3bkz - Revision history

OCA at 18:58, 20 October 2021

2021-10-20T18:58:44Z

←Older revision		Revision as of 18:58, 20 October 2021
Line 1:		Line 1:

	==X-ray structure of E coli AlkB crosslinked to dsDNA in the active site==		==X-ray structure of E coli AlkB crosslinked to dsDNA in the active site==
-	<StructureSection load='3bkz' size='340' side='right' caption='[[3bkz]], [[Resolution\|resolution]] 1.65Å' scene=''>	+	<StructureSection load='3bkz' size='340' side='right'caption='[[3bkz]], [[Resolution\|resolution]] 1.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3bkz]] is a 3 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=3BKZ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3BKZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3bkz]] is a 3 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=3BKZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BKZ 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=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></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></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2fd8\|2fd8]], [[2qxq\|2qxq]]</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]], [[2qxq\|2qxq]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">alkB, aidD ([~~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">alkB, aidD ([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=3bkz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bkz OCA], [~~http~~://pdbe.org/3bkz PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3bkz RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3bkz PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3bkz 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=3bkz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bkz OCA], [https://pdbe.org/3bkz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3bkz RCSB], [https://www.ebi.ac.uk/pdbsum/3bkz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3bkz 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>
	== 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: Ecoli]]		[[Category: Ecoli]]
		+	[[Category: Large Structures]]
	[[Category: He, C]]		[[Category: He, C]]
	[[Category: Yang, C G]]		[[Category: Yang, C G]]

OCA at 07:38, 31 October 2018

2018-10-31T07:38:10Z

←Older revision		Revision as of 07:38, 31 October 2018
Line 1:		Line 1:
		+
	==X-ray structure of E coli AlkB crosslinked to dsDNA in the active site==		==X-ray structure of E coli AlkB crosslinked to dsDNA in the active site==
	<StructureSection load='3bkz' size='340' side='right' caption='[[3bkz]], [[Resolution\|resolution]] 1.65Å' scene=''>		<StructureSection load='3bkz' size='340' side='right' caption='[[3bkz]], [[Resolution\|resolution]] 1.65Å' scene=''>
Line 7:		Line 8:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2fd8\|2fd8]], [[2qxq\|2qxq]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2fd8\|2fd8]], [[2qxq\|2qxq]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">alkB, aidD ([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">alkB, aidD ([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=3bkz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bkz OCA], [http://pdbe.org/3bkz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3bkz RCSB], [http://www.ebi.ac.uk/pdbsum/3bkz 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=3bkz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bkz OCA], [http://pdbe.org/3bkz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3bkz RCSB], [http://www.ebi.ac.uk/pdbsum/3bkz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3bkz 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/bk/3bkz_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bk/3bkz_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 18:02, 8 February 2016

2016-02-08T18:02:04Z

←Older revision		Revision as of 18:02, 8 February 2016
Line 7:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2fd8\|2fd8]], [[2qxq\|2qxq]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2fd8\|2fd8]], [[2qxq\|2qxq]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">alkB, aidD ([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">alkB, aidD ([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=3bkz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bkz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3bkz RCSB], [http://www.ebi.ac.uk/pdbsum/3bkz 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=3bkz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bkz OCA], [http://pdbe.org/3bkz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3bkz RCSB], [http://www.ebi.ac.uk/pdbsum/3bkz 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=3bkz 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 3bkz" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==

OCA at 01:10, 25 December 2014

2014-12-25T01:10:57Z

←Older revision		Revision as of 01:10, 25 December 2014
Line 9:		Line 9:
	<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=3bkz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bkz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3bkz RCSB], [http://www.ebi.ac.uk/pdbsum/3bkz 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=3bkz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bkz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3bkz RCSB], [http://www.ebi.ac.uk/pdbsum/3bkz 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>
	== 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: Ecoli]]		[[Category: Ecoli]]
-	[[Category: He, C.]]	+	[[Category: He, C]]
-	[[Category: Yang, C G.]]	+	[[Category: Yang, C G]]
-	[[Category: Yi, C.]]	+	[[Category: Yi, C]]
	[[Category: Alkylation repair]]		[[Category: Alkylation repair]]
	[[Category: Cross-linking]]		[[Category: Cross-linking]]

OCA at 06:27, 10 October 2014

2014-10-10T06:27:10Z

←Older revision		Revision as of 06:27, 10 October 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3bkz]] is a 3 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=3BKZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3BKZ FirstGlance]. <br>		<table><tr><td colspan='2'>[[3bkz]] is a 3 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=3BKZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3BKZ 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></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></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2fd8\|2fd8]], [[2qxq\|2qxq]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2fd8\|2fd8]], [[2qxq\|2qxq]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">alkB, aidD ([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">alkB, aidD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=3bkz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bkz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3bkz RCSB], [http://www.ebi.ac.uk/pdbsum/3bkz 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=3bkz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bkz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3bkz RCSB], [http://www.ebi.ac.uk/pdbsum/3bkz PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 25:		Line 25:
	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 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>

-	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>
		+
		+	==See Also==
		+	*[[Dioxygenase\|Dioxygenase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 07:14, 28 May 2014

2014-05-28T07:14:37Z

←Older revision		Revision as of 07:14, 28 May 2014
Line 1:		Line 1:
-	[[~~Image:~~3bkz.~~png~~\|~~left~~\|200px]]	+	==X-ray structure of E coli AlkB crosslinked to dsDNA in the active site==
		+	<StructureSection load='3bkz' size='340' side='right' caption='[[3bkz]], [[Resolution\|resolution]] 1.65Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3bkz]] is a 3 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=3BKZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3BKZ 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></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2fd8\|2fd8]], [[2qxq\|2qxq]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">alkB, aidD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=3bkz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bkz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3bkz RCSB], [http://www.ebi.ac.uk/pdbsum/3bkz 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/bk/3bkz_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_3bkz\| PDB=3bkz \| 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>

-	~~===X-ray structure~~ of ~~E coli AlkB crosslinked to dsDNA in~~ the ~~active site===~~	+	From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_18432238}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[3bkz]] is a 3 chain structure with sequence from [http://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=3BKZ OCA].~~	+	</StructureSection>
-		+	[[Category: Ecoli]]
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:018432238<~~/~~ref~~><~~references group="xtra"~~/>	+
-	[[Category: ~~Escherichia coli k-12~~]]	+
	[[Category: He, C.]]		[[Category: He, C.]]
	[[Category: Yang, C G.]]		[[Category: Yang, C G.]]

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

2013-01-07T21:19:08Z

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

←Older revision

Revision as of 21:19, 7 January 2013

OCA at 21:19, 7 January 2013

2013-01-07T21:19:03Z

←Older revision		Revision as of 21:19, 7 January 2013
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-	{{Seed}}
	[[Image:3bkz.png\|left\|200px]]		[[Image:3bkz.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3bkz", 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_3bkz\| PDB=3bkz \| SCENE= }}		{{STRUCTURE_3bkz\| PDB=3bkz \| SCENE= }}

	===X-ray structure of E coli AlkB crosslinked to dsDNA in the active site===		===X-ray structure of E coli AlkB crosslinked to dsDNA in the 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==
-	~~3BKZ~~ is a 3 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/~~Escherichia_coli_k12~~ Escherichia coli ~~k12~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BKZ OCA].	+	[[3bkz]] is a 3 chain structure with sequence from [http://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=3BKZ OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~18432238~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:018432238</ref><references group="xtra"/>
-	[[Category: Escherichia coli ~~k12~~]]	+	[[Category: Escherichia coli k-12]]
	[[Category: He, C.]]		[[Category: He, C.]]
	[[Category: Yang, C G.]]		[[Category: Yang, C G.]]
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	[[Category: Dioxygenase]]		[[Category: Dioxygenase]]
	[[Category: Dna repair]]		[[Category: Dna repair]]
-	[[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 00:58:53 2009''

OCA at 22:58, 16 February 2009

2009-02-16T22:58:54Z

←Older revision		Revision as of 22:58, 16 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	3BKZ is a ~~[[Protein complex]]~~ structure of sequences from [http://en.wikipedia.org/wiki/Escherichia_coli_k12 Escherichia coli k12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BKZ OCA].	+	3BKZ is a 3 chains structure of sequences from [http://en.wikipedia.org/wiki/Escherichia_coli_k12 Escherichia coli k12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BKZ 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: Escherichia coli k12]]		[[Category: Escherichia coli k12]]
-	[[Category: Protein complex]]
	[[Category: He, C.]]		[[Category: He, C.]]
	[[Category: Yang, C G.]]		[[Category: Yang, C G.]]
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	[[Category: Protein dna interaction]]		[[Category: Protein dna interaction]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Wed Jul 23 10~~:13:~~18 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 00:58:53 2009''

OCA at 07:13, 23 July 2008

2008-07-23T07:13:19Z

←Older revision		Revision as of 07:13, 23 July 2008
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-	[[Image:3bkz.~~jpg~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:3bkz.png\|left\|200px]]

	<!--		<!--
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	{{STRUCTURE_3bkz\| PDB=3bkz \| SCENE= }}		{{STRUCTURE_3bkz\| PDB=3bkz \| SCENE= }}

-	~~'''~~X-ray structure of E coli AlkB crosslinked to dsDNA in the active site~~'''~~	+	===X-ray structure of E coli AlkB crosslinked to dsDNA in the 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}}

	==About this Structure==		==About this Structure==
-	3BKZ is a [[Protein complex]] structure of sequences 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=3BKZ OCA].	+	3BKZ is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Escherichia_coli_k12 Escherichia coli k12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BKZ OCA].
-	[[Category: Escherichia coli]]	+
		+	==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: Escherichia coli k12]]
	[[Category: Protein complex]]		[[Category: Protein complex]]
	[[Category: He, C.]]		[[Category: He, C.]]
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	[[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~~:48:43 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul 23 10:13:18 2008''