1lkd - Revision history

OCA at 07:33, 14 February 2024

OCA — Wed, 14 Feb 2024 07:33:45 GMT

←Older revision		Revision as of 07:33, 14 February 2024
Line 3:		Line 3:
	<StructureSection load='1lkd' size='340' side='right'caption='[[1lkd]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='1lkd' size='340' side='right'caption='[[1lkd]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1lkd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Burkholderia_cepacia_lb400 Burkholderia cepacia lb400~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LKD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1LKD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1lkd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Paraburkholderia_xenovorans_LB400 Paraburkholderia xenovorans LB400]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LKD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1LKD FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=BP6:2,6~~-~~DICHLORO-BIPHENYL-2~~,~~6-DIOL'>BP6</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=P6G:HEXAETHYLENE+GLYCOL'>P6G</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]] 1.7Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max~~-~~height: 3em;~~'>~~[[1lgt\|1lgt]], [[1han\|1han]], [[1kmy\|1kmy]], [[1knd\|1knd]], [[1knf\|1knf]]~~</~~div~~><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BP6:2,6-DICHLORO-BIPHENYL-2,6-DIOL'>BP6</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=P6G:HEXAETHYLENE+GLYCOL'>P6G</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[https://en.wikipedia.org/wiki/Biphenyl-2,3-diol_1,2-dioxygenase Biphenyl-2,3-diol 1,2-dioxygenase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.39 1.13.11.39]~~ </~~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=1lkd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lkd OCA], [https://pdbe.org/1lkd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1lkd RCSB], [https://www.ebi.ac.uk/pdbsum/1lkd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1lkd 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=1lkd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lkd OCA], [https://pdbe.org/1lkd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1lkd RCSB], [https://www.ebi.ac.uk/pdbsum/1lkd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1lkd ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/~~BPHC_BURXL BPHC_BURXL]~~] Shows a preference for catechols with groups immediately adjacent to the hydroxyl substituents.	+	[https://www.uniprot.org/uniprot/BPHC_PARXL BPHC_PARXL] Shows a preference for catechols with groups immediately adjacent to the hydroxyl substituents.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 21:		Line 20:
	</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=1lkd 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=1lkd ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The microbial degradation of polychlorinated biphenyls (PCBs) provides the potential to destroy these widespread, toxic and persistent environmental pollutants. For example, the four-step upper bph pathway transforms some of the more than 100 different PCBs found in commercial mixtures and is being engineered for more effective PCB degradation. In the critical third step of this pathway, 2,3-dihydroxybiphenyl (DHB) 1,2-dioxygenase (DHBD; EC 1.13.11.39) catalyzes aromatic ring cleavage. Here we demonstrate that ortho-chlorinated PCB metabolites strongly inhibit DHBD, promote its suicide inactivation and interfere with the degradation of other compounds. For example, k(cat)(app) for 2',6'-diCl DHB was reduced by a factor of approximately 7,000 relative to DHB, and it bound with sufficient affinity to competitively inhibit DHB cleavage at nanomolar concentrations. Crystal structures of two complexes of DHBD with ortho-chlorinated metabolites at 1.7 A resolution reveal an explanation for these phenomena, which have important implications for bioremediation strategies.
-
-	Identification and analysis of a bottleneck in PCB biodegradation.,Dai S, Vaillancourt FH, Maaroufi H, Drouin NM, Neau DB, Snieckus V, Bolin JT, Eltis LD Nat Struct Biol. 2002 Dec;9(12):934-9. PMID:12415290<ref>PMID:12415290</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1lkd" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Dioxygenase 3D structures\|Dioxygenase 3D structures]]		*[[Dioxygenase 3D structures\|Dioxygenase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Biphenyl-2,3-diol 1,2-dioxygenase]]
-	[[Category: Burkholderia cepacia lb400]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Bolin, J T~~]]	+	[[Category: Paraburkholderia xenovorans LB400]]
-	[[Category: ~~Dai, S~~]]	+	[[Category: Bolin JT]]
-	[[Category: ~~3-dihydroxybiphenyl]]~~	+	[[Category: Dai S]]
-	~~[[Category: Anaerobic]]~~	+
-	~~[[Category: Extradiol dioxygenase]]~~	+
-	~~[[Category: Non-heme iron]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Pcb biodegradation~~]]	+

OCA at 06:45, 18 August 2021

OCA — Wed, 18 Aug 2021 06:45:48 GMT

←Older revision		Revision as of 06:45, 18 August 2021
Line 3:		Line 3:
	<StructureSection load='1lkd' size='340' side='right'caption='[[1lkd]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='1lkd' size='340' side='right'caption='[[1lkd]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1lkd]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Burkholderia_cepacia_lb400 Burkholderia cepacia lb400]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LKD OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1LKD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1lkd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Burkholderia_cepacia_lb400 Burkholderia cepacia lb400]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LKD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1LKD FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BP6:2,6-DICHLORO-BIPHENYL-2,6-DIOL'>BP6</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=P6G:HEXAETHYLENE+GLYCOL'>P6G</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BP6:2,6-DICHLORO-BIPHENYL-2,6-DIOL'>BP6</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=P6G:HEXAETHYLENE+GLYCOL'>P6G</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1lgt\|1lgt]], [[1han\|1han]], [[1kmy\|1kmy]], [[1knd\|1knd]], [[1knf\|1knf]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1lgt\|1lgt]], [[1han\|1han]], [[1kmy\|1kmy]], [[1knd\|1knd]], [[1knf\|1knf]]</div></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Biphenyl-2,3-diol_1,2-dioxygenase Biphenyl-2,3-diol 1,2-dioxygenase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.39 1.13.11.39] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Biphenyl-2,3-diol_1,2-dioxygenase Biphenyl-2,3-diol 1,2-dioxygenase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.39 1.13.11.39] </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=1lkd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lkd OCA], [~~http~~://pdbe.org/1lkd PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1lkd RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1lkd PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1lkd 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=1lkd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lkd OCA], [https://pdbe.org/1lkd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1lkd RCSB], [https://www.ebi.ac.uk/pdbsum/1lkd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1lkd ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/BPHC_BURXL BPHC_BURXL]] Shows a preference for catechols with groups immediately adjacent to the hydroxyl substituents.	+	[[https://www.uniprot.org/uniprot/BPHC_BURXL BPHC_BURXL]] Shows a preference for catechols with groups immediately adjacent to the hydroxyl substituents.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 12:06, 13 November 2019

OCA — Wed, 13 Nov 2019 12:06:43 GMT

←Older revision		Revision as of 12:06, 13 November 2019
Line 1:		Line 1:

	==CRYSTAL STRUCTURE OF 2,3-DIHYDROXYBIPHENYL 1,2-DIOXYGENASE (DHBD) COMPLEXED WITH 2',6'-DICL DIHYDROXYBIPHENYL (DHB)==		==CRYSTAL STRUCTURE OF 2,3-DIHYDROXYBIPHENYL 1,2-DIOXYGENASE (DHBD) COMPLEXED WITH 2',6'-DICL DIHYDROXYBIPHENYL (DHB)==
-	<StructureSection load='1lkd' size='340' side='right' caption='[[1lkd]], [[Resolution\|resolution]] 1.70Å' scene=''>	+	<StructureSection load='1lkd' size='340' side='right'caption='[[1lkd]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1lkd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Burkholderia_cepacia_lb400 Burkholderia cepacia lb400]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LKD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LKD FirstGlance]. <br>		<table><tr><td colspan='2'>[[1lkd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Burkholderia_cepacia_lb400 Burkholderia cepacia lb400]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LKD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LKD FirstGlance]. <br>
Line 30:		Line 30:
	</div>		</div>
	<div class="pdbe-citations 1lkd" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1lkd" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Dioxygenase 3D structures\|Dioxygenase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 36:		Line 39:
	[[Category: Biphenyl-2,3-diol 1,2-dioxygenase]]		[[Category: Biphenyl-2,3-diol 1,2-dioxygenase]]
	[[Category: Burkholderia cepacia lb400]]		[[Category: Burkholderia cepacia lb400]]
		+	[[Category: Large Structures]]
	[[Category: Bolin, J T]]		[[Category: Bolin, J T]]
	[[Category: Dai, S]]		[[Category: Dai, S]]

OCA at 07:43, 31 January 2018

OCA — Wed, 31 Jan 2018 07:43:42 GMT

←Older revision		Revision as of 07:43, 31 January 2018
Line 1:		Line 1:
		+
	==CRYSTAL STRUCTURE OF 2,3-DIHYDROXYBIPHENYL 1,2-DIOXYGENASE (DHBD) COMPLEXED WITH 2',6'-DICL DIHYDROXYBIPHENYL (DHB)==		==CRYSTAL STRUCTURE OF 2,3-DIHYDROXYBIPHENYL 1,2-DIOXYGENASE (DHBD) COMPLEXED WITH 2',6'-DICL DIHYDROXYBIPHENYL (DHB)==
	<StructureSection load='1lkd' size='340' side='right' caption='[[1lkd]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='1lkd' size='340' side='right' caption='[[1lkd]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1lkd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Burxl Burxl~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LKD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LKD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1lkd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Burkholderia_cepacia_lb400 Burkholderia cepacia lb400]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LKD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LKD FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BP6:2,6-DICHLORO-BIPHENYL-2,6-DIOL'>BP6</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=P6G:HEXAETHYLENE+GLYCOL'>P6G</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BP6:2,6-DICHLORO-BIPHENYL-2,6-DIOL'>BP6</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=P6G:HEXAETHYLENE+GLYCOL'>P6G</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1lgt\|1lgt]], [[1han\|1han]], [[1kmy\|1kmy]], [[1knd\|1knd]], [[1knf\|1knf]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1lgt\|1lgt]], [[1han\|1han]], [[1kmy\|1kmy]], [[1knd\|1knd]], [[1knf\|1knf]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Biphenyl-2,3-diol_1,2-dioxygenase Biphenyl-2,3-diol 1,2-dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.39 1.13.11.39] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Biphenyl-2,3-diol_1,2-dioxygenase Biphenyl-2,3-diol 1,2-dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.39 1.13.11.39] </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=1lkd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lkd OCA], [http://pdbe.org/1lkd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1lkd RCSB], [http://www.ebi.ac.uk/pdbsum/1lkd 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=1lkd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lkd OCA], [http://pdbe.org/1lkd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1lkd RCSB], [http://www.ebi.ac.uk/pdbsum/1lkd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1lkd ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 14:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/lk/1lkd_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/lk/1lkd_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>
Line 29:		Line 30:
	</div>		</div>
	<div class="pdbe-citations 1lkd" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1lkd" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Dioxygenase\|Dioxygenase]]
	== References ==		== References ==
	<references/>		<references/>
Line 37:		Line 35:
	</StructureSection>		</StructureSection>
	[[Category: Biphenyl-2,3-diol 1,2-dioxygenase]]		[[Category: Biphenyl-2,3-diol 1,2-dioxygenase]]
-	[[Category: ~~Burxl~~]]	+	[[Category: Burkholderia cepacia lb400]]
	[[Category: Bolin, J T]]		[[Category: Bolin, J T]]
	[[Category: Dai, S]]		[[Category: Dai, S]]

OCA at 05:41, 9 February 2016

OCA — Tue, 09 Feb 2016 05:41:38 GMT

←Older revision		Revision as of 05:41, 9 February 2016
Line 18:		Line 18:
	<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=1lkd ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 19:10, 10 September 2015

OCA — Thu, 10 Sep 2015 19:10:45 GMT

←Older revision		Revision as of 19:10, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1lkd' size='340' side='right' caption='[[1lkd]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='1lkd' size='340' side='right' caption='[[1lkd]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1lkd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Burkholderia_xenovorans Burkholderia xenovorans~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LKD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LKD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1lkd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Burxl Burxl]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LKD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LKD FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BP6:2,6-DICHLORO-BIPHENYL-2,6-DIOL'>BP6</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=P6G:HEXAETHYLENE+GLYCOL'>P6G</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BP6:2,6-DICHLORO-BIPHENYL-2,6-DIOL'>BP6</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=P6G:HEXAETHYLENE+GLYCOL'>P6G</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1lgt\|1lgt]], [[1han\|1han]], [[1kmy\|1kmy]], [[1knd\|1knd]], [[1knf\|1knf]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1lgt\|1lgt]], [[1han\|1han]], [[1kmy\|1kmy]], [[1knd\|1knd]], [[1knf\|1knf]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Biphenyl-2,3-diol_1,2-dioxygenase Biphenyl-2,3-diol 1,2-dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.39 1.13.11.39] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Biphenyl-2,3-diol_1,2-dioxygenase Biphenyl-2,3-diol 1,2-dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.39 1.13.11.39] </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=1lkd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lkd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1lkd RCSB], [http://www.ebi.ac.uk/pdbsum/1lkd 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=1lkd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lkd OCA], [http://pdbe.org/1lkd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1lkd RCSB], [http://www.ebi.ac.uk/pdbsum/1lkd PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/BPHC_BURXL BPHC_BURXL]] Shows a preference for catechols with groups immediately adjacent to the hydroxyl substituents.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 26:		Line 28:
	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 1lkd" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 34:		Line 37:
	</StructureSection>		</StructureSection>
	[[Category: Biphenyl-2,3-diol 1,2-dioxygenase]]		[[Category: Biphenyl-2,3-diol 1,2-dioxygenase]]
-	[[Category: ~~Burkholderia xenovorans~~]]	+	[[Category: Burxl]]
	[[Category: Bolin, J T]]		[[Category: Bolin, J T]]
	[[Category: Dai, S]]		[[Category: Dai, S]]

OCA at 15:25, 5 January 2015

OCA — Mon, 05 Jan 2015 15:25:06 GMT

←Older revision		Revision as of 15:25, 5 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1lkd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Burkholderia_xenovorans Burkholderia xenovorans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LKD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LKD FirstGlance]. <br>		<table><tr><td colspan='2'>[[1lkd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Burkholderia_xenovorans Burkholderia xenovorans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LKD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LKD FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BP6:2,6-DICHLORO-BIPHENYL-2,6-DIOL'>BP6</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=P6G:HEXAETHYLENE+GLYCOL'>P6G</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BP6:2,6-DICHLORO-BIPHENYL-2,6-DIOL'>BP6</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=P6G:HEXAETHYLENE+GLYCOL'>P6G</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1lgt\|1lgt]], [[1han\|1han]], [[1kmy\|1kmy]], [[1knd\|1knd]], [[1knf\|1knf]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1lgt\|1lgt]], [[1han\|1han]], [[1kmy\|1kmy]], [[1knd\|1knd]], [[1knf\|1knf]]</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Biphenyl-2,3-diol_1,2-dioxygenase Biphenyl-2,3-diol 1,2-dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.39 1.13.11.39] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Biphenyl-2,3-diol_1,2-dioxygenase Biphenyl-2,3-diol 1,2-dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.39 1.13.11.39] </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=1lkd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lkd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1lkd RCSB], [http://www.ebi.ac.uk/pdbsum/1lkd 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=1lkd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lkd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1lkd RCSB], [http://www.ebi.ac.uk/pdbsum/1lkd 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 35:		Line 35:
	[[Category: Biphenyl-2,3-diol 1,2-dioxygenase]]		[[Category: Biphenyl-2,3-diol 1,2-dioxygenase]]
	[[Category: Burkholderia xenovorans]]		[[Category: Burkholderia xenovorans]]
-	[[Category: Bolin, J T.]]	+	[[Category: Bolin, J T]]
-	[[Category: Dai, S.]]	+	[[Category: Dai, S]]
	[[Category: 3-dihydroxybiphenyl]]		[[Category: 3-dihydroxybiphenyl]]
	[[Category: Anaerobic]]		[[Category: Anaerobic]]

OCA at 15:25, 28 September 2014

OCA — Sun, 28 Sep 2014 15:25:41 GMT

←Older revision		Revision as of 15:25, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1lkd.~~png~~\|~~left~~\|200px]]	+	==CRYSTAL STRUCTURE OF 2,3-DIHYDROXYBIPHENYL 1,2-DIOXYGENASE (DHBD) COMPLEXED WITH 2',6'-DICL DIHYDROXYBIPHENYL (DHB)==
		+	<StructureSection load='1lkd' size='340' side='right' caption='[[1lkd]], [[Resolution\|resolution]] 1.70Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1lkd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Burkholderia_xenovorans Burkholderia xenovorans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LKD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LKD FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BP6:2,6-DICHLORO-BIPHENYL-2,6-DIOL'>BP6</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=P6G:HEXAETHYLENE+GLYCOL'>P6G</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1lgt\|1lgt]], [[1han\|1han]], [[1kmy\|1kmy]], [[1knd\|1knd]], [[1knf\|1knf]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Biphenyl-2,3-diol_1,2-dioxygenase Biphenyl-2,3-diol 1,2-dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.39 1.13.11.39] </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=1lkd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lkd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1lkd RCSB], [http://www.ebi.ac.uk/pdbsum/1lkd 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/lk/1lkd_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 ==
		+	The microbial degradation of polychlorinated biphenyls (PCBs) provides the potential to destroy these widespread, toxic and persistent environmental pollutants. For example, the four-step upper bph pathway transforms some of the more than 100 different PCBs found in commercial mixtures and is being engineered for more effective PCB degradation. In the critical third step of this pathway, 2,3-dihydroxybiphenyl (DHB) 1,2-dioxygenase (DHBD; EC 1.13.11.39) catalyzes aromatic ring cleavage. Here we demonstrate that ortho-chlorinated PCB metabolites strongly inhibit DHBD, promote its suicide inactivation and interfere with the degradation of other compounds. For example, k(cat)(app) for 2',6'-diCl DHB was reduced by a factor of approximately 7,000 relative to DHB, and it bound with sufficient affinity to competitively inhibit DHB cleavage at nanomolar concentrations. Crystal structures of two complexes of DHBD with ortho-chlorinated metabolites at 1.7 A resolution reveal an explanation for these phenomena, which have important implications for bioremediation strategies.

-	~~{{STRUCTURE_1lkd\| PDB=1lkd \| SCENE= }}~~	+	Identification and analysis of a bottleneck in PCB biodegradation.,Dai S, Vaillancourt FH, Maaroufi H, Drouin NM, Neau DB, Snieckus V, Bolin JT, Eltis LD Nat Struct Biol. 2002 Dec;9(12):934-9. PMID:12415290<ref>PMID:12415290</ref>

-	~~===CRYSTAL STRUCTURE OF 2~~,~~3-DIHYDROXYBIPHENYL 1,2-DIOXYGENASE (DHBD) COMPLEXED WITH 2',6'-DICL DIHYDROXYBIPHENYL (DHB)===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

-	~~{{ABSTRACT_PUBMED_12415290}}~~	+	==See Also==
-		+	*[[Dioxygenase\|Dioxygenase]]
-	==~~About this Structure~~==	+	== References ==
-	[[~~1lkd~~]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Burkholderia_xenovorans Burkholderia xenovorans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LKD OCA].	+	<references/>
-		+	__TOC__
-	==~~Reference~~==	+	</StructureSection>
-	<~~ref group="xtra">PMID:012415290<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Biphenyl-2,3-diol 1,2-dioxygenase]]		[[Category: Biphenyl-2,3-diol 1,2-dioxygenase]]
	[[Category: Burkholderia xenovorans]]		[[Category: Burkholderia xenovorans]]

OCA: Protected "1lkd" [edit=sysop:move=sysop]

OCA — Wed, 05 Dec 2012 19:40:11 GMT

Protected "1lkd" [edit=sysop:move=sysop]

←Older revision

Revision as of 19:40, 5 December 2012

OCA at 19:40, 5 December 2012

OCA — Wed, 05 Dec 2012 19:40:07 GMT

←Older revision		Revision as of 19:40, 5 December 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1lkd.png\|left\|200px]]		[[Image:1lkd.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1lkd", 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_1lkd\| PDB=1lkd \| SCENE= }}		{{STRUCTURE_1lkd\| PDB=1lkd \| SCENE= }}

	===CRYSTAL STRUCTURE OF 2,3-DIHYDROXYBIPHENYL 1,2-DIOXYGENASE (DHBD) COMPLEXED WITH 2',6'-DICL DIHYDROXYBIPHENYL (DHB)===		===CRYSTAL STRUCTURE OF 2,3-DIHYDROXYBIPHENYL 1,2-DIOXYGENASE (DHBD) COMPLEXED WITH 2',6'-DICL DIHYDROXYBIPHENYL (DHB)===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_12415290}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 12415290 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_12415290}}		{{ABSTRACT_PUBMED_12415290}}

	==About this Structure==		==About this Structure==
-	~~1LKD~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/~~Burkholderia_sp.~~ Burkholderia ~~sp.~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LKD OCA].	+	[[1lkd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Burkholderia_xenovorans Burkholderia xenovorans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LKD OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~12415290~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:012415290</ref><references group="xtra"/>
	[[Category: Biphenyl-2,3-diol 1,2-dioxygenase]]		[[Category: Biphenyl-2,3-diol 1,2-dioxygenase]]
-	[[Category: Burkholderia ~~sp.~~]]	+	[[Category: Burkholderia xenovorans]]
	[[Category: Bolin, J T.]]		[[Category: Bolin, J T.]]
	[[Category: Dai, S.]]		[[Category: Dai, S.]]
-	[[Category: 2,3-dihydroxybiphenyl]]	+	[[Category: 3-dihydroxybiphenyl]]
	[[Category: Anaerobic]]		[[Category: Anaerobic]]
	[[Category: Extradiol dioxygenase]]		[[Category: Extradiol dioxygenase]]
	[[Category: Non-heme iron]]		[[Category: Non-heme iron]]
		+	[[Category: Oxidoreductase]]
	[[Category: Pcb biodegradation]]		[[Category: Pcb biodegradation]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 06:55:28 2009''