3s57 - Revision history

OCA at 08:36, 20 March 2024

OCA — Wed, 20 Mar 2024 08:36:31 GMT

←Older revision		Revision as of 08:36, 20 March 2024
Line 3:		Line 3:
	<StructureSection load='3s57' size='340' side='right'caption='[[3s57]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='3s57' size='340' side='right'caption='[[3s57]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3s57]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3S57 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3S57 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3s57]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3S57 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3S57 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=XL3:PROPANE-1-THIOL'>XL3</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]] 1.6Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3bty\|3bty]], [[3s5a\|3s5a]]</div></td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=XL3:PROPANE-1-THIOL'>XL3</scene></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ABH2, ALKBH2 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])~~</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=3s57 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s57 OCA], [https://pdbe.org/3s57 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3s57 RCSB], [https://www.ebi.ac.uk/pdbsum/3s57 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3s57 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=3s57 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s57 OCA], [https://pdbe.org/3s57 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3s57 RCSB], [https://www.ebi.ac.uk/pdbsum/3s57 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3s57 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/ALKB2_HUMAN ALKB2_HUMAN]] Dioxygenase that repairs alkylated DNA and RNA containing 1-methyladenine and 3-methylcytosine by oxidative demethylation. Can also repair alkylated DNA containing 1-ethenoadenine (in vitro). Has strong preference for double-stranded DNA. Has low efficiency with single-stranded substrates. Requires molecular oxygen, alpha-ketoglutarate and iron.<ref>PMID:12486230</ref> <ref>PMID:12594517</ref> <ref>PMID:16174769</ref> <ref>PMID:18519673</ref> <ref>PMID:18432238</ref>	+	[https://www.uniprot.org/uniprot/ALKB2_HUMAN ALKB2_HUMAN] Dioxygenase that repairs alkylated DNA and RNA containing 1-methyladenine and 3-methylcytosine by oxidative demethylation. Can also repair alkylated DNA containing 1-ethenoadenine (in vitro). Has strong preference for double-stranded DNA. Has low efficiency with single-stranded substrates. Requires molecular oxygen, alpha-ketoglutarate and iron.<ref>PMID:12486230</ref> <ref>PMID:12594517</ref> <ref>PMID:16174769</ref> <ref>PMID:18519673</ref> <ref>PMID:18432238</ref>
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	ALKBH2 is a direct DNA repair dioxygenase guarding the mammalian genome against N(1)-methyladenine, N(3)-methylcytosine and 1,N(6)-ethenoadenine damage. A prerequisite for repair is to identify these lesions in the genome. Here we present crystal structures of human ALKBH2 bound to different duplex DNAs. Together with computational and biochemical analyses, our results suggest that DNA interrogation by ALKBH2 has two previously unknown features: (i) ALKBH2 probes base-pair stability and detects base pairs with reduced stability, and (ii) ALKBH2 does not have nor need a damage-checking site, which is critical for preventing spurious base cleavage for several glycosylases. The demethylation mechanism of ALKBH2 insures that only cognate lesions are oxidized and reversed to normal bases, and that a flipped, non-substrate base remains intact in the active site. Overall, the combination of duplex interrogation and oxidation chemistry allows ALKBH2 to detect and process diverse lesions efficiently and correctly.	+
-		+
-	Duplex interrogation by a direct DNA repair protein in search of base damage.,Yi C, Chen B, Qi B, Zhang W, Jia G, Zhang L, Li CJ, Dinner AR, Yang CG, He C Nat Struct Mol Biol. 2012 Jun 3;19(7):671-6. doi: 10.1038/nsmb.2320. PMID:22659876<ref>PMID:22659876</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 3s57" style="background-color:#fffaf0;"></div~~>	+

	==See Also==		==See Also==
Line 27:		Line 17:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Chen, B]]	+	[[Category: Chen B]]
-	[[Category: Dinner~~, A R~~]]	+	[[Category: Dinner AR]]
-	[[Category: He, C]]	+	[[Category: He C]]
-	[[Category: Jia, G]]	+	[[Category: Jia G]]
-	[[Category: Li~~, C Q~~]]	+	[[Category: Li CQ]]
-	[[Category: Qi, B]]	+	[[Category: Qi B]]
-	[[Category: Ramirez, B]]	+	[[Category: Ramirez B]]
-	[[Category: Yang, C G]]	+	[[Category: Yang C-G]]
-	[[Category: Yi, C]]	+	[[Category: Yi C]]
-	[[Category: Zhang, L]]	+	[[Category: Zhang L]]
-	[[Category: Zhang, W]]	+	[[Category: Zhang W]]
-	~~[[Category: Dioxygenase]]~~	+
-	~~[[Category: Dsdna binding]]~~	+
-	~~[[Category: Jelly-roll fold]]~~	+
-	~~[[Category: Oxidoreductase-dna complex]]~~	+
-	~~[[Category: Plasma]]~~	+
-	~~[[Category: Protein-dna complex~~]]	+

OCA at 10:38, 22 June 2022

OCA — Wed, 22 Jun 2022 10:38:45 GMT

←Older revision		Revision as of 10:38, 22 June 2022
Line 1:		Line 1:

	==ABH2 cross-linked with undamaged dsDNA-1 containing cofactors==		==ABH2 cross-linked with undamaged dsDNA-1 containing cofactors==
-	<StructureSection load='3s57' size='340' side='right' caption='[[3s57]], [[Resolution\|resolution]] 1.60Å' scene=''>	+	<StructureSection load='3s57' size='340' side='right'caption='[[3s57]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3s57]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3S57 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3S57 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3s57]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3S57 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3S57 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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=XL3:PROPANE-1-THIOL'>XL3</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=XL3:PROPANE-1-THIOL'>XL3</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3bty\|3bty]], [[3s5a\|3s5a]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3bty\|3bty]], [[3s5a\|3s5a]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ABH2, ALKBH2 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ABH2, ALKBH2 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=3s57 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s57 OCA], [~~http~~://pdbe.org/3s57 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3s57 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3s57 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3s57 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=3s57 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s57 OCA], [https://pdbe.org/3s57 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3s57 RCSB], [https://www.ebi.ac.uk/pdbsum/3s57 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3s57 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/ALKB2_HUMAN ALKB2_HUMAN]] Dioxygenase that repairs alkylated DNA and RNA containing 1-methyladenine and 3-methylcytosine by oxidative demethylation. Can also repair alkylated DNA containing 1-ethenoadenine (in vitro). Has strong preference for double-stranded DNA. Has low efficiency with single-stranded substrates. Requires molecular oxygen, alpha-ketoglutarate and iron.<ref>PMID:12486230</ref> <ref>PMID:12594517</ref> <ref>PMID:16174769</ref> <ref>PMID:18519673</ref> <ref>PMID:18432238</ref>	+	[[https://www.uniprot.org/uniprot/ALKB2_HUMAN ALKB2_HUMAN]] Dioxygenase that repairs alkylated DNA and RNA containing 1-methyladenine and 3-methylcytosine by oxidative demethylation. Can also repair alkylated DNA containing 1-ethenoadenine (in vitro). Has strong preference for double-stranded DNA. Has low efficiency with single-stranded substrates. Requires molecular oxygen, alpha-ketoglutarate and iron.<ref>PMID:12486230</ref> <ref>PMID:12594517</ref> <ref>PMID:16174769</ref> <ref>PMID:18519673</ref> <ref>PMID:18432238</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 22:

	==See Also==		==See Also==
-	*[[Dioxygenase\|Dioxygenase]]	+	*[[Dioxygenase 3D structures\|Dioxygenase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 28:		Line 28:
	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Chen, B]]		[[Category: Chen, B]]
	[[Category: Dinner, A R]]		[[Category: Dinner, A R]]

OCA at 09:02, 4 August 2016

OCA — Thu, 04 Aug 2016 09:02:33 GMT

←Older revision		Revision as of 09:02, 4 August 2016
Line 1:		Line 1:
		+
	==ABH2 cross-linked with undamaged dsDNA-1 containing cofactors==		==ABH2 cross-linked with undamaged dsDNA-1 containing cofactors==
	<StructureSection load='3s57' size='340' side='right' caption='[[3s57]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='3s57' size='340' side='right' caption='[[3s57]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3s57]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Homo_sapiens Homo sapiens~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3S57 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3S57 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3s57]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3S57 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3S57 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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=XL3:PROPANE-1-THIOL'>XL3</scene></td></tr>		</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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=XL3:PROPANE-1-THIOL'>XL3</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3bty\|3bty]], [[3s5a\|3s5a]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3bty\|3bty]], [[3s5a\|3s5a]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ABH2, ALKBH2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 ~~Homo sapiens~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ABH2, ALKBH2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=3s57 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s57 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3s57 RCSB], [http://www.ebi.ac.uk/pdbsum/3s57 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=3s57 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s57 OCA], [http://pdbe.org/3s57 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3s57 RCSB], [http://www.ebi.ac.uk/pdbsum/3s57 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3s57 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 3s57" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 25:		Line 27:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Homo sapiens~~]]	+	[[Category: Human]]
	[[Category: Chen, B]]		[[Category: Chen, B]]
	[[Category: Dinner, A R]]		[[Category: Dinner, A R]]

OCA at 07:59, 24 December 2014

OCA — Wed, 24 Dec 2014 07:59:22 GMT

←Older revision		Revision as of 07:59, 24 December 2014
Line 8:		Line 8:
	<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=3s57 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s57 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3s57 RCSB], [http://www.ebi.ac.uk/pdbsum/3s57 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=3s57 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s57 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3s57 RCSB], [http://www.ebi.ac.uk/pdbsum/3s57 PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/ALKB2_HUMAN ALKB2_HUMAN]] Dioxygenase that repairs alkylated DNA and RNA containing 1-methyladenine and 3-methylcytosine by oxidative demethylation. Can also repair alkylated DNA containing 1-ethenoadenine (in vitro). Has strong preference for double-stranded DNA. Has low efficiency with single-stranded substrates. Requires molecular oxygen, alpha-ketoglutarate and iron.<ref>PMID:12486230</ref> <ref>PMID:12594517</ref> <ref>PMID:16174769</ref> <ref>PMID:18519673</ref> <ref>PMID:18432238</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 10:38, 19 December 2014

OCA — Fri, 19 Dec 2014 10:38:00 GMT

←Older revision		Revision as of 10:38, 19 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_3s57\| PDB=3s57 \| SCENE= }}~~	+	==ABH2 cross-linked with undamaged dsDNA-1 containing cofactors==
-	===ABH2 cross-linked with undamaged dsDNA-1 containing cofactors===	+	<StructureSection load='3s57' size='340' side='right' caption='[[3s57]], [[Resolution\|resolution]] 1.60Å' scene=''>
-	~~{{ABSTRACT_PUBMED_22659876}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3s57]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3S57 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3S57 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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=XL3:PROPANE-1-THIOL'>XL3</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3bty\|3bty]], [[3s5a\|3s5a]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ABH2, ALKBH2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</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=3s57 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s57 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3s57 RCSB], [http://www.ebi.ac.uk/pdbsum/3s57 PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	ALKBH2 is a direct DNA repair dioxygenase guarding the mammalian genome against N(1)-methyladenine, N(3)-methylcytosine and 1,N(6)-ethenoadenine damage. A prerequisite for repair is to identify these lesions in the genome. Here we present crystal structures of human ALKBH2 bound to different duplex DNAs. Together with computational and biochemical analyses, our results suggest that DNA interrogation by ALKBH2 has two previously unknown features: (i) ALKBH2 probes base-pair stability and detects base pairs with reduced stability, and (ii) ALKBH2 does not have nor need a damage-checking site, which is critical for preventing spurious base cleavage for several glycosylases. The demethylation mechanism of ALKBH2 insures that only cognate lesions are oxidized and reversed to normal bases, and that a flipped, non-substrate base remains intact in the active site. Overall, the combination of duplex interrogation and oxidation chemistry allows ALKBH2 to detect and process diverse lesions efficiently and correctly.

-	~~==Function==~~	+	Duplex interrogation by a direct DNA repair protein in search of base damage.,Yi C, Chen B, Qi B, Zhang W, Jia G, Zhang L, Li CJ, Dinner AR, Yang CG, He C Nat Struct Mol Biol. 2012 Jun 3;19(7):671-6. doi: 10.1038/nsmb.2320. PMID:22659876<ref>PMID:22659876</ref>
-	~~[[http://www~~.~~uniprot~~.~~org/uniprot/ALKB2_HUMAN ALKB2_HUMAN]] Dioxygenase that repairs alkylated DNA and RNA containing 1-methyladenine and~~ 3~~-methylcytosine by oxidative demethylation. Can also repair alkylated DNA containing 1-ethenoadenine~~ (~~in vitro~~)~~. Has strong preference for double~~-~~stranded DNA~~. ~~Has low efficiency with single-stranded substrates~~. ~~Requires molecular oxygen, alpha-ketoglutarate and iron~~.~~<ref>~~PMID:~~12486230</ref> <ref>PMID:12594517</ref> <ref>PMID:16174769</ref> <ref>PMID:18519673</ref>~~ <ref>PMID:~~18432238~~</ref>	+

-	~~==About this Structure==~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[3s57]] is~~ a ~~3 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Homo_sapiens Homo sapiens]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3S57 OCA].~~	+	</div>

-	==~~Reference~~==	+	==See Also==
-	~~<ref group~~=~~"xtra">PMID:022659876</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	*[[Dioxygenase\|Dioxygenase]]
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
-	[[Category: Chen, B.]]	+	[[Category: Chen, B]]
-	[[Category: Dinner, A R.]]	+	[[Category: Dinner, A R]]
-	[[Category: He, C.]]	+	[[Category: He, C]]
-	[[Category: Jia, G.]]	+	[[Category: Jia, G]]
-	[[Category: Li, C Q.]]	+	[[Category: Li, C Q]]
-	[[Category: Qi, B.]]	+	[[Category: Qi, B]]
-	[[Category: Ramirez, B.]]	+	[[Category: Ramirez, B]]
-	[[Category: Yang, C G.]]	+	[[Category: Yang, C G]]
-	[[Category: Yi, C.]]	+	[[Category: Yi, C]]
-	[[Category: Zhang, L.]]	+	[[Category: Zhang, L]]
-	[[Category: Zhang, W.]]	+	[[Category: Zhang, W]]
	[[Category: Dioxygenase]]		[[Category: Dioxygenase]]
	[[Category: Dsdna binding]]		[[Category: Dsdna binding]]

OCA at 12:42, 3 July 2013

OCA — Wed, 03 Jul 2013 12:42:30 GMT

←Older revision		Revision as of 12:42, 3 July 2013
Line 1:		Line 1:
-	[[Image:3s57.jpg\|left\|200px]]
-
-	<!--
-	The line below this paragraph, containing "STRUCTURE_3s57", 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_3s57\| PDB=3s57 \| SCENE= }}		{{STRUCTURE_3s57\| PDB=3s57 \| SCENE= }}
-
	===ABH2 cross-linked with undamaged dsDNA-1 containing cofactors===		===ABH2 cross-linked with undamaged dsDNA-1 containing cofactors===
		+	{{ABSTRACT_PUBMED_22659876}}

		+	==Function==
		+	[[http://www.uniprot.org/uniprot/ALKB2_HUMAN ALKB2_HUMAN]] Dioxygenase that repairs alkylated DNA and RNA containing 1-methyladenine and 3-methylcytosine by oxidative demethylation. Can also repair alkylated DNA containing 1-ethenoadenine (in vitro). Has strong preference for double-stranded DNA. Has low efficiency with single-stranded substrates. Requires molecular oxygen, alpha-ketoglutarate and iron.<ref>PMID:12486230</ref> <ref>PMID:12594517</ref> <ref>PMID:16174769</ref> <ref>PMID:18519673</ref> <ref>PMID:18432238</ref>

	==About this Structure==		==About this Structure==
	[[3s57]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3S57 OCA].		[[3s57]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3S57 OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:022659876</ref><references group="xtra"/><references/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Chen, B.]]		[[Category: Chen, B.]]

OCA at 07:49, 6 June 2012

OCA — Wed, 06 Jun 2012 07:49:30 GMT

←Older revision		Revision as of 07:49, 6 June 2012
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:3s57.jpg\|left\|200px]]

-	The ~~entry 3s57~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3s57", 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_3s57\| PDB=3s57 \| SCENE= }}

-	~~Authors: Yi, C., Chen, B., Qi, B., Ramirez, B., Zhang, W., Jia, G., Zhang, L., Li, C.Q., Dinner, A.R., Yang, C.~~-~~G., He, C.~~	+	===ABH2 cross-linked with undamaged dsDNA-1 containing cofactors===

-	~~Description~~: ~~ABH2 cross~~-~~linked with undamaged dsDNA~~-~~1 containing cofactors~~	+
		+	==About this Structure==
		+	[[3s57]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3S57 OCA].
		+	[[Category: Homo sapiens]]
		+	[[Category: Chen, B.]]
		+	[[Category: Dinner, A R.]]
		+	[[Category: He, C.]]
		+	[[Category: Jia, G.]]
		+	[[Category: Li, C Q.]]
		+	[[Category: Qi, B.]]
		+	[[Category: Ramirez, B.]]
		+	[[Category: Yang, C G.]]
		+	[[Category: Yi, C.]]
		+	[[Category: Zhang, L.]]
		+	[[Category: Zhang, W.]]
		+	[[Category: Dioxygenase]]
		+	[[Category: Dsdna binding]]
		+	[[Category: Jelly-roll fold]]
		+	[[Category: Oxidoreductase-dna complex]]
		+	[[Category: Plasma]]
		+	[[Category: Protein-dna complex]]

OCA at 18:23, 6 July 2011

OCA — Wed, 06 Jul 2011 18:23:35 GMT

←Older revision		Revision as of 18:23, 6 July 2011
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3s57 is ON HOLD	+	The entry 3s57 is ON HOLD until Paper Publication

	Authors: Yi, C., Chen, B., Qi, B., Ramirez, B., Zhang, W., Jia, G., Zhang, L., Li, C.Q., Dinner, A.R., Yang, C.-G., He, C.		Authors: Yi, C., Chen, B., Qi, B., Ramirez, B., Zhang, W., Jia, G., Zhang, L., Li, C.Q., Dinner, A.R., Yang, C.-G., He, C.

	Description: ABH2 cross-linked with undamaged dsDNA-1 containing cofactors		Description: ABH2 cross-linked with undamaged dsDNA-1 containing cofactors

OCA at 05:54, 15 June 2011

OCA — Wed, 15 Jun 2011 05:54:23 GMT

←Older revision		Revision as of 05:54, 15 June 2011
Line 3:		Line 3:
	The entry 3s57 is ON HOLD		The entry 3s57 is ON HOLD

-	Authors: Yi, C., Chen, B., Qi, B., Ramirez, B., Zhang, W., Jia, G., Zhang, L., Li, C. Q., Dinner, A.R., Yang, C.-G., He, C.	+	Authors: Yi, C., Chen, B., Qi, B., Ramirez, B., Zhang, W., Jia, G., Zhang, L., Li, C.Q., Dinner, A.R., Yang, C.-G., He, C.

	Description: ABH2 cross-linked with undamaged dsDNA-1 containing cofactors		Description: ABH2 cross-linked with undamaged dsDNA-1 containing cofactors

OCA: Protected "3s57" [edit=sysop:move=sysop]

OCA — Wed, 01 Jun 2011 05:26:45 GMT

Protected "3s57" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:26, 1 June 2011