3bty - Revision history

OCA at 19:02, 20 October 2021

2021-10-20T19:02:23Z

←Older revision		Revision as of 19:02, 20 October 2021
Line 1:		Line 1:

	==Crystal structure of human ABH2 bound to dsDNA containing 1meA through cross-linking away from active site==		==Crystal structure of human ABH2 bound to dsDNA containing 1meA through cross-linking away from active site==
-	<StructureSection load='3bty' size='340' side='right' caption='[[3bty]], [[Resolution\|resolution]] 2.35Å' scene=''>	+	<StructureSection load='3bty' size='340' side='right'caption='[[3bty]], [[Resolution\|resolution]] 2.35Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3bty]] 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=3BTY OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3BTY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3bty]] 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=3BTY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BTY FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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=XL3:PROPANE-1-THIOL'>XL3</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MA7:1N-METHYLADENOSINE-5-MONOPHOSPHATE'>MA7</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MA7:1N-METHYLADENOSINE-5-MONOPHOSPHATE'>MA7</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2fd8\|2fd8]], [[2iuw\|2iuw]], [[3btx\|3btx]], [[3btz\|3btz]], [[3bu0\|3bu0]], [[3buc\|3buc]]</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]], [[2iuw\|2iuw]], [[3btx\|3btx]], [[3btz\|3btz]], [[3bu0\|3bu0]], [[3buc\|3buc]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ALKBH2, ABH2 ([~~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">ALKBH2, ABH2 ([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=3bty FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bty OCA], [~~http~~://pdbe.org/3bty PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3bty RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3bty PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3bty 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=3bty FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bty OCA], [https://pdbe.org/3bty PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3bty RCSB], [https://www.ebi.ac.uk/pdbsum/3bty PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3bty 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>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 33:		Line 33:

	==See Also==		==See Also==
-	*[[Dioxygenase\|Dioxygenase]]	+	*[[Dioxygenase 3D structures\|Dioxygenase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 39:		Line 39:
	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: He, C]]		[[Category: He, C]]
	[[Category: Yang, C G]]		[[Category: Yang, C G]]

OCA at 07:52, 31 October 2018

2018-10-31T07:52:23Z

←Older revision		Revision as of 07:52, 31 October 2018
Line 1:		Line 1:
		+
	==Crystal structure of human ABH2 bound to dsDNA containing 1meA through cross-linking away from active site==		==Crystal structure of human ABH2 bound to dsDNA containing 1meA through cross-linking away from active site==
	<StructureSection load='3bty' size='340' side='right' caption='[[3bty]], [[Resolution\|resolution]] 2.35Å' scene=''>		<StructureSection load='3bty' size='340' side='right' caption='[[3bty]], [[Resolution\|resolution]] 2.35Å' scene=''>
Line 7:		Line 8:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2fd8\|2fd8]], [[2iuw\|2iuw]], [[3btx\|3btx]], [[3btz\|3btz]], [[3bu0\|3bu0]], [[3buc\|3buc]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2fd8\|2fd8]], [[2iuw\|2iuw]], [[3btx\|3btx]], [[3btz\|3btz]], [[3bu0\|3bu0]], [[3buc\|3buc]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ALKBH2, ABH2 ([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">ALKBH2, ABH2 ([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=3bty FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bty OCA], [http://pdbe.org/3bty PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3bty RCSB], [http://www.ebi.ac.uk/pdbsum/3bty 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=3bty FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bty OCA], [http://pdbe.org/3bty PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3bty RCSB], [http://www.ebi.ac.uk/pdbsum/3bty PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3bty ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 15:		Line 16:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bt/3bty_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bt/3bty_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>

OCA at 07:47, 9 February 2016

2016-02-09T07:47:25Z

←Older revision		Revision as of 07:47, 9 February 2016
Line 2:		Line 2:
	<StructureSection load='3bty' size='340' side='right' caption='[[3bty]], [[Resolution\|resolution]] 2.35Å' scene=''>		<StructureSection load='3bty' size='340' side='right' caption='[[3bty]], [[Resolution\|resolution]] 2.35Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3bty]] 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=3BTY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3BTY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3bty]] 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=3BTY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3BTY FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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=XL3:PROPANE-1-THIOL'>XL3</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MA7:1N-METHYLADENOSINE-5-MONOPHOSPHATE'>MA7</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MA7:1N-METHYLADENOSINE-5-MONOPHOSPHATE'>MA7</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2fd8\|2fd8]], [[2iuw\|2iuw]], [[3btx\|3btx]], [[3btz\|3btz]], [[3bu0\|3bu0]], [[3buc\|3buc]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2fd8\|2fd8]], [[2iuw\|2iuw]], [[3btx\|3btx]], [[3btz\|3btz]], [[3bu0\|3bu0]], [[3buc\|3buc]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ALKBH2, ABH2 ([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">ALKBH2, ABH2 ([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=3bty FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bty OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3bty RCSB], [http://www.ebi.ac.uk/pdbsum/3bty 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=3bty FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bty OCA], [http://pdbe.org/3bty PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3bty RCSB], [http://www.ebi.ac.uk/pdbsum/3bty PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 19:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3bty ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 29:		Line 29:
	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 3bty" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 36:		Line 37:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Homo sapiens~~]]	+	[[Category: Human]]
	[[Category: He, C]]		[[Category: He, C]]
	[[Category: Yang, C G]]		[[Category: Yang, C G]]

OCA at 05:29, 25 December 2014

2014-12-25T05:29:04Z

←Older revision		Revision as of 05:29, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3bty]] 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=3BTY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3BTY FirstGlance]. <br>		<table><tr><td colspan='2'>[[3bty]] 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=3BTY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3BTY FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=XL3:PROPANE-1-THIOL'>XL3</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=XL3:PROPANE-1-THIOL'>XL3</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MA7:1N-METHYLADENOSINE-5-MONOPHOSPHATE'>MA7</scene></td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MA7:1N-METHYLADENOSINE-5-MONOPHOSPHATE'>MA7</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2fd8\|2fd8]], [[2iuw\|2iuw]], [[3btx\|3btx]], [[3btz\|3btz]], [[3bu0\|3bu0]], [[3buc\|3buc]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2fd8\|2fd8]], [[2iuw\|2iuw]], [[3btx\|3btx]], [[3btz\|3btz]], [[3bu0\|3bu0]], [[3buc\|3buc]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ALKBH2, ABH2 ([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">ALKBH2, ABH2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</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=3bty FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bty OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3bty RCSB], [http://www.ebi.ac.uk/pdbsum/3bty 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=3bty FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bty OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3bty RCSB], [http://www.ebi.ac.uk/pdbsum/3bty 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>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 37:
	</StructureSection>		</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
-	[[Category: He, C.]]	+	[[Category: He, C]]
-	[[Category: Yang, C G.]]	+	[[Category: Yang, C G]]
-	[[Category: Yi, C.]]	+	[[Category: Yi, C]]
	[[Category: Cross-linking]]		[[Category: Cross-linking]]
	[[Category: Dna damage]]		[[Category: Dna damage]]

OCA at 21:07, 2 October 2014

2014-10-02T21:07:17Z

←Older revision		Revision as of 21:07, 2 October 2014
Line 1:		Line 1:
-	[[~~Image:~~3bty.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of human ABH2 bound to dsDNA containing 1meA through cross-linking away from active site==
		+	<StructureSection load='3bty' size='340' side='right' caption='[[3bty]], [[Resolution\|resolution]] 2.35Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3bty]] 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=3BTY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3BTY FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=XL3:PROPANE-1-THIOL'>XL3</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MA7:1N-METHYLADENOSINE-5-MONOPHOSPHATE'>MA7</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2fd8\|2fd8]], [[2iuw\|2iuw]], [[3btx\|3btx]], [[3btz\|3btz]], [[3bu0\|3bu0]], [[3buc\|3buc]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ALKBH2, ABH2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</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=3bty FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bty OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3bty RCSB], [http://www.ebi.ac.uk/pdbsum/3bty PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bt/3bty_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Escherichia coli AlkB and its human homologues ABH2 and ABH3 repair DNA/RNA base lesions by using a direct oxidative dealkylation mechanism. ABH2 has the primary role of guarding mammalian genomes against 1-meA damage by repairing this lesion in double-stranded DNA (dsDNA), whereas AlkB and ABH3 preferentially repair single-stranded DNA (ssDNA) lesions and can repair damaged bases in RNA. Here we show the first crystal structures of AlkB-dsDNA and ABH2-dsDNA complexes, stabilized by a chemical cross-linking strategy. This study reveals that AlkB uses an unprecedented base-flipping mechanism to access the damaged base: it squeezes together the two bases flanking the flipped-out one to maintain the base stack, explaining the preference of AlkB for repairing ssDNA lesions over dsDNA ones. In addition, the first crystal structure of ABH2, presented here, provides a structural basis for designing inhibitors of this human DNA repair protein.

-	~~{{STRUCTURE_3bty\| PDB=3bty \| SCENE= }}~~	+	Crystal structures of DNA/RNA repair enzymes AlkB and ABH2 bound to dsDNA.,Yang CG, Yi C, Duguid EM, Sullivan CT, Jian X, Rice PA, He C Nature. 2008 Apr 24;452(7190):961-5. PMID:18432238<ref>PMID:18432238</ref>

-	~~===Crystal structure~~ of ~~human ABH2 bound to dsDNA containing 1meA through cross-linking away from active site===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

-	~~{{ABSTRACT_PUBMED_18432238}}~~	+	==See Also==
-		+	*[[Dioxygenase\|Dioxygenase]]
-	==~~About this Structure~~==	+	== References ==
-	[[~~3bty~~]] 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=3BTY OCA].	+	<references/>
-		+	__TOC__
-	==~~Reference~~==	+	</StructureSection>
-	<~~ref group="xtra">PMID:018432238<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: He, C.]]		[[Category: He, C.]]

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

2013-01-07T21:27:00Z

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

←Older revision

Revision as of 21:27, 7 January 2013

OCA at 21:26, 7 January 2013

2013-01-07T21:26:56Z

←Older revision		Revision as of 21:26, 7 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:3bty.png\|left\|200px]]		[[Image:3bty.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3bty", 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_3bty\| PDB=3bty \| SCENE= }}		{{STRUCTURE_3bty\| PDB=3bty \| SCENE= }}

	===Crystal structure of human ABH2 bound to dsDNA containing 1meA through cross-linking away from active site===		===Crystal structure of human ABH2 bound to dsDNA containing 1meA through cross-linking away from active site===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_18432238}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 18432238 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_18432238}}		{{ABSTRACT_PUBMED_18432238}}

	==About this Structure==		==About this Structure==
-	~~3BTY~~ is a 3 ~~chains~~ structure ~~of sequences~~ 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=3BTY OCA].	+	[[3bty]] 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=3BTY OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~18432238~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:018432238</ref><references group="xtra"/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: He, C.]]		[[Category: He, C.]]
Line 36:		Line 24:
	[[Category: Nucleus]]		[[Category: Nucleus]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
-	[[Category: Oxidoreductase/dna complex]]	+	[[Category: Oxidoreductase-dna complex]]
	[[Category: Protein/dna interaction]]		[[Category: Protein/dna interaction]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 08:05:44 2009''

OCA at 06:05, 17 February 2009

2009-02-17T06:05:45Z

←Older revision		Revision as of 06:05, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	3BTY is a ~~[[Protein complex]]~~ structure of sequences 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=3BTY OCA].	+	3BTY is a 3 chains structure of sequences 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=3BTY OCA].

	==Reference==		==Reference==
-	~~Crystal structures of DNA/RNA repair enzymes AlkB and ABH2 bound to dsDNA., Yang CG, Yi C, Duguid EM, Sullivan CT, Jian X, Rice PA, He C, Nature. 2008 Apr 24;452(7190):961-5.~~ PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/18432238 18432238]~~	+	<ref group="xtra">PMID:18432238</ref><references group="xtra"/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
-	[[Category: Protein complex]]
	[[Category: He, C.]]		[[Category: He, C.]]
	[[Category: Yang, C G.]]		[[Category: Yang, C G.]]
Line 40:		Line 39:
	[[Category: Protein/dna interaction]]		[[Category: Protein/dna interaction]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Mon Jul 28 11~~:28:~~17 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 08:05:44 2009''

OCA at 08:28, 28 July 2008

2008-07-28T08:28:19Z

←Older revision		Revision as of 08:28, 28 July 2008
Line 1:		Line 1:
-	[[Image:3bty.~~jpg~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:3bty.png\|left\|200px]]

	<!--		<!--
Line 9:		Line 10:
	{{STRUCTURE_3bty\| PDB=3bty \| SCENE= }}		{{STRUCTURE_3bty\| PDB=3bty \| SCENE= }}

-	~~'''~~Crystal structure of human ABH2 bound to dsDNA containing 1meA through cross-linking away from active site~~'''~~	+	===Crystal structure of human ABH2 bound to dsDNA containing 1meA through cross-linking away from active site===


-	~~==Overview==~~	+	<!--
-	Escherichia coli AlkB and its human homologues ABH2 and ABH3 repair DNA/RNA base lesions by using a direct oxidative dealkylation mechanism. ABH2 has the primary role of guarding mammalian genomes against 1-meA damage by repairing this ~~lesion in double-stranded DNA (dsDNA)~~, ~~whereas AlkB and ABH3 preferentially repair single-stranded DNA (ssDNA) lesions and can repair damaged bases in RNA. Here we show~~ the ~~first crystal structures of AlkB-dsDNA and ABH2-dsDNA complexes, stabilized by a chemical cross-linking strategy. This study reveals that AlkB uses an unprecedented base-flipping mechanism~~ to ~~access~~ the ~~damaged base~~: ~~it squeezes together the two bases flanking the flipped-out one to maintain the base stack, explaining the preference of AlkB for repairing ssDNA lesions over dsDNA ones~~. ~~In addition~~, the ~~first crystal structure of ABH2, presented here, provides a structural basis for designing inhibitors of this human DNA repair protein~~.	+	The line below this paragraph, {{ABSTRACT_PUBMED_18432238}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 18432238 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_18432238}}

	==About this Structure==		==About this Structure==
Line 35:		Line 39:
	[[Category: Oxidoreductase/dna complex]]		[[Category: Oxidoreductase/dna complex]]
	[[Category: Protein/dna interaction]]		[[Category: Protein/dna interaction]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Wed Jun~~ 11 10:57:25 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 11:28:17 2008''

OCA at 07:57, 11 June 2008

2008-06-11T07:57:26Z

←Older revision		Revision as of 07:57, 11 June 2008
Line 11:		Line 11:
	'''Crystal structure of human ABH2 bound to dsDNA containing 1meA through cross-linking away from active site'''		'''Crystal structure of human ABH2 bound to dsDNA containing 1meA through cross-linking away from active site'''

		+
		+	==Overview==
		+	Escherichia coli AlkB and its human homologues ABH2 and ABH3 repair DNA/RNA base lesions by using a direct oxidative dealkylation mechanism. ABH2 has the primary role of guarding mammalian genomes against 1-meA damage by repairing this lesion in double-stranded DNA (dsDNA), whereas AlkB and ABH3 preferentially repair single-stranded DNA (ssDNA) lesions and can repair damaged bases in RNA. Here we show the first crystal structures of AlkB-dsDNA and ABH2-dsDNA complexes, stabilized by a chemical cross-linking strategy. This study reveals that AlkB uses an unprecedented base-flipping mechanism to access the damaged base: it squeezes together the two bases flanking the flipped-out one to maintain the base stack, explaining the preference of AlkB for repairing ssDNA lesions over dsDNA ones. In addition, the first crystal structure of ABH2, presented here, provides a structural basis for designing inhibitors of this human DNA repair protein.

	==About this Structure==		==About this Structure==
	3BTY is a [[Protein complex]] structure of sequences 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=3BTY OCA].		3BTY is a [[Protein complex]] structure of sequences 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=3BTY OCA].
		+
		+	==Reference==
		+	Crystal structures of DNA/RNA repair enzymes AlkB and ABH2 bound to dsDNA., Yang CG, Yi C, Duguid EM, Sullivan CT, Jian X, Rice PA, He C, Nature. 2008 Apr 24;452(7190):961-5. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18432238 18432238]
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Protein complex]]		[[Category: Protein complex]]
Line 29:		Line 35:
	[[Category: Oxidoreductase/dna complex]]		[[Category: Oxidoreductase/dna complex]]
	[[Category: Protein/dna interaction]]		[[Category: Protein/dna interaction]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Thu Apr 24 09~~:49:18 2008''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jun 11 10:57:25 2008''