7v92 - Revision history

OCA at 17:22, 29 November 2023

OCA — Wed, 29 Nov 2023 17:22:12 GMT

←Older revision		Revision as of 17:22, 29 November 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7v92]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Ficus_microcarpa Ficus microcarpa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7V92 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7V92 FirstGlance]. <br>		<table><tr><td colspan='2'>[[7v92]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Ficus_microcarpa Ficus microcarpa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7V92 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7V92 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=7v92 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7v92 OCA], [https://pdbe.org/7v92 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7v92 RCSB], [https://www.ebi.ac.uk/pdbsum/7v92 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7v92 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]] 1.607Å</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=7v92 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7v92 OCA], [https://pdbe.org/7v92 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7v92 RCSB], [https://www.ebi.ac.uk/pdbsum/7v92 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7v92 ProSAT]</span></td></tr>
	</table>		</table>
		+
		+	==See Also==
		+	*[[Chitinase 3D structures\|Chitinase 3D structures]]
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 07:24, 8 September 2022

OCA — Thu, 08 Sep 2022 07:24:07 GMT

←Older revision		Revision as of 07:24, 8 September 2022
Line 3:		Line 3:
	<StructureSection load='7v92' size='340' side='right'caption='[[7v92]], [[Resolution\|resolution]] 1.61Å' scene=''>		<StructureSection load='7v92' size='340' side='right'caption='[[7v92]], [[Resolution\|resolution]] 1.61Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7v92]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7V92 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7V92 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7v92]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Ficus_microcarpa Ficus microcarpa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7V92 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7V92 FirstGlance]. <br>
-	</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Chitinase Chitinase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.14 3.2.1.14] </span></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=7v92 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7v92 OCA], [https://pdbe.org/7v92 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7v92 RCSB], [https://www.ebi.ac.uk/pdbsum/7v92 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7v92 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=7v92 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7v92 OCA], [https://pdbe.org/7v92 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7v92 RCSB], [https://www.ebi.ac.uk/pdbsum/7v92 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7v92 ProSAT]</span></td></tr>	+
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Chitin is a biopolymer of N-acetyl-d-glucosamine with beta-1,4-bond and is the main component of arthropod exoskeletons and the cell walls of many fungi. Chitinase (EC 3.2.1.14) is an enzyme that hydrolyzes the beta-1,4-bond in chitin and degrades chitin into oligomers. It has been found in a wide range of organisms. Chitinase from Gazyumaru (Ficus microcarpa) latex exhibits antifungal activity by degrading chitin in the cell wall of fungi and is expected to be used in medical and agricultural fields. However, the enzyme's thermostability is an important factor; chitinase is not thermostable enough to maintain its activity under the actual application conditions. In addition to the fact that thermostable chitinases exhibiting antifungal activity can be used under various conditions, they have some advantages for the production process and long-term preservation, which are highly demanded in industrial use. We solved the crystal structure of chitinase to explore the target sites to improve its thermostability. We rationally introduced proline residues, a disulfide bond, and salt bridges in the chitinase using protein-engineering methods based on the crystal structure and sequence alignment among other chitinases. As a result, we successfully constructed the thermostable mutant chitinases rationally with high antifungal and specific activities. The results provide a useful strategy to enhance the thermostability of this enzyme family. IMPORTANCE We solved the crystal structure of the chitinase from Gazyumaru (Ficus microcarpa) latex exhibiting antifungal activity. Furthermore, we demonstrated that the thermostable mutant enzyme with a melting temperature (Tm) 6.9 degrees C higher than wild type (WT) and a half-life at 60 degrees C that is 15 times longer than WT was constructed through 10 amino acid substitutions, including 5 proline residues substitutions, making disulfide bonding, and building a salt bridge network in the enzyme. These mutations do not affect its high antifungal activity and chitinase activity, and the principle for the construction of the thermostable chitinase was well explained by its crystal structure. Our results provide a useful strategy to enhance the thermostability of this enzyme family and to use the thermostable mutant as a seed for antifungal agents for practical use.
-
-	Structural Analysis and Construction of a Thermostable Antifungal Chitinase.,Kozome D, Uechi K, Taira T, Fukada H, Kubota T, Ishikawa K Appl Environ Microbiol. 2022 Jun 2:e0065222. doi: 10.1128/aem.00652-22. PMID:35652665<ref>PMID:35652665</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 7v92" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Chitinase~~]]	+	[[Category: Ficus microcarpa]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Ishikawa, K]]	+	[[Category: Ishikawa K]]
-	[[Category: Kozome, D]]	+	[[Category: Kozome D]]
-	[[Category: Kubota, T]]	+	[[Category: Kubota T]]
-	~~[[Category: Class i chitinase gh19 antifungal activity]]~~	+
-	~~[[Category: Hydrolase~~]]	+

OCA at 05:23, 15 June 2022

OCA — Wed, 15 Jun 2022 05:23:06 GMT

←Older revision		Revision as of 05:23, 15 June 2022
Line 1:		Line 1:

	==Crystal Structure of a thermostable mutant of the Catalytic Domain of GH19 Chitinase from Gazyumaru, Ficus microcarpa==		==Crystal Structure of a thermostable mutant of the Catalytic Domain of GH19 Chitinase from Gazyumaru, Ficus microcarpa==
-	<StructureSection load='7v92' size='340' side='right'caption='[[7v92]]' scene=''>	+	<StructureSection load='7v92' size='340' side='right'caption='[[7v92]], [[Resolution\|resolution]] 1.61Å' 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=7V92 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7V92 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7v92]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7V92 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7V92 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=7v92 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7v92 OCA], [https://pdbe.org/7v92 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7v92 RCSB], [https://www.ebi.ac.uk/pdbsum/7v92 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7v92 ProSAT]</span></td></tr>	+	</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Chitinase Chitinase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.14 3.2.1.14] </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=7v92 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7v92 OCA], [https://pdbe.org/7v92 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7v92 RCSB], [https://www.ebi.ac.uk/pdbsum/7v92 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7v92 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Chitin is a biopolymer of N-acetyl-d-glucosamine with beta-1,4-bond and is the main component of arthropod exoskeletons and the cell walls of many fungi. Chitinase (EC 3.2.1.14) is an enzyme that hydrolyzes the beta-1,4-bond in chitin and degrades chitin into oligomers. It has been found in a wide range of organisms. Chitinase from Gazyumaru (Ficus microcarpa) latex exhibits antifungal activity by degrading chitin in the cell wall of fungi and is expected to be used in medical and agricultural fields. However, the enzyme's thermostability is an important factor; chitinase is not thermostable enough to maintain its activity under the actual application conditions. In addition to the fact that thermostable chitinases exhibiting antifungal activity can be used under various conditions, they have some advantages for the production process and long-term preservation, which are highly demanded in industrial use. We solved the crystal structure of chitinase to explore the target sites to improve its thermostability. We rationally introduced proline residues, a disulfide bond, and salt bridges in the chitinase using protein-engineering methods based on the crystal structure and sequence alignment among other chitinases. As a result, we successfully constructed the thermostable mutant chitinases rationally with high antifungal and specific activities. The results provide a useful strategy to enhance the thermostability of this enzyme family. IMPORTANCE We solved the crystal structure of the chitinase from Gazyumaru (Ficus microcarpa) latex exhibiting antifungal activity. Furthermore, we demonstrated that the thermostable mutant enzyme with a melting temperature (Tm) 6.9 degrees C higher than wild type (WT) and a half-life at 60 degrees C that is 15 times longer than WT was constructed through 10 amino acid substitutions, including 5 proline residues substitutions, making disulfide bonding, and building a salt bridge network in the enzyme. These mutations do not affect its high antifungal activity and chitinase activity, and the principle for the construction of the thermostable chitinase was well explained by its crystal structure. Our results provide a useful strategy to enhance the thermostability of this enzyme family and to use the thermostable mutant as a seed for antifungal agents for practical use.
		+
		+	Structural Analysis and Construction of a Thermostable Antifungal Chitinase.,Kozome D, Uechi K, Taira T, Fukada H, Kubota T, Ishikawa K Appl Environ Microbiol. 2022 Jun 2:e0065222. doi: 10.1128/aem.00652-22. PMID:35652665<ref>PMID:35652665</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7v92" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Chitinase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Ishikawa K]]	+	[[Category: Ishikawa, K]]
-	[[Category: Kozome D]]	+	[[Category: Kozome, D]]
-	[[Category: Kubota T]]	+	[[Category: Kubota, T]]
		+	[[Category: Class i chitinase gh19 antifungal activity]]
		+	[[Category: Hydrolase]]

OCA at 11:39, 27 April 2022

OCA — Wed, 27 Apr 2022 11:39:58 GMT

←Older revision		Revision as of 11:39, 27 April 2022
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 7v92 is ON HOLD until Paper Publication~~	+	==Crystal Structure of a thermostable mutant of the Catalytic Domain of GH19 Chitinase from Gazyumaru, Ficus microcarpa==
-		+	<StructureSection load='7v92' size='340' side='right'caption='[[7v92]]' scene=''>
-	~~Authors: Kozome, D., Kubota, T., Ishikawa, K.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7V92 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7V92 FirstGlance]. <br>
-	~~Description:~~ Crystal Structure of a thermostable mutant of the Catalytic Domain of GH19 Chitinase from Gazyumaru, Ficus microcarpa	+	</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=7v92 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7v92 OCA], [https://pdbe.org/7v92 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7v92 RCSB], [https://www.ebi.ac.uk/pdbsum/7v92 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7v92 ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[[~~Category~~: ~~Kozome~~, D]]	+	__TOC__
-	[[Category: ~~Kubota, T~~]]	+	</StructureSection>
-	[[Category: Ishikawa, K]]	+	[[Category: Large Structures]]
		+	[[Category: Ishikawa K]]
		+	[[Category: Kozome D]]
		+	[[Category: Kubota T]]

OCA at 12:16, 29 December 2021

OCA — Wed, 29 Dec 2021 12:16:14 GMT

←Older revision		Revision as of 12:16, 29 December 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7v92 is ON HOLD	+	The entry 7v92 is ON HOLD until Paper Publication

	Authors: Kozome, D., Kubota, T., Ishikawa, K.		Authors: Kozome, D., Kubota, T., Ishikawa, K.

OCA: Protected "7v92" [edit=sysop:move=sysop]

OCA — Wed, 08 Sep 2021 07:59:30 GMT

Protected "7v92" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:59, 8 September 2021

OCA: New page: '''Unreleased structure''' The entry 7v92 is ON HOLD Authors: Kozome, D., Kubota, T., Ishikawa, K. Description: Crystal Structure of a thermostable mutant of the Catalytic Domain of GH...

OCA — Wed, 08 Sep 2021 07:59:29 GMT

New page: '''Unreleased structure''' The entry 7v92 is ON HOLD Authors: Kozome, D., Kubota, T., Ishikawa, K. Description: Crystal Structure of a thermostable mutant of the Catalytic Domain of GH...

New page

'''Unreleased structure'''

The entry 7v92 is ON HOLD

Authors: Kozome, D., Kubota, T., Ishikawa, K.

Description: Crystal Structure of a thermostable mutant of the Catalytic Domain of GH19 Chitinase from Gazyumaru, Ficus microcarpa
[[Category: Unreleased Structures]]
[[Category: Kozome, D]]
[[Category: Kubota, T]]
[[Category: Ishikawa, K]]