3o1o: Difference between revisions

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-[[Image:3o1o.png|left|200px]]
+==Iron-Catalyzed Oxidation Intermediates Captured in A DNA Repair Dioxygenase==
+<StructureSection load='3o1o' size='340' side='right' caption='[[3o1o]], [[Resolution|resolution]] 1.92&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[3o1o]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3O1O OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3O1O FirstGlance]. <br>
+</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene><br>
+<tr><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=2YR:2-DEOXY-N-(2-SULFANYLETHYL)CYTIDINE+5-(DIHYDROGEN+PHOSPHATE)'>2YR</scene>, <scene name='pdbligand=MFT:3-METHYLTHYMIDINE+5-(DIHYDROGEN+PHOSPHATE)'>MFT</scene></td></tr>
+<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3o1m|3o1m]], [[3o1p|3o1p]], [[3o1r|3o1r]], [[3o1s|3o1s]], [[3o1t|3o1t]], [[3o1u|3o1u]], [[3o1v|3o1v]]</td></tr>
+<tr><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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3o1o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3o1o OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3o1o RCSB], [http://www.ebi.ac.uk/pdbsum/3o1o PDBsum]</span></td></tr>
+<table>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Mononuclear 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<ref>PMID:21068844</ref>
-The line below this paragraph, containing "STRUCTURE_3o1o", creates the "Structure Box" on the page.
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-or leave the SCENE parameter empty for the default display.
--->
-{{STRUCTURE_3o1o|  PDB=3o1o  |  SCENE=  }}
-===Iron-Catalyzed Oxidation Intermediates Captured in A DNA Repair Dioxygenase===
+From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
+</div>
+== References ==
-<!--
+<references/>
-The line below this paragraph, {{ABSTRACT_PUBMED_21068844}}, adds the Publication Abstract to the page
+__TOC__
-(as it appears on PubMed at http://www.pubmed.gov), where 21068844 is the PubMed ID number.
+</StructureSection>
--->
+[[Category: Ecoli]]
-{{ABSTRACT_PUBMED_21068844}}
-==About this Structure==
-[[3o1o]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3O1O OCA].
-==Reference==
-<ref group="xtra">PMID:021068844</ref><references group="xtra"/>
-[[Category: Escherichia coli]]
 [[Category: Cui, Q.]]
 [[Category: Dai, Q.]]