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3t4v

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==Crystal Structure of AlkB in complex with Fe(III) and N-Oxalyl-S-(2-napthalenemethyl)-L-cysteine==
==Crystal Structure of AlkB in complex with Fe(III) and N-Oxalyl-S-(2-napthalenemethyl)-L-cysteine==
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<StructureSection load='3t4v' size='340' side='right' caption='[[3t4v]], [[Resolution|resolution]] 1.73&Aring;' scene=''>
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<StructureSection load='3t4v' size='340' side='right'caption='[[3t4v]], [[Resolution|resolution]] 1.73&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[3t4v]] is a 1 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=3T4V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3T4V FirstGlance]. <br>
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<table><tr><td colspan='2'>[[3t4v]] is a 1 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=3T4V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3T4V FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MD3:N-(CARBOXYCARBONYL)-S-(NAPHTHALEN-2-YLMETHYL)-L-CYSTEINE'>MD3</scene></td></tr>
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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]] 1.732&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2fd8|2fd8]], [[2fdf|2fdf]], [[2fdg|2fdg]], [[2fdh|2fdh]], [[2fdi|2fdi]], [[2fdj|2fdj]], [[2fdk|2fdk]], [[3bi3|3bi3]], [[3bie|3bie]], [[3bkz|3bkz]], [[3h8o|3h8o]], [[3h8r|3h8r]], [[3h8x|3h8x]], [[3i2o|3i2o]], [[3i3m|3i3m]], [[3i3q|3i3q]], [[3i49|3i49]], [[3khb|3khb]], [[3khc|3khc]], [[3o1m|3o1m]], [[3o1o|3o1o]], [[3o1p|3o1p]], [[3o1r|3o1r]], [[3o1s|3o1s]], [[3o1t|3o1t]], [[3o1u|3o1u]], [[3o1v|3o1v]], [[3t3y|3t3y]], [[3t4h|3t4h]]</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=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MD3:N-(CARBOXYCARBONYL)-S-(NAPHTHALEN-2-YLMETHYL)-L-CYSTEINE'>MD3</scene></td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">aidD, alkB, b2212, JW2200 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=3t4v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3t4v OCA], [https://pdbe.org/3t4v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3t4v RCSB], [https://www.ebi.ac.uk/pdbsum/3t4v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3t4v ProSAT]</span></td></tr>
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<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=3t4v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3t4v OCA], [http://pdbe.org/3t4v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3t4v RCSB], [http://www.ebi.ac.uk/pdbsum/3t4v PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3t4v ProSAT]</span></td></tr>
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</table>
</table>
== Function ==
== Function ==
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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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[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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2-Oxoglutarate-dependent nucleic acid demethylases are of biological interest because of their roles in nucleic acid repair and modification. Although some of these enzymes are linked to physiology, their regulatory roles are unclear. Hence, there is a desire to develop selective inhibitors for them; we report studies on AlkB, which reveal it as being amenable to selective inhibition by small molecules. Dynamic combinatorial chemistry linked to mass spectrometric analyses (DCMS) led to the identification of lead compounds, one of which was analyzed by crystallography. Subsequent structure-guided studies led to the identification of inhibitors of improved potency, some of which were shown to be selective over two other 2OG oxygenases. The work further validates the use of the DCMS method and will help to enable the development of inhibitors of nucleic acid modifying 2OG oxygenases both for use as functional probes and, in the longer term, for potential therapeutic use.
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Dynamic Combinatorial Mass Spectrometry Leads to Inhibitors of a 2-Oxoglutarate-Dependent Nucleic Acid Demethylase.,Woon EC, Demetriades M, Bagg EA, Aik W, Krylova SM, Ma JH, Chan M, Walport LJ, Wegman DW, Dack KN, McDonough MA, Krylov SN, Schofield CJ J Med Chem. 2012 Feb 22. PMID:22263962<ref>PMID:22263962</ref>
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==See Also==
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*[[Dioxygenase 3D structures|Dioxygenase 3D structures]]
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 3t4v" style="background-color:#fffaf0;"></div>
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== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Ecoli]]
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[[Category: Escherichia coli K-12]]
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[[Category: Aik, W S]]
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[[Category: Large Structures]]
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[[Category: McDonough, M A]]
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[[Category: Aik WS]]
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[[Category: Schofield, C J]]
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[[Category: McDonough MA]]
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[[Category: Double-stranded beta-helix]]
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[[Category: Schofield CJ]]
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[[Category: Nucleic acid demethylase]]
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[[Category: Oxidoreductase-oxidoreductase inhibitor complex]]
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Current revision

Crystal Structure of AlkB in complex with Fe(III) and N-Oxalyl-S-(2-napthalenemethyl)-L-cysteine

PDB ID 3t4v

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