6k0v - Revision history

OCA at 10:24, 22 November 2023

OCA — Wed, 22 Nov 2023 10:24:48 GMT

←Older revision		Revision as of 10:24, 22 November 2023
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	<StructureSection load='6k0v' size='340' side='right'caption='[[6k0v]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='6k0v' size='340' side='right'caption='[[6k0v]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6k0v]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6K0V OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6K0V FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6k0v]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Paenibacillus_glycanilyticus Paenibacillus glycanilyticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6K0V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6K0V FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=~~SO4~~:~~SULFATE+ION~~'>~~SO4~~</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]] 2.504Å</td></tr>
-	~~<tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b~~></td>~~<td class="sblockDat">[[6k0m\|6k0m]], [[6k0n\|6k0n]], [[6k0p\|6k0p]], [[6k0q\|6k0q]], [[6k0s\|6k0s]], [[6k0u\|6k0u]]~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=PRD_900052:alpha-nigerose'>PRD_900052</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=6k0v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k0v OCA], [~~http~~://pdbe.org/6k0v PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6k0v RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6k0v PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6k0v 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=6k0v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k0v OCA], [https://pdbe.org/6k0v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6k0v RCSB], [https://www.ebi.ac.uk/pdbsum/6k0v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6k0v ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A068PS59_9BACL A0A068PS59_9BACL]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 6k0v" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6k0v" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Glucanase 3D structures\|Glucanase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Hayashi, J]]	+	[[Category: Paenibacillus glycanilyticus]]
-	[[Category: Hibi, T]]	+	[[Category: Hayashi J]]
-	[[Category: Intuy, R]]	+	[[Category: Hibi T]]
-	[[Category: Itoh, T]]	+	[[Category: Intuy R]]
-	[[Category: Makabe, K]]	+	[[Category: Itoh T]]
-	[[Category: Suyotha, W]]	+	[[Category: Makabe K]]
-	[[Category: Wakayama, M]]	+	[[Category: Suyotha W]]
-	[[Category: Yano, S]]	+	[[Category: Wakayama M]]
-	~~[[Category: 3-glucanase]]~~	+	[[Category: Yano S]]
-	~~[[Category: Catalytic domain]]~~	+
-	~~[[Category: Gh87 alpha-1]]~~	+
-	~~[[Category: Hydrolase~~]]	+

OCA at 09:04, 25 December 2019

OCA — Wed, 25 Dec 2019 09:04:19 GMT

←Older revision		Revision as of 09:04, 25 December 2019
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-	'''Unreleased structure'''

-	~~The entry~~ 6k0v is ~~ON HOLD until Paper~~ Publication	+	==Catalytic domain of GH87 alpha-1,3-glucanase D1069A in complex with tetrasaccharides==
		+	<StructureSection load='6k0v' size='340' side='right'caption='[[6k0v]], [[Resolution\|resolution]] 2.50Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6k0v]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6K0V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6K0V FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6k0m\|6k0m]], [[6k0n\|6k0n]], [[6k0p\|6k0p]], [[6k0q\|6k0q]], [[6k0s\|6k0s]], [[6k0u\|6k0u]]</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=6k0v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k0v OCA], [http://pdbe.org/6k0v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6k0v RCSB], [http://www.ebi.ac.uk/pdbsum/6k0v PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6k0v ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The alpha-1,3-glucanase from Paenibacillus glycanilyticus FH11 (Agl-FH1), a member of the glycoside hydrolase family 87 (GH87), hydrolyzes alpha-1,3-glucan with an endo-action. GH87 enzymes are known to degrade dental plaque produced by oral pathogenic Streptococcus species. In this study, the kinetic analyses revealed that this enzyme hydrolyzed alpha-1,3-tetraglucan into glucose and alpha-1,3-triglucan with beta-configuration at the reducing end by an inverting mechanism. The crystal structures of the catalytic domain (CatAgl-FH1) complexed with or without oligosaccharides at 1.4-2.5 or 1.6 A resolutions, respectively, are also presented. The initial crystal structure of CatAgl-FH1 was determined by native single-wavelength anomalous diffraction. The catalytic domain was composed of two modules, a beta-sandwich fold module, and a right-handed beta-helix fold module. The structure of the beta-sandwich was similar to those of the carbohydrate-binding module family 35 members. The glycerol or nigerose enzyme complex structures demonstrated that this beta-sandwich fold module is a novel carbohydrate-binding module with the capabilities to bind saccharides and to promote the degradation of polysaccharides. The structures of the inactive mutant in complexes with oligosaccharide showed that at least eight subsites for glucose binding were located in the active cleft of the beta-helix fold and the architecture of the active cleft was suitable for the recognition and hydrolysis of alpha-1,3-glucan by the inverting mechanism. The structural similarity to GH28 and GH49 enzymes and the results of site-directed mutagenesis indicated that three Asp residues, Asp1045, Asp1068, and Asp1069, are the most likely candidates for the catalytic residues of Agl-FH1. DATABASE: Structural data are available in RCSB Protein Data Bank under the accession numbers 6K0M (CatAgl-FH1), 6K0N (WT/nigerose), 6K0P (D1045A/nigerose), 6K0Q (D1068A/nigerose), 6K0S (D1069A/ nigerose), 6K0U (D1068A/oligo), and 6K0V (D1069A/oligo). ENZYMES: Agl-FH1, alpha-1,3-glucanase (EC3.2.1.59) from Paenibacillus glycanilyticus FH11.

-	~~Authors: Itoh~~, T., Intuy, R., Suyotha, W., Hayashi, J., Yano, S., Makabe, K., Wakayama, M., Hibi, T.	+	Structural insights into substrate recognition and catalysis by glycoside hydrolase family 87 alpha-1,3-glucanase from Paenibacillus glycanilyticus FH11.,Itoh T, Intuy R, Suyotha W, Hayashi J, Yano S, Makabe K, Wakayama M, Hibi T FEBS J. 2019 Dec 2. doi: 10.1111/febs.15161. PMID:31788942<ref>PMID:31788942</ref>

-	~~Description: Catalytic domain~~ of ~~GH87 alpha~~-~~1,3~~-~~glucanase D1069A in complex with tetrasaccharides~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 6k0v" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Hayashi, J]]
		+	[[Category: Hibi, T]]
	[[Category: Intuy, R]]		[[Category: Intuy, R]]
		+	[[Category: Itoh, T]]
		+	[[Category: Makabe, K]]
	[[Category: Suyotha, W]]		[[Category: Suyotha, W]]
	[[Category: Wakayama, M]]		[[Category: Wakayama, M]]
-	[[Category: Hibi, T]]
-	[[Category: Itoh, T]]
-	[[Category: Hayashi, J]]
	[[Category: Yano, S]]		[[Category: Yano, S]]
-	[[Category: ~~Makabe, K~~]]	+	[[Category: 3-glucanase]]
		+	[[Category: Catalytic domain]]
		+	[[Category: Gh87 alpha-1]]
		+	[[Category: Hydrolase]]

OCA at 20:56, 5 June 2019

OCA — Wed, 05 Jun 2019 20:56:47 GMT

←Older revision		Revision as of 20:56, 5 June 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6k0v is ON HOLD	+	The entry 6k0v is ON HOLD until Paper Publication

	Authors: Itoh, T., Intuy, R., Suyotha, W., Hayashi, J., Yano, S., Makabe, K., Wakayama, M., Hibi, T.		Authors: Itoh, T., Intuy, R., Suyotha, W., Hayashi, J., Yano, S., Makabe, K., Wakayama, M., Hibi, T.
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	Description: Catalytic domain of GH87 alpha-1,3-glucanase D1069A in complex with tetrasaccharides		Description: Catalytic domain of GH87 alpha-1,3-glucanase D1069A in complex with tetrasaccharides
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
		+	[[Category: Intuy, R]]
		+	[[Category: Suyotha, W]]
		+	[[Category: Wakayama, M]]
	[[Category: Hibi, T]]		[[Category: Hibi, T]]
	[[Category: Itoh, T]]		[[Category: Itoh, T]]
	[[Category: Hayashi, J]]		[[Category: Hayashi, J]]
	[[Category: Yano, S]]		[[Category: Yano, S]]
-	[[Category: Intuy, R]]
-	[[Category: Suyotha, W]]
	[[Category: Makabe, K]]		[[Category: Makabe, K]]
-	[[Category: Wakayama, M]]

OCA: Protected "6k0v" [edit=sysop:move=sysop]

OCA — Tue, 21 May 2019 05:40:23 GMT

Protected "6k0v" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:40, 21 May 2019

OCA: New page: '''Unreleased structure''' The entry 6k0v is ON HOLD Authors: Itoh, T., Intuy, R., Suyotha, W., Hayashi, J., Yano, S., Makabe, K., Wakayama, M., Hibi, T. Description: Catalytic domain ...

OCA — Tue, 21 May 2019 05:40:22 GMT

New page: '''Unreleased structure''' The entry 6k0v is ON HOLD Authors: Itoh, T., Intuy, R., Suyotha, W., Hayashi, J., Yano, S., Makabe, K., Wakayama, M., Hibi, T. Description: Catalytic domain ...

New page

'''Unreleased structure'''

The entry 6k0v is ON HOLD

Authors: Itoh, T., Intuy, R., Suyotha, W., Hayashi, J., Yano, S., Makabe, K., Wakayama, M., Hibi, T.

Description: Catalytic domain of GH87 alpha-1,3-glucanase D1069A in complex with tetrasaccharides
[[Category: Unreleased Structures]]
[[Category: Hibi, T]]
[[Category: Itoh, T]]
[[Category: Hayashi, J]]
[[Category: Yano, S]]
[[Category: Intuy, R]]
[[Category: Suyotha, W]]
[[Category: Makabe, K]]
[[Category: Wakayama, M]]