3o1o: Difference between revisions

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-[[Image:3o1o.png|left|200px]]
-<!--
+==Iron-Catalyzed Oxidation Intermediates Captured in A DNA Repair Dioxygenase==
-The line below this paragraph, containing "STRUCTURE_3o1o", creates the "Structure Box" on the page.
+<StructureSection load='3o1o' size='340' side='right'caption='[[3o1o]], [[Resolution|resolution]] 1.92&Aring;' 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'>[[3o1o]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. 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 [https://proteopedia.org/fgij/fg.htm?mol=3O1O 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">X-ray diffraction, [[Resolution|Resolution]] 1.92&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2YR:2-DEOXY-N-(2-SULFANYLETHYL)CYTIDINE+5-(DIHYDROGEN+PHOSPHATE)'>2YR</scene>, <scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=MFT:3-METHYLTHYMIDINE+5-(DIHYDROGEN+PHOSPHATE)'>MFT</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
-{{STRUCTURE_3o1o|  PDB=3o1o  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3o1o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3o1o OCA], [https://pdbe.org/3o1o PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3o1o RCSB], [https://www.ebi.ac.uk/pdbsum/3o1o PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3o1o ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/ALKB_ECOLI 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).<ref>PMID:12226668</ref> <ref>PMID:12594517</ref> <ref>PMID:16482161</ref> <ref>PMID:19706517</ref> <ref>PMID:21068844</ref> <ref>PMID:20084272</ref>
+<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-Catalyzed Oxidation Intermediates Captured in A DNA Repair Dioxygenase===
+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>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3o1o" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_21068844}}, adds the Publication Abstract to the page
+*[[Dioxygenase 3D structures|Dioxygenase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 21068844 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_21068844}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Escherichia coli K-12]]
-[[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].
+[[Category: Large Structures]]
+[[Category: Cui Q]]
-==Reference==
+[[Category: Dai Q]]
-<ref group="xtra">PMID:021068844</ref><references group="xtra"/>
+[[Category: He C]]
-[[Category: Escherichia coli]]
+[[Category: Hou G]]
-[[Category: Cui, Q.]]
+[[Category: Jia G]]
-[[Category: Dai, Q.]]
+[[Category: Jian X]]
-[[Category: He, C.]]
+[[Category: Yang C-G]]
-[[Category: Hou, G.]]
+[[Category: Yi C]]
-[[Category: Jia, G.]]
+[[Category: Zhang W]]
-[[Category: Jian, X.]]
+[[Category: Zheng G]]
-[[Category: Yang, C G.]]
-[[Category: Yi, C.]]
-[[Category: Zhang, W.]]
-[[Category: Zheng, G.]]
-[[Category: Demethylase]]
-[[Category: Jelly-roll fold.]]
-[[Category: Oxidoreductase]]