8in1 - Revision history

OCA: Replacing page with ''''Unreleased structure''' The entry 8in1 is ON HOLD until Paper Publication Authors: Sun, X.M., Ye, Y.X., Kato, K., Yu, J., Yao, M. Description: beta-glucosidase protein f...'

OCA — Wed, 22 Nov 2023 05:31:18 GMT

Replacing page with ''''Unreleased structure''' The entry 8in1 is ON HOLD until Paper Publication Authors: Sun, X.M., Ye, Y.X., Kato, K., Yu, J., Yao, M. Description: beta-glucosidase protein f...'

←Older revision		Revision as of 05:31, 22 November 2023
Line 1:		Line 1:
		+	'''Unreleased structure'''

-	~~==beta-glucosidase protein from Aplysia kurodai==~~	+	The entry 8in1 is ON HOLD until Paper Publication
-	~~<StructureSection load='~~8in1~~' size='340' side='right'caption='[[8in1]], [[Resolution\|resolution]] 2.70Å' scene=''>~~	+
-	~~== Structural highlights ==~~	+
-	~~<table><tr><td colspan='2'>[[8in1]]~~ is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Aplysia_kurodai Aplysia kurodai]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8IN1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8IN1 FirstGlance]. <br>	+
-	~~</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.7Å</td></tr>~~	+
-	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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=8in1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8in1 OCA], [https://pdbe.org/8in1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8in1 RCSB], [https://www.ebi.ac.uk/pdbsum/8in1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8in1 ProSAT]</span></td></tr>	+
-	~~</table>~~	+
-	~~== Function ==~~	+
-	~~[https://www.uniprot.org/uniprot/A0A1V1FXL2_APLKU A0A1V1FXL2_APLKU]~~	+
-	~~<div style="background-color:#fffaf0;">~~	+
-	== Publication ~~Abstract from PubMed ==~~	+
-	The defensive-offensive associations between algae and herbivores determine marine ecology. Brown algae utilize phlorotannin as their chemical defense against the predator Aplysia kurodai, which uses beta-glucosidase (akuBGL) to digest the laminarin in algae into glucose. Moreover, A. kurodai employs Eisenia hydrolysis-enhancing protein (EHEP) as an offense to protect akuBGL activity from phlorotannin inhibition by precipitating phlorotannin. To underpin the molecular mechanism of this digestive-defensive-offensive system, we determined the structures of the apo and tannic acid (TNA, a phlorotannin analog) bound forms of EHEP, as well as the apo akuBGL. EHEP consisted of three peritrophin-A domains arranged in a triangular shape and bound TNA in the center without significant conformational changes. Structural comparison between EHEP and EHEP-TNA led us to find that EHEP can be resolubilized from phlorotannin precipitation at an alkaline pH, which reflects a requirement in the digestive tract. akuBGL contained two GH1 domains, only one of which conserved the active site. Combining docking analysis, we propose the mechanisms by which phlorotannin inhibits akuBGL by occupying the substrate-binding pocket, and EHEP protects akuBGL against this inhibition by binding with phlorotannin to free the akuBGL pocket.	+

-	~~Structural basis of EHEP-mediated offense against phlorotannin-induced defense from brown algae to protect akuBGL activity.,~~Sun X, Ye Y~~, Sakurai N, Wang H~~, Kato K, Yu J, ~~Yuasa K~~, ~~Tsuji A, Yao~~ M ~~Elife~~. ~~2023 Nov 1;12:RP88939. doi: 10.7554/eLife.88939. PMID:37910430<ref>PMID:37910430</ref>~~	+	Authors: Sun, X.M., Ye, Y.X., Kato, K., Yu, J., Yao, M.

-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+	Description: beta-glucosidase protein from Aplysia kurodai
-	~~</div>~~	+	[[Category: Unreleased Structures]]
-	~~<div class="pdbe~~-~~citations 8in1" style="background-color:#fffaf0;"></div>~~	+	[[Category: Kato, K]]
-	~~== References ==~~	+	[[Category: Sun, X.M]]
-	~~<references/>~~	+	[[Category: Yao, M]]
-	~~__TOC__~~	+	[[Category: Yu, J]]
-	~~</StructureSection>~~	+	[[Category: Ye, Y.X]]
-	~~[[Category:~~ Aplysia kurodai]]	+
-	[[Category: ~~Large~~ Structures]]	+
-	[[Category: Kato K]]	+
-	[[Category: Sun XM]]	+
-	[[Category: Yao M]]	+
-	[[Category: ~~Ye YX~~]]	+
-	[[Category: ~~Yu J~~]]	+

OCA at 07:35, 15 November 2023

OCA — Wed, 15 Nov 2023 07:35:41 GMT

←Older revision		Revision as of 07:35, 15 November 2023
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 8in1 is ~~ON HOLD until Paper~~ Publication	+	==beta-glucosidase protein from Aplysia kurodai==
		+	<StructureSection load='8in1' size='340' side='right'caption='[[8in1]], [[Resolution\|resolution]] 2.70Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[8in1]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Aplysia_kurodai Aplysia kurodai]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8IN1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8IN1 FirstGlance]. <br>
		+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.7Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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=8in1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8in1 OCA], [https://pdbe.org/8in1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8in1 RCSB], [https://www.ebi.ac.uk/pdbsum/8in1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8in1 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A1V1FXL2_APLKU A0A1V1FXL2_APLKU]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The defensive-offensive associations between algae and herbivores determine marine ecology. Brown algae utilize phlorotannin as their chemical defense against the predator Aplysia kurodai, which uses beta-glucosidase (akuBGL) to digest the laminarin in algae into glucose. Moreover, A. kurodai employs Eisenia hydrolysis-enhancing protein (EHEP) as an offense to protect akuBGL activity from phlorotannin inhibition by precipitating phlorotannin. To underpin the molecular mechanism of this digestive-defensive-offensive system, we determined the structures of the apo and tannic acid (TNA, a phlorotannin analog) bound forms of EHEP, as well as the apo akuBGL. EHEP consisted of three peritrophin-A domains arranged in a triangular shape and bound TNA in the center without significant conformational changes. Structural comparison between EHEP and EHEP-TNA led us to find that EHEP can be resolubilized from phlorotannin precipitation at an alkaline pH, which reflects a requirement in the digestive tract. akuBGL contained two GH1 domains, only one of which conserved the active site. Combining docking analysis, we propose the mechanisms by which phlorotannin inhibits akuBGL by occupying the substrate-binding pocket, and EHEP protects akuBGL against this inhibition by binding with phlorotannin to free the akuBGL pocket.

-	~~Authors: Sun~~, X~~.M.~~, Ye, Y~~.X.~~, ~~Kato~~, K., Yu, J., ~~Yao~~, M.	+	Structural basis of EHEP-mediated offense against phlorotannin-induced defense from brown algae to protect akuBGL activity.,Sun X, Ye Y, Sakurai N, Wang H, Kato K, Yu J, Yuasa K, Tsuji A, Yao M Elife. 2023 Nov 1;12:RP88939. doi: 10.7554/eLife.88939. PMID:37910430<ref>PMID:37910430</ref>

-	~~Description: beta~~-~~glucosidase protein from~~ Aplysia kurodai	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
-	[[Category: Kato, K]]	+	<div class="pdbe-citations 8in1" style="background-color:#fffaf0;"></div>
-	[[Category: Sun~~, X.M~~]]	+	== References ==
-	[[Category: Yao, M]]	+	<references/>
-	[[Category: ~~Yu, J~~]]	+	__TOC__
-	[[Category: ~~Ye, Y.X~~]]	+	</StructureSection>
		+	[[Category: Aplysia kurodai]]
		+	[[Category: Large Structures]]
		+	[[Category: Kato K]]
		+	[[Category: Sun XM]]
		+	[[Category: Yao M]]
		+	[[Category: Ye YX]]
		+	[[Category: Yu J]]

OCA at 05:24, 3 May 2023

OCA — Wed, 03 May 2023 05:24:05 GMT

←Older revision		Revision as of 05:24, 3 May 2023
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 8in1 is ON HOLD	+	The entry 8in1 is ON HOLD until Paper Publication

	Authors: Sun, X.M., Ye, Y.X., Kato, K., Yu, J., Yao, M.		Authors: Sun, X.M., Ye, Y.X., Kato, K., Yu, J., Yao, M.

OCA: Protected "8in1" [edit=sysop:move=sysop]

OCA — Wed, 15 Mar 2023 08:14:29 GMT

Protected "8in1" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:14, 15 March 2023

OCA: New page: '''Unreleased structure''' The entry 8in1 is ON HOLD Authors: Sun, X.M., Ye, Y.X., Kato, K., Yu, J., Yao, M. Description: beta-glucosidase protein from Aplysia kurodai [[Category: Unre...

OCA — Wed, 15 Mar 2023 08:14:28 GMT

New page: '''Unreleased structure''' The entry 8in1 is ON HOLD Authors: Sun, X.M., Ye, Y.X., Kato, K., Yu, J., Yao, M. Description: beta-glucosidase protein from Aplysia kurodai [[Category: Unre...

New page

'''Unreleased structure'''

The entry 8in1 is ON HOLD

Authors: Sun, X.M., Ye, Y.X., Kato, K., Yu, J., Yao, M.

Description: beta-glucosidase protein from Aplysia kurodai
[[Category: Unreleased Structures]]
[[Category: Kato, K]]
[[Category: Sun, X.M]]
[[Category: Yao, M]]
[[Category: Yu, J]]
[[Category: Ye, Y.X]]