4nig - Revision history

OCA at 16:57, 20 September 2023

OCA — Wed, 20 Sep 2023 16:57:52 GMT

←Older revision		Revision as of 16:57, 20 September 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4nig]] 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=4NIG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4NIG FirstGlance]. <br>		<table><tr><td colspan='2'>[[4nig]] 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=4NIG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4NIG FirstGlance]. <br>
-	</td></tr><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>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.52Å</td></tr>
		+	<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>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4nig FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nig OCA], [https://pdbe.org/4nig PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4nig RCSB], [https://www.ebi.ac.uk/pdbsum/4nig PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4nig 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=4nig FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nig OCA], [https://pdbe.org/4nig PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4nig RCSB], [https://www.ebi.ac.uk/pdbsum/4nig PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4nig ProSAT]</span></td></tr>
	</table>		</table>

OCA at 08:30, 11 January 2023

OCA — Wed, 11 Jan 2023 08:30:01 GMT

←Older revision		Revision as of 08:30, 11 January 2023
Line 1:		Line 1:

	==Crystal structure of AlkB D135I/E136H mutant protein with cofactors bound to dsDNA containing m6A/A==		==Crystal structure of AlkB D135I/E136H mutant protein with cofactors bound to dsDNA containing m6A/A==
-	<StructureSection load='4nig' size='340' side='right' caption='[[4nig]], [[Resolution\|resolution]] 1.52Å' scene=''>	+	<StructureSection load='4nig' size='340' side='right'caption='[[4nig]], [[Resolution\|resolution]] 1.52Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4nig]] 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=4NIG OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4NIG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4nig]] 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=4NIG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4NIG FirstGlance]. <br>
-	</td></tr><tr id='ligand'><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></td></tr>~~	+	</td></tr><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>
-	~~<tr~~ id~~='NonStdRes'><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>~~	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4nig FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nig OCA], [https://pdbe.org/4nig PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4nig RCSB], [https://www.ebi.ac.uk/pdbsum/4nig PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4nig ProSAT]</span></td></tr>
-	~~<tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b~~></td>~~<td class="sblockDat">[[4nid\|4nid]]~~, ~~[[4nih\|4nih]], [[4nii\|4nii]]~~<~~/td></tr>~~	+
-	~~<tr id~~='~~gene'><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>~~	+
-	~~<tr id='activity~~'>~~<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>	+
-	<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=4nig FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nig OCA], [~~http~~://pdbe.org/4nig PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4nig RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4nig PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4nig 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 24:		Line 20:

	==See Also==		==See Also==
-	*[[Dioxygenase\|Dioxygenase]]	+	*[[Dioxygenase 3D structures\|Dioxygenase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus~~ coli ~~migula 1895~~]]	+	[[Category: Escherichia coli]]
-	[[Category: ~~DNA oxidative demethylase~~]]	+	[[Category: Large Structures]]
-	[[Category: Yi~~, C Q~~]]	+	[[Category: Yi CQ]]
-	[[Category: Zhu~~, C X]]~~	+	[[Category: Zhu CX]]
-	~~[[Category: 2-kg]]~~	+
-	~~[[Category: Dna/rna demethylation repair]]~~	+
-	~~[[Category: Dna/rna direct repair]]~~	+
-	~~[[Category: Jelly-roll fold]]~~	+
-	~~[[Category: Oxidoreductase-dna complex~~]]	+

OCA at 13:43, 4 August 2016

OCA — Thu, 04 Aug 2016 13:43:36 GMT

←Older revision		Revision as of 13:43, 4 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of AlkB D135I/E136H mutant protein with cofactors bound to dsDNA containing m6A/A==		==Crystal structure of AlkB D135I/E136H mutant protein with cofactors bound to dsDNA containing m6A/A==
	<StructureSection load='4nig' size='340' side='right' caption='[[4nig]], [[Resolution\|resolution]] 1.52Å' scene=''>		<StructureSection load='4nig' size='340' side='right' caption='[[4nig]], [[Resolution\|resolution]] 1.52Å' scene=''>
Line 8:		Line 9:
	<tr id='gene'><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>		<tr id='gene'><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>
	<tr id='activity'><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>		<tr id='activity'><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>
-	<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=4nig FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nig OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4nig RCSB], [http://www.ebi.ac.uk/pdbsum/4nig 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=4nig FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nig OCA], [http://pdbe.org/4nig PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4nig RCSB], [http://www.ebi.ac.uk/pdbsum/4nig PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4nig ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 20:		Line 21:
	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 4nig" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Dioxygenase\|Dioxygenase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 09:50, 25 December 2014

OCA — Thu, 25 Dec 2014 09:50:07 GMT

←Older revision		Revision as of 09:50, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4nig]] 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=4NIG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4NIG FirstGlance]. <br>		<table><tr><td colspan='2'>[[4nig]] 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=4NIG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4NIG FirstGlance]. <br>
-	</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>	+	</td></tr><tr id='ligand'><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></td></tr>
-	<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>	+	<tr id='NonStdRes'><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>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4nid\|4nid]], [[4nih\|4nih]], [[4nii\|4nii]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4nid\|4nid]], [[4nih\|4nih]], [[4nii\|4nii]]</td></tr>
-	<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>	+	<tr id='gene'><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>
-	<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>	+	<tr id='activity'><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>
-	<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=4nig FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nig OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4nig RCSB], [http://www.ebi.ac.uk/pdbsum/4nig 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=4nig FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nig OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4nig RCSB], [http://www.ebi.ac.uk/pdbsum/4nig PDBsum]</span></td></tr>
-	<table>	+	</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;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 16:		Line 18:
	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>		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>

-	From ~~MEDLINEÂ®~~/~~PubMedÂ®~~, 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>
	== References ==		== References ==
Line 24:		Line 26:
	[[Category: Bacillus coli migula 1895]]		[[Category: Bacillus coli migula 1895]]
	[[Category: DNA oxidative demethylase]]		[[Category: DNA oxidative demethylase]]
-	[[Category: Yi, C Q.]]	+	[[Category: Yi, C Q]]
-	[[Category: Zhu, C X.]]	+	[[Category: Zhu, C X]]
	[[Category: 2-kg]]		[[Category: 2-kg]]
	[[Category: Dna/rna demethylation repair]]		[[Category: Dna/rna demethylation repair]]

OCA at 07:02, 28 May 2014

OCA — Wed, 28 May 2014 07:02:27 GMT

←Older revision		Revision as of 07:02, 28 May 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_4nig\| PDB=4nig \| SCENE= }}~~	+	==Crystal structure of AlkB D135I/E136H mutant protein with cofactors bound to dsDNA containing m6A/A==
-	===Crystal structure of AlkB D135I/E136H mutant protein with cofactors bound to dsDNA containing m6A/A===	+	<StructureSection load='4nig' size='340' side='right' caption='[[4nig]], [[Resolution\|resolution]] 1.52Å' scene=''>
-	~~{{ABSTRACT_PUBMED_24596302}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4nig]] 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=4NIG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4NIG FirstGlance]. <br>
		+	</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>
		+	<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>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4nid\|4nid]], [[4nih\|4nih]], [[4nii\|4nii]]</td></tr>
		+	<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>
		+	<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>
		+	<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=4nig FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nig OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4nig RCSB], [http://www.ebi.ac.uk/pdbsum/4nig PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	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.

-	~~==Function==~~	+	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>
-	~~[[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>	+

-	~~==About this Structure==~~	+	From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
-	~~[[4nig]] is~~ a ~~3 chain structure~~. ~~Full crystallographic information is available from [http://oca~~.~~weizmann~~.~~ac.il~~/~~oca-bin/ocashort?id=4NIG OCA].~~	+	</div>
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	~~<ref group="xtra">PMID:024596302</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	__TOC__
		+	</StructureSection>
		+	[[Category: Bacillus coli migula 1895]]
	[[Category: DNA oxidative demethylase]]		[[Category: DNA oxidative demethylase]]
	[[Category: Yi, C Q.]]		[[Category: Yi, C Q.]]

OCA at 09:39, 16 April 2014

OCA — Wed, 16 Apr 2014 09:39:50 GMT

←Older revision		Revision as of 09:39, 16 April 2014
Line 1:		Line 1:
-	~~'''Unreleased~~ structure~~'''~~	+	{{STRUCTURE_4nig\| PDB=4nig \| SCENE= }}
		+	===Crystal structure of AlkB D135I/E136H mutant protein with cofactors bound to dsDNA containing m6A/A===
		+	{{ABSTRACT_PUBMED_24596302}}

-	~~The entry 4nig is ON HOLD~~ ~~until Paper Publication~~	+	==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>

-	~~Authors~~: ~~Yi, C~~.Q.~~, Zhu, C~~.X.	+	==About this Structure==
		+	[[4nig]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NIG OCA].

-	~~Description~~: ~~Crystal structure of AlkB D135I~~/~~E136H mutant protein with cofactors bound to dsDNA containing m6A~~/A	+	==Reference==
		+	<ref group="xtra">PMID:024596302</ref><references group="xtra"/><references/>
		+	[[Category: DNA oxidative demethylase]]
		+	[[Category: Yi, C Q.]]
		+	[[Category: Zhu, C X.]]
		+	[[Category: 2-kg]]
		+	[[Category: Dna/rna demethylation repair]]
		+	[[Category: Dna/rna direct repair]]
		+	[[Category: Jelly-roll fold]]
		+	[[Category: Oxidoreductase-dna complex]]

OCA at 09:24, 25 December 2013

OCA — Wed, 25 Dec 2013 09:24:11 GMT

←Older revision		Revision as of 09:24, 25 December 2013
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4nig is ON HOLD	+	The entry 4nig is ON HOLD until Paper Publication

	Authors: Yi, C.Q., Zhu, C.X.		Authors: Yi, C.Q., Zhu, C.X.

	Description: Crystal structure of AlkB D135I/E136H mutant protein with cofactors bound to dsDNA containing m6A/A		Description: Crystal structure of AlkB D135I/E136H mutant protein with cofactors bound to dsDNA containing m6A/A

OCA at 12:58, 20 November 2013

OCA — Wed, 20 Nov 2013 12:58:38 GMT

←Older revision		Revision as of 12:58, 20 November 2013
Line 5:		Line 5:
	Authors: Yi, C.Q., Zhu, C.X.		Authors: Yi, C.Q., Zhu, C.X.

-	Description: Crystal structure of AlkB D135I/E136H mutant protein bound to dsDNA containing m6A/A ~~with cofactors~~	+	Description: Crystal structure of AlkB D135I/E136H mutant protein with cofactors bound to dsDNA containing m6A/A

OCA: Protected "4nig" [edit=sysop:move=sysop]

OCA — Wed, 13 Nov 2013 07:50:35 GMT

Protected "4nig" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:50, 13 November 2013

OCA: New page: '''Unreleased structure''' The entry 4nig is ON HOLD Authors: Yi, C.Q., Zhu, C.X. Description: Crystal structure of AlkB D135I/E136H mutant protein bound to dsDNA containing m6A/A with...

OCA — Wed, 13 Nov 2013 07:50:35 GMT

New page: '''Unreleased structure''' The entry 4nig is ON HOLD Authors: Yi, C.Q., Zhu, C.X. Description: Crystal structure of AlkB D135I/E136H mutant protein bound to dsDNA containing m6A/A with...

New page

'''Unreleased structure'''

The entry 4nig is ON HOLD

Authors: Yi, C.Q., Zhu, C.X.

Description: Crystal structure of AlkB D135I/E136H mutant protein bound to dsDNA containing m6A/A with cofactors