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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{{ABSTRACT_PUBMED_24596302}}
 
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==Function==
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==Crystal structure of AlkB protein with cofactors bound to dsDNA containing m6A==
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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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<StructureSection load='4nid' size='340' side='right'caption='[[4nid]], [[Resolution|resolution]] 1.58&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[4nid]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. 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 [https://proteopedia.org/fgij/fg.htm?mol=4NID FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.58&#8491;</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=2YR:2-DEOXY-N-(2-SULFANYLETHYL)CYTIDINE+5-(DIHYDROGEN+PHOSPHATE)'>2YR</scene>, <scene name='pdbligand=6MA:N6-METHYL-DEOXY-ADENOSINE-5-MONOPHOSPHATE'>6MA</scene>, <scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></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=4nid FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nid OCA], [https://pdbe.org/4nid PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4nid RCSB], [https://www.ebi.ac.uk/pdbsum/4nid PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4nid ProSAT]</span></td></tr>
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</table>
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== Function ==
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[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>
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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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==About this Structure==
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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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[[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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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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<ref group="xtra">PMID:024596302</ref><references group="xtra"/><references/>
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</div>
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[[Category: DNA oxidative demethylase]]
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<div class="pdbe-citations 4nid" style="background-color:#fffaf0;"></div>
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[[Category: Yi, C Q.]]
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[[Category: Zhu, C X.]]
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==See Also==
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[[Category: 2-kg]]
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*[[Dioxygenase 3D structures|Dioxygenase 3D structures]]
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[[Category: Dna/rna demethylation repair]]
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== References ==
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[[Category: Dna/rna direct repair]]
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<references/>
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[[Category: Jelly-roll fold]]
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__TOC__
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[[Category: Oxidoreductase-dna complex]]
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</StructureSection>
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[[Category: Escherichia coli]]
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[[Category: Large Structures]]
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[[Category: Yi CQ]]
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[[Category: Zhu CX]]

Current revision

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

PDB ID 4nid

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