3t4v - Revision history

OCA at 13:17, 14 March 2024

2024-03-14T13:17:43Z

←Older revision		Revision as of 13:17, 14 March 2024
Line 3:		Line 3:
	<StructureSection load='3t4v' size='340' side='right'caption='[[3t4v]], [[Resolution\|resolution]] 1.73Å' scene=''>		<StructureSection load='3t4v' size='340' side='right'caption='[[3t4v]], [[Resolution\|resolution]] 1.73Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3t4v]] 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=3T4V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3T4V FirstGlance]. <br>	+	<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>
-	</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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MD3:N-(CARBOXYCARBONYL)-S-(NAPHTHALEN-2-YLMETHYL)-L-CYSTEINE'>MD3</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]] 1.732Å</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]], [[3t3y\|3t3y]], [[3t4h\|3t4h]]</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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MD3:N-(CARBOXYCARBONYL)-S-(NAPHTHALEN-2-YLMETHYL)-L-CYSTEINE'>MD3</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=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>		<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>
	</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 3t4v" style="background-color:#fffaf0;"></div~~>	+

	==See Also==		==See Also==
Line 27:		Line 17:
	__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 16:43, 6 July 2022

2022-07-06T16:43:07Z

←Older revision		Revision as of 16:43, 6 July 2022
Line 1:		Line 1:

	==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==
-	<StructureSection load='3t4v' size='340' side='right' caption='[[3t4v]], [[Resolution\|resolution]] 1.73Å' scene=''>	+	<StructureSection load='3t4v' size='340' side='right'caption='[[3t4v]], [[Resolution\|resolution]] 1.73Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<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>	+	<table><tr><td colspan='2'>[[3t4v]] 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=3T4V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3T4V 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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MD3:N-(CARBOXYCARBONYL)-S-(NAPHTHALEN-2-YLMETHYL)-L-CYSTEINE'>MD3</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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MD3:N-(CARBOXYCARBONYL)-S-(NAPHTHALEN-2-YLMETHYL)-L-CYSTEINE'>MD3</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]], [[3t3y\|3t3y]], [[3t4h\|3t4h]]</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]], [[3t3y\|3t3y]], [[3t4h\|3t4h]]</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=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>	+	<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>
	</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 ==
Line 20:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 3t4v" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3t4v" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Dioxygenase 3D structures\|Dioxygenase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 25:		Line 28:
	</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 09:48, 8 November 2017

2017-11-08T09:48:11Z

←Older revision		Revision as of 09:48, 8 November 2017
Line 20:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 3t4v" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3t4v" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Dioxygenase\|Dioxygenase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 07:14, 4 August 2016

2016-08-04T07:14:16Z

←Older revision		Revision as of 07:14, 4 August 2016
Line 1:		Line 1:
		+
	==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==
	<StructureSection load='3t4v' size='340' side='right' caption='[[3t4v]], [[Resolution\|resolution]] 1.73Å' scene=''>		<StructureSection load='3t4v' size='340' side='right' caption='[[3t4v]], [[Resolution\|resolution]] 1.73Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3t4v]] 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=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>	+	<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>
	</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>		</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>
	<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>		<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>
-	<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=3t4v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3t4v OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3t4v RCSB], [http://www.ebi.ac.uk/pdbsum/3t4v 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=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>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 19:
	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 3t4v" 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 06:38, 24 December 2014

2014-12-24T06:38:05Z

←Older revision		Revision as of 06:38, 24 December 2014
Line 1:		Line 1:
-	[[~~Image:~~3t4v.~~png~~\|~~left~~\|~~200px~~]]	+	==Crystal Structure of AlkB in complex with Fe(III) and N-Oxalyl-S-(2-napthalenemethyl)-L-cysteine==
		+	<StructureSection load='3t4v' size='340' side='right' caption='[[3t4v]], [[Resolution\|resolution]] 1.73Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3t4v]] 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=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>
		+	</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>
		+	<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>
		+	<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=3t4v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3t4v OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3t4v RCSB], [http://www.ebi.ac.uk/pdbsum/3t4v 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_3t4v"~~, ~~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_3t4v\| PDB=3t4v \| SCENE= }}~~	+

-	~~===Crystal Structure~~ of ~~AlkB in complex with Fe(III) and N-Oxalyl-~~S~~-(2-napthalenemethyl)-L-cysteine===~~	+	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~~==	+
-	[[~~3t4v~~]] 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=3T4V 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 06:10, 21 March 2012

2012-03-21T06:10:51Z

←Older revision		Revision as of 06:10, 21 March 2012
Line 1:		Line 1:
-	[[Image:3t4v.~~jpg~~\|left\|200px]]	+	[[Image:3t4v.png\|left\|200px]]

	<!--		<!--

OCA at 05:43, 8 March 2012

2012-03-08T05:43:23Z

←Older revision		Revision as of 05:43, 8 March 2012
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:3t4v.jpg\|left\|200px]]

-	The ~~entry 3t4v~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3t4v", 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_3t4v\| PDB=3t4v \| SCENE= }}

-	~~Authors: Aik, W.~~S~~., McDonough, M.A., Schofield, C.J.~~	+	===Crystal Structure of AlkB in complex with Fe(III) and N-Oxalyl-S-(2-napthalenemethyl)-L-cysteine===

-	~~Description: Crystal Structure of AlkB in complex with Fe~~(~~III~~) ~~and N~~-~~Oxalyl~~-S-(2-~~napthalenemethyl)~~-~~L-cysteine~~	+
		+	<!--
		+	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==
		+	[[3t4v]] 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=3T4V 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 06:21, 31 August 2011

2011-08-31T06:21:00Z

←Older revision		Revision as of 06:21, 31 August 2011
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3t4v is ON HOLD	+	The entry 3t4v 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 N-Oxalyl-S-(2-napthalenemethyl)-L-cysteine		Description: Crystal Structure of AlkB in complex with Fe(III) and N-Oxalyl-S-(2-napthalenemethyl)-L-cysteine

OCA at 05:53, 17 August 2011

2011-08-17T05:53:49Z

←Older revision		Revision as of 05:53, 17 August 2011
Line 3:		Line 3:
	The entry 3t4v is ON HOLD		The entry 3t4v 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 N-Oxalyl-S-(2-napthalenemethyl)-L-cysteine		Description: Crystal Structure of AlkB in complex with Fe(III) and N-Oxalyl-S-(2-napthalenemethyl)-L-cysteine

OCA: Protected "3t4v" [edit=sysop:move=sysop]

2011-08-03T08:27:07Z

Protected "3t4v" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:27, 3 August 2011