3en1 - Revision history

OCA at 09:48, 21 February 2024

2024-02-21T09:48:25Z

←Older revision		Revision as of 09:48, 21 February 2024
Line 3:		Line 3:
	<StructureSection load='3en1' size='340' side='right'caption='[[3en1]], [[Resolution\|resolution]] 3.20Å' scene=''>		<StructureSection load='3en1' size='340' side='right'caption='[[3en1]], [[Resolution\|resolution]] 3.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3en1]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"bacillus_fluorescens_putidus"_flugge_1886 "bacillus fluorescens putidus" flugge 1886~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EN1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3EN1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3en1]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_putida Pseudomonas putida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EN1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3EN1 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=MBN:TOLUENE'>MBN</scene>, <scene name='pdbligand=PE3:3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL'>PE3</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]] 3.2Å</td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3dqy\|3dqy]], [[3ef6\|3ef6]], [[3eqq\|3eqq]]</div></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=MBN:TOLUENE'>MBN</scene>, <scene name='pdbligand=PE3:3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL'>PE3</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bnzA, TodA, todC1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=303 "Bacillus fluorescens putidus" Flugge 1886]), bnzB, TodB, todC2 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=303 "Bacillus fluorescens putidus" Flugge 1886])</td></tr>	+
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Toluene_dioxygenase Toluene dioxygenase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.12.11 1.14.12.11] </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=3en1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3en1 OCA], [https://pdbe.org/3en1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3en1 RCSB], [https://www.ebi.ac.uk/pdbsum/3en1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3en1 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=3en1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3en1 OCA], [https://pdbe.org/3en1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3en1 RCSB], [https://www.ebi.ac.uk/pdbsum/3en1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3en1 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/~~BNZA_PSEPU BNZA_PSEPU]~~] Catalyzes both the oxidation of benzene and toluene~~. [[https://www.uniprot.org/uniprot/BNZB_PSEPU BNZB_PSEPU]] Catalyzes both the oxidation of benzene and toluene. The beta subunit may be responsible for the substrate specificity of the enzyme~~.	+	[https://www.uniprot.org/uniprot/BNZA_PSEP1 BNZA_PSEP1] Catalyzes both the oxidation of benzene and toluene.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 22:		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=3en1 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=3en1 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Bacterial Rieske non-heme iron oxygenases catalyze the initial hydroxylation of aromatic hydrocarbon substrates. The structures of all three components of one such system, the toluene 2,3-dioxygenase system, have now been determined. This system consists of a reductase, a ferredoxin and a terminal dioxygenase. The dioxygenase, which was cocrystallized with toluene, is a heterohexamer containing a catalytic and a structural subunit. The catalytic subunit contains a Rieske [2Fe-2S] cluster and mononuclear iron at the active site. This iron is not strongly bound and is easily removed during enzyme purification. The structures of the enzyme with and without mononuclear iron demonstrate that part of the structure is flexible in the absence of iron. The orientation of the toluene substrate in the active site is consistent with the regiospecificity of oxygen incorporation seen in the product formed. The ferredoxin is Rieske type and contains a [2Fe-2S] cluster close to the protein surface. The reductase belongs to the glutathione reductase family of flavoenzymes and consists of three domains: an FAD-binding domain, an NADH-binding domain and a C-terminal domain. A model for electron transfer from NADH via FAD in the reductase and the ferredoxin to the terminal active-site mononuclear iron of the dioxygenase is proposed.
-
-	Structures of the multicomponent Rieske non-heme iron toluene 2,3-dioxygenase enzyme system.,Friemann R, Lee K, Brown EN, Gibson DT, Eklund H, Ramaswamy S Acta Crystallogr D Biol Crystallogr. 2009 Jan;65(Pt 1):24-33. Epub 2008, Dec 18. PMID:19153463<ref>PMID:19153463</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 3en1" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Bacillus fluorescens putidus flugge 1886]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Toluene dioxygenase~~]]	+	[[Category: Pseudomonas putida]]
-	[[Category: Brown~~, E N~~]]	+	[[Category: Brown EN]]
-	[[Category: Eklund, H]]	+	[[Category: Eklund H]]
-	[[Category: Friemann, R]]	+	[[Category: Friemann R]]
-	[[Category: Gibson~~, D T~~]]	+	[[Category: Gibson DT]]
-	[[Category: Lee, K]]	+	[[Category: Lee K]]
-	[[Category: Ramaswamy, S]]	+	[[Category: Ramaswamy S]]
-	~~[[Category: 2fe-2]]~~	+
-	~~[[Category: Aromatic hydrocarbons catabolism]]~~	+
-	~~[[Category: Dioxygenase]]~~	+
-	~~[[Category: Iron]]~~	+
-	~~[[Category: Iron-sulfur]]~~	+
-	~~[[Category: Iron-sulfur cluster]]~~	+
-	~~[[Category: Metal-binding]]~~	+
-	~~[[Category: Mononuclear iron]]~~	+
-	~~[[Category: Nad]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 09:10, 23 February 2022

2022-02-23T09:10:25Z

←Older revision		Revision as of 09:10, 23 February 2022
Line 1:		Line 1:

	==Crystal structure of Toluene 2,3-Dioxygenase==		==Crystal structure of Toluene 2,3-Dioxygenase==
-	<StructureSection load='3en1' size='340' side='right' caption='[[3en1]], [[Resolution\|resolution]] 3.20Å' scene=''>	+	<StructureSection load='3en1' size='340' side='right'caption='[[3en1]], [[Resolution\|resolution]] 3.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3en1]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacillus_fluorescens_putidus"_flugge_1886 "bacillus fluorescens putidus" flugge 1886]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EN1 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3EN1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3en1]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_fluorescens_putidus"_flugge_1886 "bacillus fluorescens putidus" flugge 1886]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EN1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3EN1 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=MBN:TOLUENE'>MBN</scene>, <scene name='pdbligand=PE3:3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL'>PE3</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=MBN:TOLUENE'>MBN</scene>, <scene name='pdbligand=PE3:3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL'>PE3</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3dqy\|3dqy]], [[3ef6\|3ef6]], [[3eqq\|3eqq]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3dqy\|3dqy]], [[3ef6\|3ef6]], [[3eqq\|3eqq]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bnzA, TodA, todC1 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=303 "Bacillus fluorescens putidus" Flugge 1886]), bnzB, TodB, todC2 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=303 "Bacillus fluorescens putidus" Flugge 1886])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bnzA, TodA, todC1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=303 "Bacillus fluorescens putidus" Flugge 1886]), bnzB, TodB, todC2 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=303 "Bacillus fluorescens putidus" Flugge 1886])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Toluene_dioxygenase Toluene dioxygenase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.12.11 1.14.12.11] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Toluene_dioxygenase Toluene dioxygenase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.12.11 1.14.12.11] </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=3en1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3en1 OCA], [~~http~~://pdbe.org/3en1 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3en1 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3en1 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3en1 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=3en1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3en1 OCA], [https://pdbe.org/3en1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3en1 RCSB], [https://www.ebi.ac.uk/pdbsum/3en1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3en1 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/BNZA_PSEPU BNZA_PSEPU]] Catalyzes both the oxidation of benzene and toluene. [[~~http~~://www.uniprot.org/uniprot/BNZB_PSEPU BNZB_PSEPU]] Catalyzes both the oxidation of benzene and toluene. The beta subunit may be responsible for the substrate specificity of the enzyme.	+	[[https://www.uniprot.org/uniprot/BNZA_PSEPU BNZA_PSEPU]] Catalyzes both the oxidation of benzene and toluene. [[https://www.uniprot.org/uniprot/BNZB_PSEPU BNZB_PSEPU]] Catalyzes both the oxidation of benzene and toluene. The beta subunit may be responsible for the substrate specificity of the enzyme.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 36:		Line 36:
	</StructureSection>		</StructureSection>
	[[Category: Bacillus fluorescens putidus flugge 1886]]		[[Category: Bacillus fluorescens putidus flugge 1886]]
		+	[[Category: Large Structures]]
	[[Category: Toluene dioxygenase]]		[[Category: Toluene dioxygenase]]
	[[Category: Brown, E N]]		[[Category: Brown, E N]]

OCA at 19:15, 24 January 2018

2018-01-24T19:15:39Z

←Older revision		Revision as of 19:15, 24 January 2018
Line 16:		Line 16:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/en/3en1_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/en/3en1_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 09:15, 25 October 2017

2017-10-25T09:15:25Z

←Older revision		Revision as of 09:15, 25 October 2017
Line 1:		Line 1:
		+
	==Crystal structure of Toluene 2,3-Dioxygenase==		==Crystal structure of Toluene 2,3-Dioxygenase==
	<StructureSection load='3en1' size='340' side='right' caption='[[3en1]], [[Resolution\|resolution]] 3.20Å' scene=''>		<StructureSection load='3en1' size='340' side='right' caption='[[3en1]], [[Resolution\|resolution]] 3.20Å' scene=''>
Line 7:		Line 8:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bnzA, TodA, todC1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=303 "Bacillus fluorescens putidus" Flugge 1886]), bnzB, TodB, todC2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=303 "Bacillus fluorescens putidus" Flugge 1886])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bnzA, TodA, todC1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=303 "Bacillus fluorescens putidus" Flugge 1886]), bnzB, TodB, todC2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=303 "Bacillus fluorescens putidus" Flugge 1886])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Toluene_dioxygenase Toluene dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.12.11 1.14.12.11] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Toluene_dioxygenase Toluene dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.12.11 1.14.12.11] </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=3en1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3en1 OCA], [http://pdbe.org/3en1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3en1 RCSB], [http://www.ebi.ac.uk/pdbsum/3en1 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=3en1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3en1 OCA], [http://pdbe.org/3en1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3en1 RCSB], [http://www.ebi.ac.uk/pdbsum/3en1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3en1 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 42:		Line 43:
	[[Category: Lee, K]]		[[Category: Lee, K]]
	[[Category: Ramaswamy, S]]		[[Category: Ramaswamy, S]]
		+	[[Category: 2fe-2]]
	[[Category: Aromatic hydrocarbons catabolism]]		[[Category: Aromatic hydrocarbons catabolism]]
	[[Category: Dioxygenase]]		[[Category: Dioxygenase]]

OCA at 07:59, 8 February 2016

2016-02-08T07:59:13Z

←Older revision		Revision as of 07:59, 8 February 2016
Line 2:		Line 2:
	<StructureSection load='3en1' size='340' side='right' caption='[[3en1]], [[Resolution\|resolution]] 3.20Å' scene=''>		<StructureSection load='3en1' size='340' side='right' caption='[[3en1]], [[Resolution\|resolution]] 3.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3en1]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Pseudomonas_putida Pseudomonas putida~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EN1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3EN1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3en1]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_fluorescens_putidus"_flugge_1886 "bacillus fluorescens putidus" flugge 1886]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EN1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3EN1 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=MBN:TOLUENE'>MBN</scene>, <scene name='pdbligand=PE3:3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL'>PE3</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=MBN:TOLUENE'>MBN</scene>, <scene name='pdbligand=PE3:3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL'>PE3</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3dqy\|3dqy]], [[3ef6\|3ef6]], [[3eqq\|3eqq]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3dqy\|3dqy]], [[3ef6\|3ef6]], [[3eqq\|3eqq]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bnzA, TodA, todC1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=303 ~~Pseudomonas putida~~]), bnzB, TodB, todC2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=303 ~~Pseudomonas putida~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bnzA, TodA, todC1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=303 "Bacillus fluorescens putidus" Flugge 1886]), bnzB, TodB, todC2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=303 "Bacillus fluorescens putidus" Flugge 1886])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Toluene_dioxygenase Toluene dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.12.11 1.14.12.11] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Toluene_dioxygenase Toluene dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.12.11 1.14.12.11] </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=3en1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3en1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3en1 RCSB], [http://www.ebi.ac.uk/pdbsum/3en1 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=3en1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3en1 OCA], [http://pdbe.org/3en1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3en1 RCSB], [http://www.ebi.ac.uk/pdbsum/3en1 PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/BNZA_PSEPU BNZA_PSEPU]] Catalyzes both the oxidation of benzene and toluene. [[http://www.uniprot.org/uniprot/BNZB_PSEPU BNZB_PSEPU]] Catalyzes both the oxidation of benzene and toluene. The beta subunit may be responsible for the substrate specificity of the enzyme.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 17:		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=3en1 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 27:		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 3en1" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Pseudomonas putida~~]]	+	[[Category: Bacillus fluorescens putidus flugge 1886]]
	[[Category: Toluene dioxygenase]]		[[Category: Toluene dioxygenase]]
	[[Category: Brown, E N]]		[[Category: Brown, E N]]

OCA at 11:33, 20 January 2015

2015-01-20T11:33:27Z

←Older revision		Revision as of 11:33, 20 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3en1]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_putida Pseudomonas putida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EN1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3EN1 FirstGlance]. <br>		<table><tr><td colspan='2'>[[3en1]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_putida Pseudomonas putida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EN1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3EN1 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=MBN:TOLUENE'>MBN</scene>, <scene name='pdbligand=PE3:3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL'>PE3</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=MBN:TOLUENE'>MBN</scene>, <scene name='pdbligand=PE3:3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL'>PE3</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3dqy\|3dqy]], [[3ef6\|3ef6]], [[3eqq\|3eqq]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3dqy\|3dqy]], [[3ef6\|3ef6]], [[3eqq\|3eqq]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bnzA, TodA, todC1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=303 Pseudomonas putida]), bnzB, TodB, todC2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=303 Pseudomonas putida])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bnzA, TodA, todC1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=303 Pseudomonas putida]), bnzB, TodB, todC2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=303 Pseudomonas putida])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Toluene_dioxygenase Toluene dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.12.11 1.14.12.11] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Toluene_dioxygenase Toluene dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.12.11 1.14.12.11] </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=3en1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3en1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3en1 RCSB], [http://www.ebi.ac.uk/pdbsum/3en1 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=3en1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3en1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3en1 RCSB], [http://www.ebi.ac.uk/pdbsum/3en1 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 33:		Line 33:
	[[Category: Pseudomonas putida]]		[[Category: Pseudomonas putida]]
	[[Category: Toluene dioxygenase]]		[[Category: Toluene dioxygenase]]
-	[[Category: Brown, E N.]]	+	[[Category: Brown, E N]]
-	[[Category: Eklund, H.]]	+	[[Category: Eklund, H]]
-	[[Category: Friemann, R.]]	+	[[Category: Friemann, R]]
-	[[Category: Gibson, D T.]]	+	[[Category: Gibson, D T]]
-	[[Category: Lee, K.]]	+	[[Category: Lee, K]]
-	[[Category: Ramaswamy, S.]]	+	[[Category: Ramaswamy, S]]
	[[Category: Aromatic hydrocarbons catabolism]]		[[Category: Aromatic hydrocarbons catabolism]]
	[[Category: Dioxygenase]]		[[Category: Dioxygenase]]

OCA at 13:16, 29 September 2014

2014-09-29T13:16:18Z

←Older revision		Revision as of 13:16, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~3en1.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of Toluene 2,3-Dioxygenase==
		+	<StructureSection load='3en1' size='340' side='right' caption='[[3en1]], [[Resolution\|resolution]] 3.20Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3en1]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_putida Pseudomonas putida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EN1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3EN1 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=MBN:TOLUENE'>MBN</scene>, <scene name='pdbligand=PE3:3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL'>PE3</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3dqy\|3dqy]], [[3ef6\|3ef6]], [[3eqq\|3eqq]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bnzA, TodA, todC1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=303 Pseudomonas putida]), bnzB, TodB, todC2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=303 Pseudomonas putida])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Toluene_dioxygenase Toluene dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.12.11 1.14.12.11] </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=3en1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3en1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3en1 RCSB], [http://www.ebi.ac.uk/pdbsum/3en1 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/en/3en1_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 ==
		+	Bacterial Rieske non-heme iron oxygenases catalyze the initial hydroxylation of aromatic hydrocarbon substrates. The structures of all three components of one such system, the toluene 2,3-dioxygenase system, have now been determined. This system consists of a reductase, a ferredoxin and a terminal dioxygenase. The dioxygenase, which was cocrystallized with toluene, is a heterohexamer containing a catalytic and a structural subunit. The catalytic subunit contains a Rieske [2Fe-2S] cluster and mononuclear iron at the active site. This iron is not strongly bound and is easily removed during enzyme purification. The structures of the enzyme with and without mononuclear iron demonstrate that part of the structure is flexible in the absence of iron. The orientation of the toluene substrate in the active site is consistent with the regiospecificity of oxygen incorporation seen in the product formed. The ferredoxin is Rieske type and contains a [2Fe-2S] cluster close to the protein surface. The reductase belongs to the glutathione reductase family of flavoenzymes and consists of three domains: an FAD-binding domain, an NADH-binding domain and a C-terminal domain. A model for electron transfer from NADH via FAD in the reductase and the ferredoxin to the terminal active-site mononuclear iron of the dioxygenase is proposed.

-	~~{{STRUCTURE_3en1\| PDB=3en1 \| SCENE= }}~~	+	Structures of the multicomponent Rieske non-heme iron toluene 2,3-dioxygenase enzyme system.,Friemann R, Lee K, Brown EN, Gibson DT, Eklund H, Ramaswamy S Acta Crystallogr D Biol Crystallogr. 2009 Jan;65(Pt 1):24-33. Epub 2008, Dec 18. PMID:19153463<ref>PMID:19153463</ref>

-	~~===Crystal structure of Toluene 2~~,~~3-Dioxygenase===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_19153463}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[3en1]] is~~ a ~~2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Pseudomonas_putida Pseudomonas putida]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3EN1 OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:019153463<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Pseudomonas putida]]		[[Category: Pseudomonas putida]]
	[[Category: Toluene dioxygenase]]		[[Category: Toluene dioxygenase]]

OCA: Protected "3en1" [edit=sysop:move=sysop]

2012-10-21T11:21:52Z

Protected "3en1" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:21, 21 October 2012

OCA at 11:21, 21 October 2012

2012-10-21T11:21:46Z

←Older revision		Revision as of 11:21, 21 October 2012
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:3en1.png\|left\|200px]]

-	~~The entry~~ 3en1 ~~is ON HOLD~~ ~~until Paper Publication~~	+	{{STRUCTURE_3en1\| PDB=3en1 \| SCENE= }}

-	~~Authors: Friemann~~, ~~R., Lee, K., Brown, E.N., Gibson, D.T., Eklund, H., Ramaswamy, S.~~	+	===Crystal structure of Toluene 2,3-Dioxygenase===

-	~~Description: Crystal structure of Toluene 2,3-Dioxygenase~~	+	{{ABSTRACT_PUBMED_19153463}}

-	~~''Page seeded by~~ [http://oca.weizmann.ac.il/oca OCA ] ~~on Wed Oct 15 14~~:06:~~02 2008''~~	+	==About this Structure==
		+	[[3en1]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_putida Pseudomonas putida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EN1 OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:019153463</ref><references group="xtra"/>
		+	[[Category: Pseudomonas putida]]
		+	[[Category: Toluene dioxygenase]]
		+	[[Category: Brown, E N.]]
		+	[[Category: Eklund, H.]]
		+	[[Category: Friemann, R.]]
		+	[[Category: Gibson, D T.]]
		+	[[Category: Lee, K.]]
		+	[[Category: Ramaswamy, S.]]
		+	[[Category: Aromatic hydrocarbons catabolism]]
		+	[[Category: Dioxygenase]]
		+	[[Category: Iron]]
		+	[[Category: Iron-sulfur]]
		+	[[Category: Iron-sulfur cluster]]
		+	[[Category: Metal-binding]]
		+	[[Category: Mononuclear iron]]
		+	[[Category: Nad]]
		+	[[Category: Oxidoreductase]]

OCA at 12:06, 15 October 2008

2008-10-15T12:06:02Z

←Older revision		Revision as of 12:06, 15 October 2008
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3en1 is ON HOLD	+	The entry 3en1 is ON HOLD until Paper Publication

-	Authors: Friemann, R., Lee, K, Brown, E.N., Gibson, D.T., Eklund, H., Ramaswamy, S.	+	Authors: Friemann, R., Lee, K., Brown, E.N., Gibson, D.T., Eklund, H., Ramaswamy, S.

	Description: Crystal structure of Toluene 2,3-Dioxygenase		Description: Crystal structure of Toluene 2,3-Dioxygenase

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Oct ~~1 21~~:16:42 2008''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Oct 15 14:06:02 2008''