4nid

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{{STRUCTURE_4nid| PDB=4nid | SCENE= }}
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==Crystal structure of AlkB protein with cofactors bound to dsDNA containing m6A==
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===Crystal structure of AlkB protein with cofactors bound to dsDNA containing m6A===
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<StructureSection load='4nid' size='340' side='right' caption='[[4nid]], [[Resolution|resolution]] 1.58&Aring;' scene=''>
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{{ABSTRACT_PUBMED_24596302}}
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== Structural highlights ==
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<table><tr><td colspan='2'>[[4nid]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NID OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4NID FirstGlance]. <br>
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</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>
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<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=6MA:N6-METHYL-DEOXY-ADENOSINE-5-MONOPHOSPHATE'>6MA</scene></td></tr>
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<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4nig|4nig]], [[4nih|4nih]], [[4nii|4nii]]</td></tr>
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<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=562 "Bacillus coli" Migula 1895])</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/DNA_oxidative_demethylase DNA oxidative demethylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.11.33 1.14.11.33] </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=4nid FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nid OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4nid RCSB], [http://www.ebi.ac.uk/pdbsum/4nid PDBsum]</span></td></tr>
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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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The AlkB family demethylases AlkB, FTO, and ALKBH5 recognize differentially methylated RNA/DNA substrates, which results in their distinct biological roles. Here we identify key active-site residues that contribute to their substrate specificity. Swapping such active-site residues between the demethylases leads to partially switched demethylation activities. Combined evidence from X-ray structures and enzyme kinetics suggests a role of the active-site residues in substrate recognition. Such a divergent active-site sequence may aid the design of selective inhibitors that can discriminate these homologue RNA/DNA demethylases.
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==Function==
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Switching Demethylation Activities between AlkB Family RNA/DNA Demethylases through Exchange of Active-Site Residues.,Zhu C, Yi C Angew Chem Int Ed Engl. 2014 Apr 1;53(14):3659-62. doi: 10.1002/anie.201310050., Epub 2014 Mar 5. PMID:24596302<ref>PMID:24596302</ref>
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[[http://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>
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==About this Structure==
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From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
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[[4nid]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NID OCA].
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</div>
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== References ==
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==Reference==
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<references/>
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<ref group="xtra">PMID:024596302</ref><references group="xtra"/><references/>
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__TOC__
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</StructureSection>
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[[Category: Bacillus coli migula 1895]]
[[Category: DNA oxidative demethylase]]
[[Category: DNA oxidative demethylase]]
[[Category: Yi, C Q.]]
[[Category: Yi, C Q.]]

Revision as of 07:00, 28 May 2014

Crystal structure of AlkB protein with cofactors bound to dsDNA containing m6A

4nid, resolution 1.58Å

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