3t3y - Revision history

OCA at 13:16, 14 March 2024

OCA — Thu, 14 Mar 2024 13:16:45 GMT

←Older revision		Revision as of 13:16, 14 March 2024
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	<StructureSection load='3t3y' size='340' side='right'caption='[[3t3y]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='3t3y' size='340' side='right'caption='[[3t3y]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3t3y]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Ecoli Ecoli~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3T3Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3T3Y FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3t3y]] 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=3T3Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3T3Y FirstGlance]. <br>
-	</td></tr><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=MD6:N-~~[~~(3-HYDROXYPYRIDIN-~~2~~-YL)CARBONYL]GLYCINE'>MD6</scene>~~</td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.001Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>[[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]], [[3t4h\|3t4h]], [[3t4v\|3t4v]]</~~div~~><~~/td></tr>~~	+	<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=MD6:N-[(3-HYDROXYPYRIDIN-2-YL)CARBONYL]GLYCINE'>MD6</scene></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>~~[~~[Gene\|Gene:~~]~~]</b~~></td>~~<td class="sblockDat">aidD, alkB, b2212, JW2200 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])~~</td></tr>	+
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3t3y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3t3y OCA], [https://pdbe.org/3t3y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3t3y RCSB], [https://www.ebi.ac.uk/pdbsum/3t3y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3t3y ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3t3y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3t3y OCA], [https://pdbe.org/3t3y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3t3y RCSB], [https://www.ebi.ac.uk/pdbsum/3t3y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3t3y ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== 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>	+	[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 ==~~	+
-	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.	+
-		+
-	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>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 3t3y" style="background-color:#fffaf0;"></div~~>	+

	==See Also==		==See Also==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Ecoli~~]]	+	[[Category: Escherichia coli K-12]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Aik~~, W S~~]]	+	[[Category: Aik WS]]
-	[[Category: McDonough~~, M A~~]]	+	[[Category: McDonough MA]]
-	[[Category: Schofield~~, C J]]~~	+	[[Category: Schofield CJ]]
-	~~[[Category: Double-stranded beta-helix]]~~	+
-	~~[[Category: Nucleic acid demethylase]]~~	+
-	~~[[Category: Oxidoreductase-oxidoreductase inhibitor complex~~]]	+

OCA at 16:42, 6 July 2022

OCA — Wed, 06 Jul 2022 16:42:01 GMT

←Older revision		Revision as of 16:42, 6 July 2022
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	==Crystal structure of AlkB in complex with Fe(III) and 2-(3-hydroxypicolinomido)acetic acid==		==Crystal structure of AlkB in complex with Fe(III) and 2-(3-hydroxypicolinomido)acetic acid==
-	<StructureSection load='3t3y' size='340' side='right' caption='[[3t3y]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='3t3y' size='340' side='right'caption='[[3t3y]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3t3y]] 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=3T3Y OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3T3Y FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3t3y]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3T3Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3T3Y FirstGlance]. <br>
-	</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=MD6:N-[(3-HYDROXYPYRIDIN-2-YL)CARBONYL]GLYCINE'>MD6</scene></td></tr>	+	</td></tr><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=MD6:N-[(3-HYDROXYPYRIDIN-2-YL)CARBONYL]GLYCINE'>MD6</scene></td></tr>
-	<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]], [[3t4h\|3t4h]], [[3t4v\|3t4v]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[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]], [[3t4h\|3t4h]], [[3t4v\|3t4v]]</div></td></tr>
-	<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>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">aidD, alkB, b2212, JW2200 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>
-	<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=3t3y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3t3y OCA], [~~http~~://pdbe.org/3t3y PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3t3y RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3t3y PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3t3y ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3t3y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3t3y OCA], [https://pdbe.org/3t3y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3t3y RCSB], [https://www.ebi.ac.uk/pdbsum/3t3y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3t3y ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~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>	+	[[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;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 3t3y" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3t3y" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Dioxygenase 3D structures\|Dioxygenase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Ecoli]]		[[Category: Ecoli]]
		+	[[Category: Large Structures]]
	[[Category: Aik, W S]]		[[Category: Aik, W S]]
	[[Category: McDonough, M A]]		[[Category: McDonough, M A]]

OCA at 09:47, 8 November 2017

OCA — Wed, 08 Nov 2017 09:47:31 GMT

←Older revision		Revision as of 09:47, 8 November 2017
Line 20:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 3t3y" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3t3y" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Dioxygenase\|Dioxygenase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 12:56, 4 August 2016

OCA — Thu, 04 Aug 2016 12:56:45 GMT

←Older revision		Revision as of 12:56, 4 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of AlkB in complex with Fe(III) and 2-(3-hydroxypicolinomido)acetic acid==		==Crystal structure of AlkB in complex with Fe(III) and 2-(3-hydroxypicolinomido)acetic acid==
	<StructureSection load='3t3y' size='340' side='right' caption='[[3t3y]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='3t3y' size='340' side='right' caption='[[3t3y]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3t3y]] is a 1 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=3T3Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3T3Y FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3t3y]] 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=3T3Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3T3Y FirstGlance]. <br>
	</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=MD6:N-[(3-HYDROXYPYRIDIN-2-YL)CARBONYL]GLYCINE'>MD6</scene></td></tr>		</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=MD6:N-[(3-HYDROXYPYRIDIN-2-YL)CARBONYL]GLYCINE'>MD6</scene></td></tr>
	<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]], [[3t4h\|3t4h]], [[3t4v\|3t4v]]</td></tr>		<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]], [[3t4h\|3t4h]], [[3t4v\|3t4v]]</td></tr>
-	<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=~~562 Escherichia coli~~])</td></tr>	+	<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>
-	<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=3t3y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3t3y OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3t3y RCSB], [http://www.ebi.ac.uk/pdbsum/3t3y PDBsum]</span></td></tr>	+	<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=3t3y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3t3y OCA], [http://pdbe.org/3t3y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3t3y RCSB], [http://www.ebi.ac.uk/pdbsum/3t3y PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3t3y ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 3t3y" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 25:		Line 27:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Escherichia coli~~]]	+	[[Category: Ecoli]]
	[[Category: Aik, W S]]		[[Category: Aik, W S]]
	[[Category: McDonough, M A]]		[[Category: McDonough, M A]]

OCA at 14:46, 24 December 2014

OCA — Wed, 24 Dec 2014 14:46:25 GMT

←Older revision		Revision as of 14:46, 24 December 2014
Line 1:		Line 1:
-	[[~~Image:~~3t3y.~~png~~\|~~left~~\|~~200px~~]]	+	==Crystal structure of AlkB in complex with Fe(III) and 2-(3-hydroxypicolinomido)acetic acid==
		+	<StructureSection load='3t3y' size='340' side='right' caption='[[3t3y]], [[Resolution\|resolution]] 2.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3t3y]] is a 1 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=3T3Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3T3Y FirstGlance]. <br>
		+	</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=MD6:N-[(3-HYDROXYPYRIDIN-2-YL)CARBONYL]GLYCINE'>MD6</scene></td></tr>
		+	<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]], [[3t4h\|3t4h]], [[3t4v\|3t4v]]</td></tr>
		+	<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=562 Escherichia coli])</td></tr>
		+	<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=3t3y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3t3y OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3t3y RCSB], [http://www.ebi.ac.uk/pdbsum/3t3y PDBsum]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[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>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	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.

-	<!--	+	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>
-	~~The line below this paragraph~~, ~~containing "STRUCTURE_3t3y"~~, ~~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_3t3y\| PDB=3t3y \| SCENE= }}~~	+

-	~~===Crystal structure~~ of ~~AlkB in complex with Fe(III) and 2-(3-hydroxypicolinomido)acetic acid===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

-		+	==See Also==
-	~~<!--~~	+	*[[Dioxygenase\|Dioxygenase]]
-	~~The line below this paragraph, {{ABSTRACT_PUBMED_22263962}}, adds the Publication Abstract to the page~~	+	== References ==
-	~~(as it appears on PubMed at http://www.pubmed.gov), where 22263962 is the PubMed ID number.~~	+	<references/>
-	~~-->~~	+	__TOC__
-	~~{{ABSTRACT_PUBMED_22263962}}~~	+	</StructureSection>
-		+
-	==~~About this Structure~~==	+
-	[[~~3t3y~~]] is a 1 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=3T3Y OCA].	+
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:022263962<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
-	[[Category: Aik, W S.]]	+	[[Category: Aik, W S]]
-	[[Category: McDonough, M A.]]	+	[[Category: McDonough, M A]]
-	[[Category: Schofield, C J.]]	+	[[Category: Schofield, C J]]
	[[Category: Double-stranded beta-helix]]		[[Category: Double-stranded beta-helix]]
	[[Category: Nucleic acid demethylase]]		[[Category: Nucleic acid demethylase]]
	[[Category: Oxidoreductase-oxidoreductase inhibitor complex]]		[[Category: Oxidoreductase-oxidoreductase inhibitor complex]]

OCA at 06:29, 21 March 2012

OCA — Wed, 21 Mar 2012 06:29:06 GMT

←Older revision		Revision as of 06:29, 21 March 2012
Line 1:		Line 1:
-	[[Image:3t3y.~~jpg~~\|left\|200px]]	+	[[Image:3t3y.png\|left\|200px]]

	<!--		<!--

OCA at 05:49, 8 March 2012

OCA — Thu, 08 Mar 2012 05:49:07 GMT

←Older revision		Revision as of 05:49, 8 March 2012
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:3t3y.jpg\|left\|200px]]

-	The ~~entry 3t3y~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3t3y", 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_3t3y\| PDB=3t3y \| SCENE= }}

-	~~Authors: Aik, W.S., McDonough, M.A., Schofield, C.J.~~	+	===Crystal structure of AlkB in complex with Fe(III) and 2-(3-hydroxypicolinomido)acetic acid===

-	~~Description~~: ~~Crystal~~ structure ~~of AlkB in complex~~ with ~~Fe(III) and 2~~-(3-~~hydroxypicolinomido)acetic~~ acid	+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_22263962}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 22263962 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_22263962}}
		+
		+	==About this Structure==
		+	[[3t3y]] is a 1 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=3T3Y OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:022263962</ref><references group="xtra"/>
		+	[[Category: Escherichia coli]]
		+	[[Category: Aik, W S.]]
		+	[[Category: McDonough, M A.]]
		+	[[Category: Schofield, C J.]]
		+	[[Category: Double-stranded beta-helix]]
		+	[[Category: Nucleic acid demethylase]]
		+	[[Category: Oxidoreductase-oxidoreductase inhibitor complex]]

OCA at 06:20, 31 August 2011

OCA — Wed, 31 Aug 2011 06:20:52 GMT

←Older revision		Revision as of 06:20, 31 August 2011
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3t3y is ON HOLD	+	The entry 3t3y is ON HOLD until Paper Publication

	Authors: Aik, W.S., McDonough, M.A., Schofield, C.J.		Authors: Aik, W.S., McDonough, M.A., Schofield, C.J.

	Description: Crystal structure of AlkB in complex with Fe(III) and 2-(3-hydroxypicolinomido)acetic acid		Description: Crystal structure of AlkB in complex with Fe(III) and 2-(3-hydroxypicolinomido)acetic acid

OCA at 05:53, 17 August 2011

OCA — Wed, 17 Aug 2011 05:53:25 GMT

←Older revision		Revision as of 05:53, 17 August 2011
Line 3:		Line 3:
	The entry 3t3y is ON HOLD		The entry 3t3y is ON HOLD

-	Authors: ~~AIK~~, W.S., McDonough, M.A., Schofield, C.J.	+	Authors: Aik, W.S., McDonough, M.A., Schofield, C.J.

	Description: Crystal structure of AlkB in complex with Fe(III) and 2-(3-hydroxypicolinomido)acetic acid		Description: Crystal structure of AlkB in complex with Fe(III) and 2-(3-hydroxypicolinomido)acetic acid

OCA: Protected "3t3y" [edit=sysop:move=sysop]

OCA — Wed, 03 Aug 2011 08:26:03 GMT

Protected "3t3y" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:26, 3 August 2011