5x9m - Revision history

OCA at 07:56, 22 November 2023

2023-11-22T07:56:27Z

←Older revision		Revision as of 07:56, 22 November 2023
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	<StructureSection load='5x9m' size='340' side='right'caption='[[5x9m]], [[Resolution\|resolution]] 0.93Å' scene=''>		<StructureSection load='5x9m' size='340' side='right'caption='[[5x9m]], [[Resolution\|resolution]] 0.93Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5x9m]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Katemfe Katemfe~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X9M OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5X9M FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5x9m]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thaumatococcus_daniellii Thaumatococcus daniellii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X9M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5X9M FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</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]] 0.93Å</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=5x9m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x9m OCA], [~~http~~://pdbe.org/5x9m PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5x9m RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5x9m PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5x9m ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</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=5x9m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x9m OCA], [https://pdbe.org/5x9m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5x9m RCSB], [https://www.ebi.ac.uk/pdbsum/5x9m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5x9m ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/THM1_THADA THM1_THADA] Taste-modifying protein; intensely sweet-tasting. It is 100000 times sweeter than sucrose on a molar basis.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Katemfe]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Masuda, T]]	+	[[Category: Thaumatococcus daniellii]]
-	[[Category: Mikami, B]]	+	[[Category: Masuda T]]
-	[[Category: Okubo, K]]	+	[[Category: Mikami B]]
-	[[Category: Sugahara, M]]	+	[[Category: Okubo K]]
-	[[Category: Suzuki, M]]	+	[[Category: Sugahara M]]
-	~~[[Category: Plant protein]]~~	+	[[Category: Suzuki M]]
-	~~[[Category: Sweet receptor]]~~	+
-	~~[[Category: Sweet-tasting protein~~]]	+

OCA at 06:55, 27 March 2019

2019-03-27T06:55:18Z

←Older revision		Revision as of 06:55, 27 March 2019
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	==Structure of hyper-sweet thaumatin (D21N)==		==Structure of hyper-sweet thaumatin (D21N)==
-	<StructureSection load='5x9m' size='340' side='right' caption='[[5x9m]], [[Resolution\|resolution]] 0.93Å' scene=''>	+	<StructureSection load='5x9m' size='340' side='right'caption='[[5x9m]], [[Resolution\|resolution]] 0.93Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5x9m]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X9M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5X9M FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5x9m]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Katemfe Katemfe]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X9M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5X9M FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene></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=5x9m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x9m OCA], [http://pdbe.org/5x9m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5x9m RCSB], [http://www.ebi.ac.uk/pdbsum/5x9m PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5x9m 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=5x9m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x9m OCA], [http://pdbe.org/5x9m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5x9m RCSB], [http://www.ebi.ac.uk/pdbsum/5x9m PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5x9m ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	One of the sweetest proteins found in tropical fruits (with a threshold of 50nM), thaumatin, is also used commercially as a sweetener. Our previous study successfully produced the sweetest thaumatin mutant (D21N), designated hyper-sweet thaumatin, which decreases the sweetness threshold to 31nM. To investigate why the D21N mutant is sweeter than wild-type thaumatin, we compared the structure of the D21N mutant solved at a subatomic resolution of 0.93A with that of wild-type thaumatin determined at 0.90A. Although the overall structure of the D21N mutant resembles that of wild-type thaumatin, our subatomic resolution analysis successfully assigned and discriminated the detailed atomic positions of side-chains at position 21. The relative B-factor value of the side-chain at position 21 in the D21N mutant was higher than that of wild-type thaumatin, hinting at a greater flexibility of side-chain at 21 in the hyper-sweet D21N mutant. Furthermore, alternative conformations of Lys19, which is hydrogen-bonded to Asp21 in wild-type, were found only in the D21N mutant. Subatomic resolution analysis revealed that flexible conformations at the sites adjacent to positions 19 and 21 play a crucial role in enhancing sweet potency and may serve to enhance the complementarity of electrostatic potentials for interaction with the sweet taste receptor.
		+
		+	Subatomic structure of hyper-sweet thaumatin D21N mutant reveals the importance of flexible conformations for enhanced sweetness.,Masuda T, Okubo K, Murata K, Mikami B, Sugahara M, Suzuki M, Temussi PA, Tani F Biochimie. 2019 Feb;157:57-63. doi: 10.1016/j.biochi.2018.10.020. Epub 2018 Oct, 31. PMID:30389513<ref>PMID:30389513</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5x9m" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Katemfe]]
		+	[[Category: Large Structures]]
	[[Category: Masuda, T]]		[[Category: Masuda, T]]
	[[Category: Mikami, B]]		[[Category: Mikami, B]]

OCA at 06:25, 14 March 2018

2018-03-14T06:25:55Z

←Older revision		Revision as of 06:25, 14 March 2018
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-	'''Unreleased structure'''

-	~~The entry~~ 5x9m is ~~ON HOLD until Paper Publication~~	+	==Structure of hyper-sweet thaumatin (D21N)==
-		+	<StructureSection load='5x9m' size='340' side='right' caption='[[5x9m]], [[Resolution\|resolution]] 0.93Å' scene=''>
-	~~Authors~~: ~~Masuda~~, T., ~~Okubo, K~~., ~~Sugahara, M~~., ~~Suzuki, M~~., ~~Mikami, B~~.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5x9m]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X9M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5X9M FirstGlance]. <br>
-	~~Description~~: ~~Structure of hyper-sweet thaumatin (D21N)~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<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=5x9m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x9m OCA], [http://pdbe.org/5x9m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5x9m RCSB], [http://www.ebi.ac.uk/pdbsum/5x9m PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5x9m ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Masuda, T]]
		+	[[Category: Mikami, B]]
	[[Category: Okubo, K]]		[[Category: Okubo, K]]
		+	[[Category: Sugahara, M]]
	[[Category: Suzuki, M]]		[[Category: Suzuki, M]]
-	[[Category: ~~Mikami, B~~]]	+	[[Category: Plant protein]]
-	[[Category: ~~Masuda, T~~]]	+	[[Category: Sweet receptor]]
-	[[Category: ~~Sugahara, M~~]]	+	[[Category: Sweet-tasting protein]]

OCA at 07:59, 4 October 2017

2017-10-04T07:59:55Z

←Older revision		Revision as of 07:59, 4 October 2017
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5x9m is ON HOLD	+	The entry 5x9m is ON HOLD until Paper Publication

	Authors: Masuda, T., Okubo, K., Sugahara, M., Suzuki, M., Mikami, B.		Authors: Masuda, T., Okubo, K., Sugahara, M., Suzuki, M., Mikami, B.
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	[[Category: Suzuki, M]]		[[Category: Suzuki, M]]
	[[Category: Mikami, B]]		[[Category: Mikami, B]]
-	[[Category: Sugahara, M]]
	[[Category: Masuda, T]]		[[Category: Masuda, T]]
		+	[[Category: Sugahara, M]]

OCA at 15:21, 27 September 2017

2017-09-27T15:21:01Z

←Older revision		Revision as of 15:21, 27 September 2017
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	[[Category: Suzuki, M]]		[[Category: Suzuki, M]]
	[[Category: Mikami, B]]		[[Category: Mikami, B]]
-	[[Category: Masuda, T]]
	[[Category: Sugahara, M]]		[[Category: Sugahara, M]]
		+	[[Category: Masuda, T]]

OCA: Protected "5x9m" [edit=sysop:move=sysop]

2017-03-15T20:20:46Z

Protected "5x9m" [edit=sysop:move=sysop]

←Older revision

Revision as of 20:20, 15 March 2017

OCA: New page: '''Unreleased structure''' The entry 5x9m is ON HOLD Authors: Masuda, T., Okubo, K., Sugahara, M., Suzuki, M., Mikami, B. Description: Structure of hyper-sweet thaumatin (D21N) [[Categ...

2017-03-15T20:20:45Z

New page: '''Unreleased structure''' The entry 5x9m is ON HOLD Authors: Masuda, T., Okubo, K., Sugahara, M., Suzuki, M., Mikami, B. Description: Structure of hyper-sweet thaumatin (D21N) [[Categ...

New page

'''Unreleased structure'''

The entry 5x9m is ON HOLD

Authors: Masuda, T., Okubo, K., Sugahara, M., Suzuki, M., Mikami, B.

Description: Structure of hyper-sweet thaumatin (D21N)
[[Category: Unreleased Structures]]
[[Category: Okubo, K]]
[[Category: Suzuki, M]]
[[Category: Mikami, B]]
[[Category: Masuda, T]]
[[Category: Sugahara, M]]