5zru - Revision history

OCA at 10:28, 27 March 2024

OCA — Wed, 27 Mar 2024 10:28:58 GMT

←Older revision		Revision as of 10:28, 27 March 2024
Line 3:		Line 3:
	<StructureSection load='5zru' size='340' side='right'caption='[[5zru]], [[Resolution\|resolution]] 1.83Å' scene=''>		<StructureSection load='5zru' size='340' side='right'caption='[[5zru]], [[Resolution\|resolution]] 1.83Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5zru]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Atcc_24 Atcc 24~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZRU OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5ZRU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5zru]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Niallia_circulans Niallia circulans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZRU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ZRU FirstGlance]. <br>
-	</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=PE5:3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL'>PE5</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.833Å</td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">agl ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1397 ATCC 24])~~</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=PE5:3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL'>PE5</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5zru FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zru OCA], [~~http~~://pdbe.org/5zru PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5zru RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5zru PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5zru 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=5zru FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zru OCA], [https://pdbe.org/5zru PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5zru RCSB], [https://www.ebi.ac.uk/pdbsum/5zru PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5zru ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/Q0WYG9_NIACI Q0WYG9_NIACI]
-	Glycoside hydrolase (GH) 87-type alpha-1,3-glucanase hydrolyses the alpha-1,3-glucoside linkages of alpha-1,3-glucan, which is found in fungal cell walls and extracellular polysaccharides produced by oral Streptococci. In this study, we report on the molecular structure of the catalytic unit of GH 87-type alpha-1,3-glucanase, Agl-KA, from Bacillus circulans, as determined by x-ray crystallography at a resolution of 1.82 A. The catalytic unit constitutes a complex structure of two tandemly connected domains-the N-terminal galactose-binding-like domain and the C-terminal right-handed beta-helix domain. While the beta-helix domain is widely found among polysaccharide-processing enzymes, complex formation with the galactose-binding-like domain was observed for the first time. Biochemical assays showed that Asp1067, Asp1090 and Asp1091 are important for catalysis, and these residues are indeed located at the putative substrate-binding cleft, which forms a closed end and explains the product specificity.	+

-	Crystal structure of the catalytic unit of GH 87-type alpha-1,3-glucanase Agl-KA from Bacillus circulans.,Yano S, Suyotha W, Oguro N, Matsui T, Shiga S, Itoh T, Hibi T, Tanaka Y, Wakayama M, Makabe K Sci Rep. 2019 Oct 25;9(1):15295. doi: 10.1038/s41598-019-51822-5. PMID:31653959<ref>PMID:31653959</ref>	+	==See Also==
-		+	*[[Glucanase 3D structures\|Glucanase 3D structures]]
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 5zru" style="background-color:#fffaf0;"></div>~~	+
-	== ~~References~~ ==	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Atcc 24]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Makabe, K~~]]	+	[[Category: Niallia circulans]]
-	[[Category: ~~Yano, S~~]]	+	[[Category: Makabe K]]
-	[[Category: ~~Agl-ka gh87]]~~	+	[[Category: Yano S]]
-	~~[[Category: Hydrolase~~]]	+

OCA at 06:20, 6 May 2020

OCA — Wed, 06 May 2020 06:20:01 GMT

←Older revision		Revision as of 06:20, 6 May 2020
Line 3:		Line 3:
	<StructureSection load='5zru' size='340' side='right'caption='[[5zru]], [[Resolution\|resolution]] 1.83Å' scene=''>		<StructureSection load='5zru' size='340' side='right'caption='[[5zru]], [[Resolution\|resolution]] 1.83Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5zru]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZRU OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5ZRU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5zru]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_24 Atcc 24]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZRU OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5ZRU FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=PE5:3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL'>PE5</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>	+	</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=PE5:3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL'>PE5</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=5zru FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zru OCA], [http://pdbe.org/5zru PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zru RCSB], [http://www.ebi.ac.uk/pdbsum/5zru PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zru ProSAT]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">agl ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1397 ATCC 24])</td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5zru FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zru OCA], [http://pdbe.org/5zru PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zru RCSB], [http://www.ebi.ac.uk/pdbsum/5zru PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zru ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Glycoside hydrolase (GH) 87-type alpha-1,3-glucanase hydrolyses the alpha-1,3-glucoside linkages of alpha-1,3-glucan, which is found in fungal cell walls and extracellular polysaccharides produced by oral Streptococci. In this study, we report on the molecular structure of the catalytic unit of GH 87-type alpha-1,3-glucanase, Agl-KA, from Bacillus circulans, as determined by x-ray crystallography at a resolution of 1.82 A. The catalytic unit constitutes a complex structure of two tandemly connected domains-the N-terminal galactose-binding-like domain and the C-terminal right-handed beta-helix domain. While the beta-helix domain is widely found among polysaccharide-processing enzymes, complex formation with the galactose-binding-like domain was observed for the first time. Biochemical assays showed that Asp1067, Asp1090 and Asp1091 are important for catalysis, and these residues are indeed located at the putative substrate-binding cleft, which forms a closed end and explains the product specificity.
		+
		+	Crystal structure of the catalytic unit of GH 87-type alpha-1,3-glucanase Agl-KA from Bacillus circulans.,Yano S, Suyotha W, Oguro N, Matsui T, Shiga S, Itoh T, Hibi T, Tanaka Y, Wakayama M, Makabe K Sci Rep. 2019 Oct 25;9(1):15295. doi: 10.1038/s41598-019-51822-5. PMID:31653959<ref>PMID:31653959</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5zru" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc 24]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Makabe, K]]		[[Category: Makabe, K]]

OCA at 06:43, 23 October 2019

OCA — Wed, 23 Oct 2019 06:43:10 GMT

←Older revision		Revision as of 06:43, 23 October 2019
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-	'''Unreleased structure'''

-	~~The entry~~ 5zru ~~is ON HOLD until Oct 20 2020~~	+	==Crystal structure of Agl-KA catalytic domain==
-		+	<StructureSection load='5zru' size='340' side='right'caption='[[5zru]], [[Resolution\|resolution]] 1.83Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5zru]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZRU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZRU FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=PE5:3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL'>PE5</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=5zru FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zru OCA], [http://pdbe.org/5zru PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zru RCSB], [http://www.ebi.ac.uk/pdbsum/5zru PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zru ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Makabe, K]]
		+	[[Category: Yano, S]]
		+	[[Category: Agl-ka gh87]]
		+	[[Category: Hydrolase]]

OCA at 03:55, 10 July 2019

OCA — Wed, 10 Jul 2019 03:55:24 GMT

←Older revision		Revision as of 03:55, 10 July 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5zru is ON HOLD until ~~Jun 25~~ 2020	+	The entry 5zru is ON HOLD until Oct 20 2020

	Authors:		Authors:

OCA at 03:53, 17 April 2019

OCA — Wed, 17 Apr 2019 03:53:34 GMT

←Older revision		Revision as of 03:53, 17 April 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5zru is ON HOLD until ~~Paper Publication~~	+	The entry 5zru is ON HOLD until Jun 25 2020

	Authors:		Authors:

OCA at 05:17, 6 March 2019

OCA — Wed, 06 Mar 2019 05:17:43 GMT

←Older revision		Revision as of 05:17, 6 March 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors:		Authors:

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

OCA — Wed, 02 May 2018 06:35:42 GMT

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

←Older revision

Revision as of 06:35, 2 May 2018

OCA: New page: '''Unreleased structure''' The entry 5zru is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 02 May 2018 06:35:41 GMT

New page: '''Unreleased structure''' The entry 5zru is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5zru is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]