSB], [https://www.ebi.ac.uk/pdbsum/2lt0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2lt0 ProSAT]</span></td></tr>
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<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2lt0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lt0 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2lt0 RCSB], [http://www.ebi.ac.uk/pdbsum/2lt0 PDBsum]</span></td></tr>
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</table>
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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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Acrolein, a cell metabolic product and main component of cigarette smoke, reacts with DNA generating alpha-OH-PdG lesions, which have the ability to pair with dATP during replication thereby causing G to T transversions. We describe the solution structure of an 11-mer DNA duplex containing the mutagenic alpha-OH-PdG.dA base pair intermediate, as determined by solution nuclear magnetic resonance (NMR) spectroscopy and retrained molecular dynamics (MD) simulations. The NMR data support a mostly regular right-handed helix that is only perturbed at its center by the presence of the lesion. Undamaged residues of the duplex are in anti orientation, forming standard Watson-Crick base pairs alignments. Duplication of proton signals at and near the damaged base pair reveals the presence of two enantiomeric duplexes, thus establishing the exocyclic nature of the lesion. The alpha-OH-PdG adduct assumes a syn conformation pairing to its partner dA base that is protonated at pH 6.6. The three-dimensional structure obtained by restrained molecular dynamics simulations show hydrogen bond interactions that stabilize alpha-OH-PdG in a syn conformation and across the lesion containing base pair. We discuss the implications of the structures for the mutagenic bypass of acrolein lesions.
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NMR structure of duplex DNA containing the alpha-OH-PdG.dA base pair: a mutagenic intermediate of acrolein.,Zaliznyak T, Lukin M, El-khateeb M, Bonala R, Johnson F, de los Santos C Biopolymers. 2010 Apr;93(4):391-401. PMID:20049919<ref>PMID:20049919</ref>
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From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
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</div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Bonala, R.]]
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[[Category: Large Structures]]
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[[Category: El-khateeb, M.]]
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[[Category: Bonala R]]
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[[Category: Johnson, F.]]
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[[Category: El-khateeb M]]
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[[Category: Lukin, M.]]
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[[Category: Johnson F]]
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[[Category: Santos, C de los.]]
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[[Category: Lukin M]]
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[[Category: Zaliznyak, T.]]
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[[Category: Zaliznyak T]]
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[[Category: Acrolein adduct]]
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[[Category: De los Santos C]]
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[[Category: Damaged dna structure]]
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[[Category: Dna]]
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[[Category: Dna lesion]]
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Current revision

NMR structure of duplex DNA containing the beta-OH-PdG dA base pair: A mutagenic intermediate of acrolein

PDB ID 2lt0

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