4nbb - Revision history

OCA at 14:47, 8 November 2023

2023-11-08T14:47:23Z

←Older revision		Revision as of 14:47, 8 November 2023
Line 1:		Line 1:

	==Carbazole- and oxygen-bound oxygenase with Ile262 replaced by Val and ferredoxin complex of carbazole 1,9a-dioxygenase==		==Carbazole- and oxygen-bound oxygenase with Ile262 replaced by Val and ferredoxin complex of carbazole 1,9a-dioxygenase==
-	<StructureSection load='4nbb' size='340' side='right'caption='[[4nbb]]' scene=''>	+	<StructureSection load='4nbb' size='340' side='right'caption='[[4nbb]], [[Resolution\|resolution]] 2.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NBB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4NBB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4nbb]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Janthinobacterium_sp._J3 Janthinobacterium sp. J3] and [https://en.wikipedia.org/wiki/Pseudomonas_resinovorans Pseudomonas resinovorans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NBB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4NBB FirstGlance]. <br>
-	</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=4nbb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nbb OCA], [https://pdbe.org/4nbb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4nbb RCSB], [https://www.ebi.ac.uk/pdbsum/4nbb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4nbb ProSAT]</span></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]] 2.05Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=9CA:9H-CARBAZOLE'>9CA</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene></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=4nbb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nbb OCA], [https://pdbe.org/4nbb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4nbb RCSB], [https://www.ebi.ac.uk/pdbsum/4nbb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4nbb ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q84II6_JANS3 Q84II6_JANS3]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Carbazole 1,9a-dioxygenase (CARDO), a Rieske non-heme iron oxygenase (RO), is a three-component system composed of terminal oxygenase (Oxy), ferredoxin, and ferredoxin reductase. Oxy has angular dioxygenation activity against carbazole. Previously, site-directed mutagenesis of the Oxy gene from Janthinobacterium sp. strain J3 generated the Oxy derivatives I262V, F275W, Q282N and Q282Y, which showed different oxygenation capabilities than the wild-type enzyme. To understand the structural features resulting in the different oxidation reactions, we determined the crystal structures of the derivatives, both free and complexed with substrates. I262V, F275W, and Q282Y catalyze the lateral dioxygenation of carbazole with higher yields than the wild type. A previous study determined the crystal structure of Oxy complexed with carbazole and revealed that the carbonyl oxygen of Gly178 hydrogen bonds with the imino nitrogen of carbazole. In these derivatives, the carbazole was rotated approximately 15 degrees , 25 degrees , and 25 degrees , respectively, compared to the wild type, creating space for a water molecule, which hydrogen bonds with the carbonyl oxygen of Gly178 and imino nitrogen of carbazole. In the crystal structure of F275W complexed with fluorene, C9 of fluorene, which corresponds to the imino nitrogen of carbazole, was oriented close to the mutated residue Trp275, which is on the opposite side of the binding pocket from the carbonyl oxygen of Gly178. Our structural analyses demonstrate that the fine-tuning of hydrophobic residues on the surface of the substrate-binding pocket in ROs causes a slight shift in the substrate binding position that in turn favors specific oxygenation reactions toward various substrates.
		+
		+	Structural Basis of the Divergent Oxygenation Reactions Catalyzed by the Rieske Non-heme Iron Oxygenase, Carbazole 1,9a-Dioxygenase.,Inoue K, Usami Y, Ashikawa Y, Noguchi H, Umeda T, Yamagami-Ashikawa A, Horisaki T, Uchimura H, Terada T, Nakamura S, Shimizu K, Habe H, Yamane H, Fujimoto Z, Nojiri H Appl Environ Microbiol. 2014 Feb 28. PMID:24584240<ref>PMID:24584240</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 4nbb" 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: Janthinobacterium sp. J3]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Pseudomonas resinovorans]]
	[[Category: Ashikawa Y]]		[[Category: Ashikawa Y]]
	[[Category: Inoue K]]		[[Category: Inoue K]]
	[[Category: Nojiri H]]		[[Category: Nojiri H]]
	[[Category: Usami Y]]		[[Category: Usami Y]]

OCA at 10:48, 31 August 2022

2022-08-31T10:48:54Z

←Older revision		Revision as of 10:48, 31 August 2022
Line 1:		Line 1:

	==Carbazole- and oxygen-bound oxygenase with Ile262 replaced by Val and ferredoxin complex of carbazole 1,9a-dioxygenase==		==Carbazole- and oxygen-bound oxygenase with Ile262 replaced by Val and ferredoxin complex of carbazole 1,9a-dioxygenase==
-	<StructureSection load='4nbb' size='340' side='right'caption='[[4nbb]]~~, [[Resolution\|resolution]] 2.05Å~~' scene=''>	+	<StructureSection load='4nbb' size='340' side='right'caption='[[4nbb]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>~~[[4nbb]] is a 6 chain structure.~~ Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NBB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4NBB FirstGlance]. <br>	+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NBB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4NBB FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=9CA:9H-CARBAZOLE'>9CA</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene></td></tr>	+	</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=4nbb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nbb OCA], [https://pdbe.org/4nbb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4nbb RCSB], [https://www.ebi.ac.uk/pdbsum/4nbb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4nbb ProSAT]</span></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[4nb8\|4nb8]], [[4nb9\|4nb9]], [[4nba\|4nba]], [[4nbc\|4nbc]], [[4nbd\|4nbd]], [[4nbe\|4nbe]], [[4nbf\|4nbf]], [[4nbg\|4nbg]], [[4nbh\|4nbh]]</div></td></tr>	+
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Carbazole_1,9a-dioxygenase Carbazole 1,9a-dioxygenase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.12.22 1.14.12.22] </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=4nbb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nbb OCA], [https://pdbe.org/4nbb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4nbb RCSB], [https://www.ebi.ac.uk/pdbsum/4nbb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4nbb ProSAT]</span></td></tr>	+
	</table>		</table>
-	== Function ==
-	[[https://www.uniprot.org/uniprot/CARAC_PSERE CARAC_PSERE]] Part of the multicomponent carbazole 1,9a-dioxygenase (CARDO), that converts carbazole (CAR) into 2-aminobiphenyl-2,3-diol. Acts as a mediator in the electron transfer from CarAd to CarAa.<ref>PMID:9244274</ref> <ref>PMID:12450807</ref>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Carbazole 1,9a-dioxygenase (CARDO), a Rieske non-heme iron oxygenase (RO), is a three-component system composed of terminal oxygenase (Oxy), ferredoxin, and ferredoxin reductase. Oxy has angular dioxygenation activity against carbazole. Previously, site-directed mutagenesis of the Oxy gene from Janthinobacterium sp. strain J3 generated the Oxy derivatives I262V, F275W, Q282N and Q282Y, which showed different oxygenation capabilities than the wild-type enzyme. To understand the structural features resulting in the different oxidation reactions, we determined the crystal structures of the derivatives, both free and complexed with substrates. I262V, F275W, and Q282Y catalyze the lateral dioxygenation of carbazole with higher yields than the wild type. A previous study determined the crystal structure of Oxy complexed with carbazole and revealed that the carbonyl oxygen of Gly178 hydrogen bonds with the imino nitrogen of carbazole. In these derivatives, the carbazole was rotated approximately 15 degrees , 25 degrees , and 25 degrees , respectively, compared to the wild type, creating space for a water molecule, which hydrogen bonds with the carbonyl oxygen of Gly178 and imino nitrogen of carbazole. In the crystal structure of F275W complexed with fluorene, C9 of fluorene, which corresponds to the imino nitrogen of carbazole, was oriented close to the mutated residue Trp275, which is on the opposite side of the binding pocket from the carbonyl oxygen of Gly178. Our structural analyses demonstrate that the fine-tuning of hydrophobic residues on the surface of the substrate-binding pocket in ROs causes a slight shift in the substrate binding position that in turn favors specific oxygenation reactions toward various substrates.
-
-	Structural Basis of the Divergent Oxygenation Reactions Catalyzed by the Rieske Non-heme Iron Oxygenase, Carbazole 1,9a-Dioxygenase.,Inoue K, Usami Y, Ashikawa Y, Noguchi H, Umeda T, Yamagami-Ashikawa A, Horisaki T, Uchimura H, Terada T, Nakamura S, Shimizu K, Habe H, Yamane H, Fujimoto Z, Nojiri H Appl Environ Microbiol. 2014 Feb 28. PMID:24584240<ref>PMID:24584240</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 4nbb" 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: Carbazole 1,9a-dioxygenase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Ashikawa, Y]]	+	[[Category: Ashikawa Y]]
-	[[Category: Inoue, K]]	+	[[Category: Inoue K]]
-	[[Category: Nojiri, H]]	+	[[Category: Nojiri H]]
-	[[Category: Usami, Y]]	+	[[Category: Usami Y]]
-	~~[[Category: 9a-dioxygenase]]~~	+
-	~~[[Category: Carbazole 1]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Rieske non-heme iron oxygenase~~]]	+

OCA at 05:04, 25 August 2022

2022-08-25T05:04:36Z

←Older revision		Revision as of 05:04, 25 August 2022
Line 1:		Line 1:

	==Carbazole- and oxygen-bound oxygenase with Ile262 replaced by Val and ferredoxin complex of carbazole 1,9a-dioxygenase==		==Carbazole- and oxygen-bound oxygenase with Ile262 replaced by Val and ferredoxin complex of carbazole 1,9a-dioxygenase==
-	<StructureSection load='4nbb' size='340' side='right' caption='[[4nbb]], [[Resolution\|resolution]] 2.05Å' scene=''>	+	<StructureSection load='4nbb' size='340' side='right'caption='[[4nbb]], [[Resolution\|resolution]] 2.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4nbb]] is a 6 chain structure ~~with sequence from [http://en.wikipedia.org/wiki/Atcc_14235 Atcc 14235] and [http://en.wikipedia.org/wiki/Jans3 Jans3]~~. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NBB OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4NBB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4nbb]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NBB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4NBB FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=9CA:9H-CARBAZOLE'>9CA</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=9CA:9H-CARBAZOLE'>9CA</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4nb8\|4nb8]], [[4nb9\|4nb9]], [[4nba\|4nba]], [[4nbc\|4nbc]], [[4nbd\|4nbd]], [[4nbe\|4nbe]], [[4nbf\|4nbf]], [[4nbg\|4nbg]], [[4nbh\|4nbh]]</td>~~</tr>~~	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[4nb8\|4nb8]], [[4nb9\|4nb9]], [[4nba\|4nba]], [[4nbc\|4nbc]], [[4nbd\|4nbd]], [[4nbe\|4nbe]], [[4nbf\|4nbf]], [[4nbg\|4nbg]], [[4nbh\|4nbh]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">carAa ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=213804 JANS3]), carAc ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=53412 ATCC 14235])</td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Carbazole_1,9a-dioxygenase Carbazole 1,9a-dioxygenase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.12.22 1.14.12.22] </span></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Carbazole_1,9a-dioxygenase Carbazole 1,9a-dioxygenase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.12.22 1.14.12.22] </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=4nbb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nbb OCA], [https://pdbe.org/4nbb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4nbb RCSB], [https://www.ebi.ac.uk/pdbsum/4nbb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4nbb ProSAT]</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=4nbb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nbb OCA], [~~http~~://pdbe.org/4nbb PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4nbb RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4nbb PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4nbb ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/CARAC_PSERE CARAC_PSERE]] Part of the multicomponent carbazole 1,9a-dioxygenase (CARDO), that converts carbazole (CAR) into 2-aminobiphenyl-2,3-diol. Acts as a mediator in the electron transfer from CarAd to CarAa.<ref>PMID:9244274</ref> <ref>PMID:12450807</ref>	+	[[https://www.uniprot.org/uniprot/CARAC_PSERE CARAC_PSERE]] Part of the multicomponent carbazole 1,9a-dioxygenase (CARDO), that converts carbazole (CAR) into 2-aminobiphenyl-2,3-diol. Acts as a mediator in the electron transfer from CarAd to CarAa.<ref>PMID:9244274</ref> <ref>PMID:12450807</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 22:

	==See Also==		==See Also==
-	*[[Dioxygenase\|Dioxygenase]]	+	*[[Dioxygenase 3D structures\|Dioxygenase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Atcc 14235]]
	[[Category: Carbazole 1,9a-dioxygenase]]		[[Category: Carbazole 1,9a-dioxygenase]]
-	[[Category: ~~Jans3~~]]	+	[[Category: Large Structures]]
	[[Category: Ashikawa, Y]]		[[Category: Ashikawa, Y]]
	[[Category: Inoue, K]]		[[Category: Inoue, K]]

OCA at 19:34, 5 August 2016

2016-08-05T19:34:11Z

←Older revision		Revision as of 19:34, 5 August 2016
Line 1:		Line 1:
		+
	==Carbazole- and oxygen-bound oxygenase with Ile262 replaced by Val and ferredoxin complex of carbazole 1,9a-dioxygenase==		==Carbazole- and oxygen-bound oxygenase with Ile262 replaced by Val and ferredoxin complex of carbazole 1,9a-dioxygenase==
	<StructureSection load='4nbb' size='340' side='right' caption='[[4nbb]], [[Resolution\|resolution]] 2.05Å' scene=''>		<StructureSection load='4nbb' size='340' side='right' caption='[[4nbb]], [[Resolution\|resolution]] 2.05Å' scene=''>
Line 7:		Line 8:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">carAa ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=213804 JANS3]), carAc ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=53412 ATCC 14235])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">carAa ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=213804 JANS3]), carAc ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=53412 ATCC 14235])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Carbazole_1,9a-dioxygenase Carbazole 1,9a-dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.12.22 1.14.12.22] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Carbazole_1,9a-dioxygenase Carbazole 1,9a-dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.12.22 1.14.12.22] </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=4nbb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nbb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4nbb RCSB], [http://www.ebi.ac.uk/pdbsum/4nbb 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=4nbb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nbb OCA], [http://pdbe.org/4nbb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4nbb RCSB], [http://www.ebi.ac.uk/pdbsum/4nbb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4nbb ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 20:
	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 4nbb" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Dioxygenase\|Dioxygenase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 21:20, 25 December 2014

2014-12-25T21:20:57Z

←Older revision		Revision as of 21:20, 25 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_4nbb\| PDB=4nbb \| SCENE= }}~~	+	==Carbazole- and oxygen-bound oxygenase with Ile262 replaced by Val and ferredoxin complex of carbazole 1,9a-dioxygenase==
-	===Carbazole- and oxygen-bound oxygenase with Ile262 replaced by Val and ferredoxin complex of carbazole 1,9a-dioxygenase===	+	<StructureSection load='4nbb' size='340' side='right' caption='[[4nbb]], [[Resolution\|resolution]] 2.05Å' scene=''>
-	~~{{ABSTRACT_PUBMED_24584240}}~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[4nbb]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_14235 Atcc 14235] and [http://en.wikipedia.org/wiki/Jans3 Jans3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NBB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4NBB FirstGlance]. <br>
-	==Function==	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=9CA:9H-CARBAZOLE'>9CA</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4nb8\|4nb8]], [[4nb9\|4nb9]], [[4nba\|4nba]], [[4nbc\|4nbc]], [[4nbd\|4nbd]], [[4nbe\|4nbe]], [[4nbf\|4nbf]], [[4nbg\|4nbg]], [[4nbh\|4nbh]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">carAa ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=213804 JANS3]), carAc ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=53412 ATCC 14235])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Carbazole_1,9a-dioxygenase Carbazole 1,9a-dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.12.22 1.14.12.22] </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=4nbb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nbb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4nbb RCSB], [http://www.ebi.ac.uk/pdbsum/4nbb PDBsum]</span></td></tr>
		+	</table>
		+	== Function ==
	[[http://www.uniprot.org/uniprot/CARAC_PSERE CARAC_PSERE]] Part of the multicomponent carbazole 1,9a-dioxygenase (CARDO), that converts carbazole (CAR) into 2-aminobiphenyl-2,3-diol. Acts as a mediator in the electron transfer from CarAd to CarAa.<ref>PMID:9244274</ref> <ref>PMID:12450807</ref>		[[http://www.uniprot.org/uniprot/CARAC_PSERE CARAC_PSERE]] Part of the multicomponent carbazole 1,9a-dioxygenase (CARDO), that converts carbazole (CAR) into 2-aminobiphenyl-2,3-diol. Acts as a mediator in the electron transfer from CarAd to CarAa.<ref>PMID:9244274</ref> <ref>PMID:12450807</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Carbazole 1,9a-dioxygenase (CARDO), a Rieske non-heme iron oxygenase (RO), is a three-component system composed of terminal oxygenase (Oxy), ferredoxin, and ferredoxin reductase. Oxy has angular dioxygenation activity against carbazole. Previously, site-directed mutagenesis of the Oxy gene from Janthinobacterium sp. strain J3 generated the Oxy derivatives I262V, F275W, Q282N and Q282Y, which showed different oxygenation capabilities than the wild-type enzyme. To understand the structural features resulting in the different oxidation reactions, we determined the crystal structures of the derivatives, both free and complexed with substrates. I262V, F275W, and Q282Y catalyze the lateral dioxygenation of carbazole with higher yields than the wild type. A previous study determined the crystal structure of Oxy complexed with carbazole and revealed that the carbonyl oxygen of Gly178 hydrogen bonds with the imino nitrogen of carbazole. In these derivatives, the carbazole was rotated approximately 15 degrees , 25 degrees , and 25 degrees , respectively, compared to the wild type, creating space for a water molecule, which hydrogen bonds with the carbonyl oxygen of Gly178 and imino nitrogen of carbazole. In the crystal structure of F275W complexed with fluorene, C9 of fluorene, which corresponds to the imino nitrogen of carbazole, was oriented close to the mutated residue Trp275, which is on the opposite side of the binding pocket from the carbonyl oxygen of Gly178. Our structural analyses demonstrate that the fine-tuning of hydrophobic residues on the surface of the substrate-binding pocket in ROs causes a slight shift in the substrate binding position that in turn favors specific oxygenation reactions toward various substrates.

-	~~==About this Structure==~~	+	Structural Basis of the Divergent Oxygenation Reactions Catalyzed by the Rieske Non-heme Iron Oxygenase, Carbazole 1,9a-Dioxygenase.,Inoue K, Usami Y, Ashikawa Y, Noguchi H, Umeda T, Yamagami-Ashikawa A, Horisaki T, Uchimura H, Terada T, Nakamura S, Shimizu K, Habe H, Yamane H, Fujimoto Z, Nojiri H Appl Environ Microbiol. 2014 Feb 28. PMID:24584240<ref>PMID:24584240</ref>
-	~~[[4nbb]] is a 6 chain structure~~. ~~Full crystallographic information is available from [http://oca~~.~~weizmann~~.~~ac.il~~/~~oca-bin/ocashort?id=4NBB OCA].~~	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group="xtra">PMID:024584240</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Atcc 14235]]
	[[Category: Carbazole 1,9a-dioxygenase]]		[[Category: Carbazole 1,9a-dioxygenase]]
-	[[Category: Ashikawa, Y.]]	+	[[Category: Jans3]]
-	[[Category: Inoue, K.]]	+	[[Category: Ashikawa, Y]]
-	[[Category: Nojiri, H.]]	+	[[Category: Inoue, K]]
-	[[Category: Usami, Y.]]	+	[[Category: Nojiri, H]]
		+	[[Category: Usami, Y]]
	[[Category: 9a-dioxygenase]]		[[Category: 9a-dioxygenase]]
	[[Category: Carbazole 1]]		[[Category: Carbazole 1]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
	[[Category: Rieske non-heme iron oxygenase]]		[[Category: Rieske non-heme iron oxygenase]]

OCA at 09:18, 26 March 2014

2014-03-26T09:18:21Z

←Older revision		Revision as of 09:18, 26 March 2014
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-	~~'''Unreleased structure'''~~	+	{{STRUCTURE_4nbb\| PDB=4nbb \| SCENE= }}
		+	===Carbazole- and oxygen-bound oxygenase with Ile262 replaced by Val and ferredoxin complex of carbazole 1,9a-dioxygenase===
		+	{{ABSTRACT_PUBMED_24584240}}

-	~~The entry 4nbb is ON HOLD~~ ~~until Paper Publication~~	+	==Function==
		+	[[http://www.uniprot.org/uniprot/CARAC_PSERE CARAC_PSERE]] Part of the multicomponent carbazole 1,9a-dioxygenase (CARDO), that converts carbazole (CAR) into 2-aminobiphenyl-2,3-diol. Acts as a mediator in the electron transfer from CarAd to CarAa.<ref>PMID:9244274</ref> <ref>PMID:12450807</ref>

-	~~Authors~~: ~~Ashikawa, Y~~.~~, Usami, Y~~.~~, Inoue, K~~.~~, Nojiri, H~~.	+	==About this Structure==
		+	[[4nbb]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NBB OCA].

-	~~Description~~: Carbazole~~-and oxygen-bound oxygenase with Ile262 replaced by Val and ferredoxin complex of carbazole~~ 1,9a-dioxygenase	+	==Reference==
		+	<ref group="xtra">PMID:024584240</ref><references group="xtra"/><references/>
		+	[[Category: Carbazole 1,9a-dioxygenase]]
		+	[[Category: Ashikawa, Y.]]
		+	[[Category: Inoue, K.]]
		+	[[Category: Nojiri, H.]]
		+	[[Category: Usami, Y.]]
		+	[[Category: 9a-dioxygenase]]
		+	[[Category: Carbazole 1]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Rieske non-heme iron oxygenase]]

OCA at 07:42, 13 November 2013

2013-11-13T07:42:40Z

←Older revision		Revision as of 07:42, 13 November 2013
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4nbb is ON HOLD	+	The entry 4nbb is ON HOLD until Paper Publication

-	Authors: Ashikawa, Y, Usami, Y, Inoue, K, Nojiri, H	+	Authors: Ashikawa, Y., Usami, Y., Inoue, K., Nojiri, H.

	Description: Carbazole-and oxygen-bound oxygenase with Ile262 replaced by Val and ferredoxin complex of carbazole 1,9a-dioxygenase		Description: Carbazole-and oxygen-bound oxygenase with Ile262 replaced by Val and ferredoxin complex of carbazole 1,9a-dioxygenase

OCA: Protected "4nbb" [edit=sysop:move=sysop]

2013-11-06T07:07:18Z

Protected "4nbb" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:07, 6 November 2013

OCA: New page: '''Unreleased structure''' The entry 4nbb is ON HOLD Authors: Ashikawa, Y, Usami, Y, Inoue, K, Nojiri, H Description: Carbazole-and oxygen-bound oxygenase with Ile262 replaced by Val a...

2013-11-06T07:07:17Z

New page: '''Unreleased structure''' The entry 4nbb is ON HOLD Authors: Ashikawa, Y, Usami, Y, Inoue, K, Nojiri, H Description: Carbazole-and oxygen-bound oxygenase with Ile262 replaced by Val a...

New page

'''Unreleased structure'''

The entry 4nbb is ON HOLD

Authors: Ashikawa, Y, Usami, Y, Inoue, K, Nojiri, H

Description: Carbazole-and oxygen-bound oxygenase with Ile262 replaced by Val and ferredoxin complex of carbazole 1,9a-dioxygenase