6jxs - Revision history

OCA at 10:21, 22 November 2023

2023-11-22T10:21:40Z

←Older revision		Revision as of 10:21, 22 November 2023
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	<StructureSection load='6jxs' size='340' side='right'caption='[[6jxs]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='6jxs' size='340' side='right'caption='[[6jxs]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6jxs]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Bacillus_smithii Bacillus smithii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JXS OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6JXS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6jxs]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_smithii Bacillus smithii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JXS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6JXS FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=PE8:3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL'>PE8</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]] 1.95Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[6jxn\|6jxn]]</div~~></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=PE8:3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL'>PE8</scene></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=6jxs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jxs OCA], [~~http~~://pdbe.org/6jxs PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6jxs RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6jxs PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6jxs 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=6jxs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jxs OCA], [https://pdbe.org/6jxs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6jxs RCSB], [https://www.ebi.ac.uk/pdbsum/6jxs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6jxs ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/G9QLG5_9BACI G9QLG5_9BACI]] Catalyzes the reductive cleavage of azo bond in aromatic azo compounds to the corresponding amines. Requires NADH, but not NADPH, as an electron donor for its activity.[HAMAP-Rule:MF_01216][SAAS:SAAS00016147]	+	[https://www.uniprot.org/uniprot/G9QLG5_9BACI G9QLG5_9BACI] Catalyzes the reductive cleavage of azo bond in aromatic azo compounds to the corresponding amines. Requires NADH, but not NADPH, as an electron donor for its activity.[HAMAP-Rule:MF_01216][SAAS:SAAS00016147]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	[[Category: Bacillus smithii]]		[[Category: Bacillus smithii]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Ohshima, T]]	+	[[Category: Ohshima T]]
-	[[Category: Sakuraba, H]]	+	[[Category: Sakuraba H]]
-	[[Category: Yoneda, K]]	+	[[Category: Yoneda K]]
-	~~[[Category: Indigo reductase]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Y151f~~]]	+

OCA at 07:05, 25 November 2020

2020-11-25T07:05:04Z

←Older revision		Revision as of 07:05, 25 November 2020
Line 5:		Line 5:
	<table><tr><td colspan='2'>[[6jxs]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_smithii Bacillus smithii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JXS OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6JXS FirstGlance]. <br>		<table><tr><td colspan='2'>[[6jxs]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_smithii Bacillus smithii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JXS OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6JXS FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=PE8:3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL'>PE8</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=PE8:3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL'>PE8</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6jxn\|6jxn]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[6jxn\|6jxn]]</div></td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6jxs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jxs OCA], [http://pdbe.org/6jxs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6jxs RCSB], [http://www.ebi.ac.uk/pdbsum/6jxs PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6jxs ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6jxs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jxs OCA], [http://pdbe.org/6jxs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6jxs RCSB], [http://www.ebi.ac.uk/pdbsum/6jxs PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6jxs ProSAT]</span></td></tr>
	</table>		</table>

OCA at 10:02, 16 September 2020

2020-09-16T10:02:08Z

←Older revision		Revision as of 10:02, 16 September 2020
Line 3:		Line 3:
	<StructureSection load='6jxs' size='340' side='right'caption='[[6jxs]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='6jxs' size='340' side='right'caption='[[6jxs]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6jxs]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JXS OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6JXS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6jxs]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_smithii Bacillus smithii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JXS OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6JXS FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=PE8:3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL'>PE8</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=PE8:3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL'>PE8</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6jxn\|6jxn]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6jxn\|6jxn]]</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=6jxs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jxs OCA], [http://pdbe.org/6jxs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6jxs RCSB], [http://www.ebi.ac.uk/pdbsum/6jxs PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6jxs ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6jxs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jxs OCA], [http://pdbe.org/6jxs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6jxs RCSB], [http://www.ebi.ac.uk/pdbsum/6jxs PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6jxs ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/G9QLG5_9BACI G9QLG5_9BACI]] Catalyzes the reductive cleavage of azo bond in aromatic azo compounds to the corresponding amines. Requires NADH, but not NADPH, as an electron donor for its activity.[HAMAP-Rule:MF_01216][SAAS:SAAS00016147]		[[http://www.uniprot.org/uniprot/G9QLG5_9BACI G9QLG5_9BACI]] Catalyzes the reductive cleavage of azo bond in aromatic azo compounds to the corresponding amines. Requires NADH, but not NADPH, as an electron donor for its activity.[HAMAP-Rule:MF_01216][SAAS:SAAS00016147]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The FMN-dependent NADH-indigo reductase gene from the thermophilic bacterium Bacillus smithii was overexpressed in Escherichia coli. The expressed enzyme functioned as a highly thermostable indigo reductase that retained complete activity even after incubation at 100 degrees C for 10min. Furthermore, B. smithii indigo reductase exhibited high stability over a wider pH range and longer storage periods compared with indigo reductases previously identified from other sources. The enzyme catalyzed the reduction of various azo compounds and indigo carmine. The crystal structures of the wild-type enzyme in complex with FMN/N-cyclohexyl-2-aminoethanesulfonate (CHES) and the Y151F mutant enzyme in complex with FMN were determined by the molecular replacement method and refined at resolutions of 1.97 and 1.95A, respectively. Then, indigo carmine molecule was modeled into the active site using the molecular docking simulation and the binding mode of indigo carmine was elucidated. In addition, the structure of B. smithii indigo reductase, which is relatively less stable Bacillus cohnii indigo reductase, was constructed by homology modeling. The factor contributing to the considerably higher thermostability of B. smithii indigo reductase was analyzed by comparing its structure with that of B. cohnii indigo reductase, which revealed that intersubunit aromatic interactions (F105-F172' and F172-F105') may be responsible for the high thermostability of B. smithii indigo reductase. Notably, site-directed mutagenesis results showed that F105 plays a major role in the intersubunit aromatic interaction.
		+
		+	Structural and biochemical characterization of an extremely thermostable FMN-dependent NADH-indigo reductase from Bacillus smithii.,Yoneda K, Yoshioka M, Sakuraba H, Araki T, Ohshima T Int J Biol Macromol. 2020 Aug 28. pii: S0141-8130(20)34294-X. doi:, 10.1016/j.ijbiomac.2020.08.197. PMID:32861785<ref>PMID:32861785</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6jxs" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus smithii]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Ohshima, T]]		[[Category: Ohshima, T]]
	[[Category: Sakuraba, H]]		[[Category: Sakuraba, H]]
	[[Category: Yoneda, K]]		[[Category: Yoneda, K]]
-	[[Category: Bacillus smithii]]
	[[Category: Indigo reductase]]		[[Category: Indigo reductase]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
	[[Category: Y151f]]		[[Category: Y151f]]

OCA at 09:05, 1 April 2020

2020-04-01T09:05:53Z

←Older revision		Revision as of 09:05, 1 April 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6jxs is ~~ON HOLD until Paper Publication~~	+	==Crystal Structure of Indigo reductase (Y151F) from Bacillus smithii type strain DSM 4216==
-		+	<StructureSection load='6jxs' size='340' side='right'caption='[[6jxs]], [[Resolution\|resolution]] 1.95Å' scene=''>
-	~~Authors~~: ~~Yoneda~~, K., ~~Sakuraba~~, H., ~~Ohshima~~, T.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6jxs]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JXS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6JXS FirstGlance]. <br>
-	~~Description~~: ~~Crystal Structure~~ of ~~Indigo reductase (Y151F) from Bacillus smithii type strain DSM 4216~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=PE8:3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL'>PE8</scene></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6jxn\|6jxn]]</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=6jxs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jxs OCA], [http://pdbe.org/6jxs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6jxs RCSB], [http://www.ebi.ac.uk/pdbsum/6jxs PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6jxs ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/G9QLG5_9BACI G9QLG5_9BACI]] Catalyzes the reductive cleavage of azo bond in aromatic azo compounds to the corresponding amines. Requires NADH, but not NADPH, as an electron donor for its activity.[HAMAP-Rule:MF_01216][SAAS:SAAS00016147]
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Ohshima, T]]
		+	[[Category: Sakuraba, H]]
	[[Category: Yoneda, K]]		[[Category: Yoneda, K]]
-	[[Category: ~~Sakuraba, H~~]]	+	[[Category: Bacillus smithii]]
-	[[Category: ~~Ohshima, T~~]]	+	[[Category: Indigo reductase]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Y151f]]

OCA at 05:36, 21 May 2019

2019-05-21T05:36:52Z

←Older revision		Revision as of 05:36, 21 May 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6jxs is ON HOLD	+	The entry 6jxs is ON HOLD until Paper Publication

	Authors: Yoneda, K., Sakuraba, H., Ohshima, T.		Authors: Yoneda, K., Sakuraba, H., Ohshima, T.

OCA: Protected "6jxs" [edit=sysop:move=sysop]

2019-05-01T07:00:47Z

Protected "6jxs" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:00, 1 May 2019

OCA: New page: '''Unreleased structure''' The entry 6jxs is ON HOLD Authors: Yoneda, K., Sakuraba, H., Ohshima, T. Description: Crystal Structure of Indigo reductase (Y151F) from Bacillus smithii typ...

2019-05-01T07:00:46Z

New page: '''Unreleased structure''' The entry 6jxs is ON HOLD Authors: Yoneda, K., Sakuraba, H., Ohshima, T. Description: Crystal Structure of Indigo reductase (Y151F) from Bacillus smithii typ...

New page

'''Unreleased structure'''

The entry 6jxs is ON HOLD

Authors: Yoneda, K., Sakuraba, H., Ohshima, T.

Description: Crystal Structure of Indigo reductase (Y151F) from Bacillus smithii type strain DSM 4216
[[Category: Unreleased Structures]]
[[Category: Yoneda, K]]
[[Category: Sakuraba, H]]
[[Category: Ohshima, T]]