5zbd - Revision history

OCA at 10:27, 27 March 2024

2024-03-27T10:27:23Z

←Older revision		Revision as of 10:27, 27 March 2024
Line 3:		Line 3:
	<StructureSection load='5zbd' size='340' side='right'caption='[[5zbd]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='5zbd' size='340' side='right'caption='[[5zbd]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5zbd]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZBD OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5ZBD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5zbd]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Chromobacterium_violaceum_ATCC_12472 Chromobacterium violaceum ATCC 12472]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZBD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ZBD FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=FAD:FLAVIN~~-~~ADENINE+DINUCLEOTIDE'>FAD</scene>~~, ~~<scene name='pdbligand=TRP:TRYPTOPHAN'>TRP</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]] 1.8Å</td></tr>
-	<tr id='~~activity~~'><td class="sblockLbl"><b>~~Activity~~:</b></td><td class="sblockDat"><~~span class~~='~~plainlinks~~'>~~[http:~~/~~/en.wikipedia.org/wiki/7-chloro-L-tryptophan_oxidase 7-chloro-L-tryptophan oxidase]~~, ~~with EC number [http~~:~~//www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.3.23 1.4.3.23]~~ </~~span~~></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=TRP:TRYPTOPHAN'>TRP</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=5zbd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zbd OCA], [~~http~~://pdbe.org/5zbd PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5zbd RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5zbd PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5zbd 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=5zbd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zbd OCA], [https://pdbe.org/5zbd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5zbd RCSB], [https://www.ebi.ac.uk/pdbsum/5zbd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5zbd ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/VIOA_CHRVO VIOA_CHRVO]
-	l-Tryptophan oxidase, VioA from Chromobacterium violaceum, which has a high substrate specificity for tryptophan, is useful for quantitative assay of tryptophan. However, stability of wild type VioA is not enough for its application in clinical or industrial use. To improve the thermal stability of the enzyme, we developed a VioA (C395A) mutant, with higher stability than wild type VioA. The VioA (C395A) exhibited similar specificity and kinetic parameter for tryptophan to wild type. Conventionally, the quantity of tryptophan is determined by instrumental methods, such as high-performance liquid chromatography (HPLC) after pre-column-derivatization. Using the mutant enzyme, we succeeded in the tryptophan quantification in human plasma samples, to an accuracy of <2.9% when compared to the instrumental method, and to a precision of CV <3.2%. To analyse the improvement in storage stability and substrate specificity, we further determined the crystal structures of VioA (C395A) complexed with FAD, and with FAD and tryptophan at 1.8 A resolution.	+
-		+
-	Protein engineering for improving the thermostability of tryptophan oxidase and insights from structural analysis.,Yamaguchi H, Tatsumi M, Takahashi K, Tagami U, Sugiki M, Kashiwagi T, Kameya M, Okazaki S, Mizukoshi T, Asano Y J Biochem. 2018 Nov 1;164(5):~~359-367. doi: 10.1093~~/jb/~~mvy065~~. ~~PMID:30053101<ref>PMID:30053101</ref>~~	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U~~.~~S. National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 5zbd" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references~~/>	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~7-chloro-L-tryptophan oxidase~~]]	+	[[Category: Chromobacterium violaceum ATCC 12472]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Asano, Y]]	+	[[Category: Asano Y]]
-	[[Category: Kashiwagi, T]]	+	[[Category: Kashiwagi T]]
-	[[Category: Mizukoshi, T]]	+	[[Category: Mizukoshi T]]
-	[[Category: Okazaki, S]]	+	[[Category: Okazaki S]]
-	[[Category: Sugiki, M]]	+	[[Category: Sugiki M]]
-	[[Category: Tagami, U]]	+	[[Category: Tagami U]]
-	[[Category: Takahashi, K]]	+	[[Category: Takahashi K]]
-	[[Category: Tatsumi, M]]	+	[[Category: Tatsumi M]]
-	[[Category: Yamaguchi, H]]	+	[[Category: Yamaguchi H]]
-	~~[[Category: Oxidase]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 21:17, 28 October 2020

2020-10-28T21:17:48Z

←Older revision		Revision as of 21:17, 28 October 2020
Line 1:		Line 1:

	==Crystal structure of tryptophan oxidase (C395A mutant) from Chromobacterium violaceum==		==Crystal structure of tryptophan oxidase (C395A mutant) from Chromobacterium violaceum==
-	<StructureSection load='5zbd' size='340' side='right' caption='[[5zbd]], [[Resolution\|resolution]] 1.80Å' scene=''>	+	<StructureSection load='5zbd' size='340' side='right'caption='[[5zbd]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5zbd]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZBD OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5ZBD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5zbd]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZBD OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5ZBD FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=TRP:TRYPTOPHAN'>TRP</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=TRP:TRYPTOPHAN'>TRP</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/7-chloro-L-tryptophan_oxidase 7-chloro-L-tryptophan oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.3.23 1.4.3.23] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/7-chloro-L-tryptophan_oxidase 7-chloro-L-tryptophan oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.3.23 1.4.3.23] </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=5zbd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zbd OCA], [http://pdbe.org/5zbd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zbd RCSB], [http://www.ebi.ac.uk/pdbsum/5zbd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zbd 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=5zbd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zbd OCA], [http://pdbe.org/5zbd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zbd RCSB], [http://www.ebi.ac.uk/pdbsum/5zbd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zbd ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 22:		Line 22:
	</StructureSection>		</StructureSection>
	[[Category: 7-chloro-L-tryptophan oxidase]]		[[Category: 7-chloro-L-tryptophan oxidase]]
		+	[[Category: Large Structures]]
	[[Category: Asano, Y]]		[[Category: Asano, Y]]
	[[Category: Kashiwagi, T]]		[[Category: Kashiwagi, T]]

OCA at 08:11, 19 December 2018

2018-12-19T08:11:50Z

←Older revision		Revision as of 08:11, 19 December 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5zbd is ~~ON HOLD until Feb 11 2020~~	+	==Crystal structure of tryptophan oxidase (C395A mutant) from Chromobacterium violaceum==
		+	<StructureSection load='5zbd' size='340' side='right' caption='[[5zbd]], [[Resolution\|resolution]] 1.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5zbd]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZBD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZBD FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=TRP:TRYPTOPHAN'>TRP</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/7-chloro-L-tryptophan_oxidase 7-chloro-L-tryptophan oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.3.23 1.4.3.23] </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=5zbd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zbd OCA], [http://pdbe.org/5zbd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zbd RCSB], [http://www.ebi.ac.uk/pdbsum/5zbd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zbd ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	l-Tryptophan oxidase, VioA from Chromobacterium violaceum, which has a high substrate specificity for tryptophan, is useful for quantitative assay of tryptophan. However, stability of wild type VioA is not enough for its application in clinical or industrial use. To improve the thermal stability of the enzyme, we developed a VioA (C395A) mutant, with higher stability than wild type VioA. The VioA (C395A) exhibited similar specificity and kinetic parameter for tryptophan to wild type. Conventionally, the quantity of tryptophan is determined by instrumental methods, such as high-performance liquid chromatography (HPLC) after pre-column-derivatization. Using the mutant enzyme, we succeeded in the tryptophan quantification in human plasma samples, to an accuracy of <2.9% when compared to the instrumental method, and to a precision of CV <3.2%. To analyse the improvement in storage stability and substrate specificity, we further determined the crystal structures of VioA (C395A) complexed with FAD, and with FAD and tryptophan at 1.8 A resolution.

-	~~Authors:~~ Yamaguchi, H., Tatsumi, M., Takahashi, K., Tagami, U., Sugiki, M., Kashiwagi, T., ~~Okazaki~~, S., Mizukoshi, T., Asano, Y.	+	Protein engineering for improving the thermostability of tryptophan oxidase and insights from structural analysis.,Yamaguchi H, Tatsumi M, Takahashi K, Tagami U, Sugiki M, Kashiwagi T, Kameya M, Okazaki S, Mizukoshi T, Asano Y J Biochem. 2018 Nov 1;164(5):359-367. doi: 10.1093/jb/mvy065. PMID:30053101<ref>PMID:30053101</ref>

-	~~Description: Crystal structure~~ of ~~tryptophan oxidase (C395A mutant) from Chromobacterium violaceum~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	~~[[Category~~: ~~Yamaguchi, H]]~~	+	<div class="pdbe-citations 5zbd" style="background-color:#fffaf0;"></div>
-	~~[[Category: Mizukoshi, T]]~~	+	== References ==
-	[[Category: ~~Takahashi, K~~]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: 7-chloro-L-tryptophan oxidase]]
	[[Category: Asano, Y]]		[[Category: Asano, Y]]
		+	[[Category: Kashiwagi, T]]
		+	[[Category: Mizukoshi, T]]
	[[Category: Okazaki, S]]		[[Category: Okazaki, S]]
	[[Category: Sugiki, M]]		[[Category: Sugiki, M]]
	[[Category: Tagami, U]]		[[Category: Tagami, U]]
		+	[[Category: Takahashi, K]]
	[[Category: Tatsumi, M]]		[[Category: Tatsumi, M]]
-	[[Category: ~~Kashiwagi~~, T]]	+	[[Category: Yamaguchi, H]]
		+	[[Category: Oxidase]]
		+	[[Category: Oxidoreductase]]

OCA at 04:58, 14 March 2018

2018-03-14T04:58:03Z

←Older revision		Revision as of 04:58, 14 March 2018
Line 5:		Line 5:
	Authors: Yamaguchi, H., Tatsumi, M., Takahashi, K., Tagami, U., Sugiki, M., Kashiwagi, T., Okazaki, S., Mizukoshi, T., Asano, Y.		Authors: Yamaguchi, H., Tatsumi, M., Takahashi, K., Tagami, U., Sugiki, M., Kashiwagi, T., Okazaki, S., Mizukoshi, T., Asano, Y.

-	Description: Crystal structure of ~~Se-Met~~ tryptophan oxidase from Chromobacterium violaceum	+	Description: Crystal structure of tryptophan oxidase (C395A mutant) from Chromobacterium violaceum
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Yamaguchi, H]]		[[Category: Yamaguchi, H]]

OCA: Protected "5zbd" [edit=sysop:move=sysop]

2018-03-08T03:35:49Z

Protected "5zbd" [edit=sysop:move=sysop]

←Older revision

Revision as of 03:35, 8 March 2018

OCA: New page: '''Unreleased structure''' The entry 5zbd is ON HOLD until Feb 11 2020 Authors: Yamaguchi, H., Tatsumi, M., Takahashi, K., Tagami, U., Sugiki, M., Kashiwagi, T., Okazaki, S., Mizukoshi,...

2018-03-08T03:35:48Z

New page: '''Unreleased structure''' The entry 5zbd is ON HOLD until Feb 11 2020 Authors: Yamaguchi, H., Tatsumi, M., Takahashi, K., Tagami, U., Sugiki, M., Kashiwagi, T., Okazaki, S., Mizukoshi,...

New page

'''Unreleased structure'''

The entry 5zbd is ON HOLD until Feb 11 2020

Authors: Yamaguchi, H., Tatsumi, M., Takahashi, K., Tagami, U., Sugiki, M., Kashiwagi, T., Okazaki, S., Mizukoshi, T., Asano, Y.

Description: Crystal structure of Se-Met tryptophan oxidase from Chromobacterium violaceum
[[Category: Unreleased Structures]]
[[Category: Yamaguchi, H]]
[[Category: Mizukoshi, T]]
[[Category: Takahashi, K]]
[[Category: Asano, Y]]
[[Category: Okazaki, S]]
[[Category: Sugiki, M]]
[[Category: Tagami, U]]
[[Category: Tatsumi, M]]
[[Category: Kashiwagi, T]]