7vkz - Revision history

OCA at 19:43, 29 May 2024

OCA — Wed, 29 May 2024 19:43:06 GMT

←Older revision		Revision as of 19:43, 29 May 2024
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	==The complex structure of beta-1,2-glucosyltransferase from Ignavibacterium album with 1-Deoxynojirimycin==		==The complex structure of beta-1,2-glucosyltransferase from Ignavibacterium album with 1-Deoxynojirimycin==
-	<StructureSection load='7vkz' size='340' side='right'caption='[[7vkz]]' scene=''>	+	<StructureSection load='7vkz' size='340' side='right'caption='[[7vkz]], [[Resolution\|resolution]] 2.00Å' 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=7VKZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7VKZ FirstGlance]. <br>		<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7VKZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7VKZ 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=7vkz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7vkz OCA], [https://pdbe.org/7vkz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7vkz RCSB], [https://www.ebi.ac.uk/pdbsum/7vkz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7vkz 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]] 2Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=NOJ:1-DEOXYNOJIRIMYCIN'>NOJ</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=7vkz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7vkz OCA], [https://pdbe.org/7vkz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7vkz RCSB], [https://www.ebi.ac.uk/pdbsum/7vkz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7vkz ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The IALB_1185 protein, which is encoded in the gene cluster for endo-beta-1,2-glucanase homologs in the genome of Ignavibacterium album, is a glycoside hydrolase family (GH) 35 protein. However, most known GH35 enzymes are beta-galactosidases, which is inconsistent with the components of this gene cluster. Thus, IALB_1185 is expected to possess novel enzymatic properties. Here, we showed using recombinant IALB_1185 that this protein has glycosyltransferase activity toward beta-1,2-glucooligosaccharides, and that the kinetic parameters for beta-1,2-glucooligosaccharides are not within the ranges for general GH enzymes. When various aryl- and alkyl-glucosides were used as acceptors, glycosyltransfer products derived from these acceptors were subsequently detected. Kinetic analysis further revealed that the enzyme has wide aglycone specificity regardless of the anomer, and that the beta-1,2-linked glucose dimer sophorose is an appropriate donor. In the complex of wild-type IALB_1185 with sophorose, the electron density of sophorose was clearly observed at subsites -1 and +1, whereas in the E343Q mutant-sophorose complex, the electron density of sophorose was clearly observed at subsites +1 and +2. This observation suggests that binding at subsites -1 and +2 competes through Glu102, which is consistent with the preference for sophorose as a donor and unsuitability of beta-1,2-glucooligosaccharides as acceptors. A pliable hydrophobic pocket that can accommodate various aglycone moieties was also observed in the complex structures with various glucosides. Overall, our biochemical and structural data are indicative of a novel enzymatic reaction. We propose that IALB_1185 be redefined beta-1,2-glucooligosaccharide:d-glucoside beta-d-glucosyltransferase as a systematic name and beta-1,2-glucosyltransferase as an accepted name.
		+
		+	Characterization and structural analyses of a novel glycosyltransferase acting on the beta-1,2-glucosidic linkages.,Kobayashi K, Shimizu H, Tanaka N, Kuramochi K, Nakai H, Nakajima M, Taguchi H J Biol Chem. 2022 Jan 19;298(3):101606. doi: 10.1016/j.jbc.2022.101606. PMID:35065074<ref>PMID:35065074</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7vkz" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 06:10, 9 March 2022

OCA — Wed, 09 Mar 2022 06:10:24 GMT

←Older revision		Revision as of 06:10, 9 March 2022
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-	'''Unreleased structure'''

-	The ~~entry~~ 7vkz ~~is ON HOLD until Oct 01 2023~~	+	==The complex structure of beta-1,2-glucosyltransferase from Ignavibacterium album with 1-Deoxynojirimycin==
-		+	<StructureSection load='7vkz' size='340' side='right'caption='[[7vkz]]' scene=''>
-	~~Authors~~: ~~Kobayashi, K~~.~~, Shimizu, H~~., ~~Tanaka, N~~., ~~Kuramochi, K~~., ~~Nakai, H~~., ~~Nakajima, M~~., ~~Taguchi, H~~.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7VKZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7VKZ FirstGlance]. <br>
-	~~Description: The complex structure of beta-1,2-glucosyltransferase from Ignavibacterium album with 1-Deoxynojirimycin~~	+	</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=7vkz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7vkz OCA], [https://pdbe.org/7vkz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7vkz RCSB], [https://www.ebi.ac.uk/pdbsum/7vkz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7vkz ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: ~~Kuramochi,~~ K]]	+	__TOC__
-	[[Category: ~~Tanaka, N~~]]	+	</StructureSection>
-	[[Category: ~~Taguchi,~~ H]]	+	[[Category: Large Structures]]
-	[[Category: ~~Kobayashi, K~~]]	+	[[Category: Kobayashi K]]
-	[[Category: ~~Nakajima, M~~]]	+	[[Category: Kuramochi K]]
-	[[Category: ~~Nakai,~~ H]]	+	[[Category: Nakai H]]
-	[[Category: ~~Shimizu, H~~]]	+	[[Category: Nakajima M]]
		+	[[Category: Shimizu H]]
		+	[[Category: Taguchi H]]
		+	[[Category: Tanaka N]]

OCA at 12:59, 3 November 2021

OCA — Wed, 03 Nov 2021 12:59:06 GMT

←Older revision		Revision as of 12:59, 3 November 2021
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7vkz is ON HOLD	+	The entry 7vkz is ON HOLD until Oct 01 2023

	Authors: Kobayashi, K., Shimizu, H., Tanaka, N., Kuramochi, K., Nakai, H., Nakajima, M., Taguchi, H.		Authors: Kobayashi, K., Shimizu, H., Tanaka, N., Kuramochi, K., Nakai, H., Nakajima, M., Taguchi, H.
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	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Kuramochi, K]]		[[Category: Kuramochi, K]]
		+	[[Category: Tanaka, N]]
		+	[[Category: Taguchi, H]]
	[[Category: Kobayashi, K]]		[[Category: Kobayashi, K]]
	[[Category: Nakajima, M]]		[[Category: Nakajima, M]]
	[[Category: Nakai, H]]		[[Category: Nakai, H]]
	[[Category: Shimizu, H]]		[[Category: Shimizu, H]]
-	[[Category: Tanaka, N]]
-	[[Category: Taguchi, H]]

OCA at 10:32, 13 October 2021

OCA — Wed, 13 Oct 2021 10:32:43 GMT

←Older revision		Revision as of 10:32, 13 October 2021
Line 5:		Line 5:
	Authors: Kobayashi, K., Shimizu, H., Tanaka, N., Kuramochi, K., Nakai, H., Nakajima, M., Taguchi, H.		Authors: Kobayashi, K., Shimizu, H., Tanaka, N., Kuramochi, K., Nakai, H., Nakajima, M., Taguchi, H.

-	Description: The ~~apo~~ structure of beta-1,2-glucosyltransferase from Ignavibacterium album	+	Description: The complex structure of beta-1,2-glucosyltransferase from Ignavibacterium album with 1-Deoxynojirimycin
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Kuramochi, K]]		[[Category: Kuramochi, K]]
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	[[Category: Nakajima, M]]		[[Category: Nakajima, M]]
	[[Category: Nakai, H]]		[[Category: Nakai, H]]
-	[[Category: Taguchi, H]]
	[[Category: Shimizu, H]]		[[Category: Shimizu, H]]
	[[Category: Tanaka, N]]		[[Category: Tanaka, N]]
		+	[[Category: Taguchi, H]]

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

OCA — Wed, 06 Oct 2021 04:27:23 GMT

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

←Older revision

Revision as of 04:27, 6 October 2021

OCA: New page: '''Unreleased structure''' The entry 7vkz is ON HOLD Authors: Kobayashi, K., Shimizu, H., Tanaka, N., Kuramochi, K., Nakai, H., Nakajima, M., Taguchi, H. Description: The apo structure...

OCA — Wed, 06 Oct 2021 04:27:22 GMT

New page: '''Unreleased structure''' The entry 7vkz is ON HOLD Authors: Kobayashi, K., Shimizu, H., Tanaka, N., Kuramochi, K., Nakai, H., Nakajima, M., Taguchi, H. Description: The apo structure...

New page

'''Unreleased structure'''

The entry 7vkz is ON HOLD

Authors: Kobayashi, K., Shimizu, H., Tanaka, N., Kuramochi, K., Nakai, H., Nakajima, M., Taguchi, H.

Description: The apo structure of beta-1,2-glucosyltransferase from Ignavibacterium album
[[Category: Unreleased Structures]]
[[Category: Kuramochi, K]]
[[Category: Kobayashi, K]]
[[Category: Nakajima, M]]
[[Category: Nakai, H]]
[[Category: Taguchi, H]]
[[Category: Shimizu, H]]
[[Category: Tanaka, N]]