3o1s: Difference between revisions
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==Iron-Catalyzed Oxidation Intermediates Captured in A DNA Repair Dioxygenase== | ==Iron-Catalyzed Oxidation Intermediates Captured in A DNA Repair Dioxygenase== | ||
<StructureSection load='3o1s' size='340' side='right' caption='[[3o1s]], [[Resolution|resolution]] 1.58Å' scene=''> | <StructureSection load='3o1s' size='340' side='right' caption='[[3o1s]], [[Resolution|resolution]] 1.58Å' scene=''> | ||
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3o1m|3o1m]], [[3o1o|3o1o]], [[3o1p|3o1p]], [[3o1r|3o1r]], [[3o1t|3o1t]], [[3o1u|3o1u]], [[3o1v|3o1v]]</td></tr> | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3o1m|3o1m]], [[3o1o|3o1o]], [[3o1p|3o1p]], [[3o1r|3o1r]], [[3o1t|3o1t]], [[3o1u|3o1u]], [[3o1v|3o1v]]</td></tr> | ||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">alkB, aidD, b2212, JW2200 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr> | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">alkB, aidD, b2212, JW2200 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=3o1s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3o1s OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3o1s RCSB], [http://www.ebi.ac.uk/pdbsum/3o1s 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=3o1s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3o1s OCA], [http://pdbe.org/3o1s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3o1s RCSB], [http://www.ebi.ac.uk/pdbsum/3o1s PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3o1s ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
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From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
</div> | </div> | ||
<div class="pdbe-citations 3o1s" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Dioxygenase|Dioxygenase]] | |||
== References == | == References == | ||
<references/> | <references/> | ||
Revision as of 23:36, 5 August 2016
Iron-Catalyzed Oxidation Intermediates Captured in A DNA Repair DioxygenaseIron-Catalyzed Oxidation Intermediates Captured in A DNA Repair Dioxygenase
Structural highlights
Function[ALKB_ECOLI] Dioxygenase that repairs alkylated DNA and RNA containing 3-methylcytosine or 1-methyladenine by oxidative demethylation. Has highest activity towards 3-methylcytosine. Has lower activity towards alkylated DNA containing ethenoadenine, and no detectable activity towards 1-methylguanine or 3-methylthymine. Accepts double-stranded and single-stranded substrates. Requires molecular oxygen, alpha-ketoglutarate and iron. Provides extensive resistance to alkylating agents such as MMS and DMS (SN2 agents), but not to MMNG and MNU (SN1 agents).[1] [2] [3] [4] [5] [6] Publication Abstract from PubMedMononuclear iron-containing oxygenases conduct a diverse variety of oxidation functions in biology, including the oxidative demethylation of methylated nucleic acids and histones. Escherichia coli AlkB is the first such enzyme that was discovered to repair methylated nucleic acids, which are otherwise cytotoxic and/or mutagenic. AlkB human homologues are known to play pivotal roles in various processes. Here we present structural characterization of oxidation intermediates for these demethylases. Using a chemical cross-linking strategy, complexes of AlkB-double stranded DNA (dsDNA) containing 1,N(6)-etheno adenine (epsilonA), N(3)-methyl thymine (3-meT) and N(3)-methyl cytosine (3-meC) are stabilized and crystallized, respectively. Exposing these crystals, grown under anaerobic conditions containing iron(II) and alpha-ketoglutarate (alphaKG), to dioxygen initiates oxidation in crystallo. Glycol (from epsilonA) and hemiaminal (from 3-meT) intermediates are captured; a zwitterionic intermediate (from 3-meC) is also proposed, based on crystallographic observations and computational analysis. The observation of these unprecedented intermediates provides direct support for the oxidative demethylation mechanism for these demethylases. This study also depicts a general mechanistic view of how a methyl group is oxidatively removed from different biological substrates. Iron-catalysed oxidation intermediates captured in a DNA repair dioxygenase.,Yi C, Jia G, Hou G, Dai Q, Zhang W, Zheng G, Jian X, Yang CG, Cui Q, He C Nature. 2010 Nov 11;468(7321):330-3. PMID:21068844[7] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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