7bys - Revision history

OCA at 09:21, 9 October 2024

2024-10-09T09:21:39Z

← Older revision		Revision as of 09:21, 9 October 2024
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	<StructureSection load='7bys' size='340' side='right'caption='[[7bys]], [[Resolution\|resolution]] 1.40Å' scene=''>		<StructureSection load='7bys' size='340' side='right'caption='[[7bys]], [[Resolution\|resolution]] 1.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>~~[[7bys]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Chrysosporium_pruinosum_(gilman_&_abbott)_carmich. Chrysosporium pruinosum (gilman & abbott) carmich.].~~ Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7BYS OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=7BYS FirstGlance]. <br>		<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7BYS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7BYS FirstGlance]. <br>
	</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=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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]] 1.4Å</td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[7byt\|7byt]], [[7byv\|7byv]], [[7byx\|7byx]]</div></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=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Galactan_1,3-beta-galactosidase Galactan 1,3-beta-galactosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.145 3.2.1.145] </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=7bys FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7bys OCA], [https://pdbe.org/7bys PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7bys RCSB], [https://www.ebi.ac.uk/pdbsum/7bys PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7bys ProSAT]</span></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=7bys FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7bys OCA], [~~http~~://pdbe.org/7bys PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=7bys RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/7bys PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=7bys ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	~~[[Category: Galactan 1,3-beta-galactosidase]]~~
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Fujimoto, Z]]		[[Category: Fujimoto Z]]
	[[Category: Igarashi, K]]		[[Category: Igarashi K]]
	[[Category: Ishida, T]]		[[Category: Ishida T]]
	[[Category: Kaneko, S]]		[[Category: Kaneko S]]
	[[Category: Kishine, N]]		[[Category: Kishine N]]
	[[Category: Matsuyama, K]]		[[Category: Matsuyama K]]
	~~[[Category: 3-galactanase]]~~
	~~[[Category: Apo form]]~~
	~~[[Category: Arabinogalactan degrade]]~~
	~~[[Category: Carbohydrate binding module family 35]]~~
	~~[[Category: Exo-beta-1]]~~
	~~[[Category: Glycoside hydrolase family 43]]~~
	~~[[Category: Hydrolase~~]]

OCA at 06:04, 20 January 2021

2021-01-20T06:04:10Z

← Older revision		Revision as of 06:04, 20 January 2021
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	==Crystal structure of exo-beta-1,3-galactanase from Phanerochaete chrysosporium Pc1,3Gal43A apo form==		==Crystal structure of exo-beta-1,3-galactanase from Phanerochaete chrysosporium Pc1,3Gal43A apo form==
	<StructureSection load='7bys' size='340' side='right'caption='[[7bys]]' scene=''>		<StructureSection load='7bys' size='340' side='right'caption='[[7bys]], [[Resolution\|resolution]] 1.40Å' 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=7BYS OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=7BYS FirstGlance]. <br>		<table><tr><td colspan='2'>[[7bys]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Chrysosporium_pruinosum_(gilman_&_abbott)_carmich. Chrysosporium pruinosum (gilman & abbott) carmich.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7BYS OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=7BYS FirstGlance]. <br>
	</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=7bys FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7bys OCA], [http://pdbe.org/7bys PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7bys RCSB], [http://www.ebi.ac.uk/pdbsum/7bys PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=7bys ProSAT]</span></td></tr>		</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=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
			<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[7byt\|7byt]], [[7byv\|7byv]], [[7byx\|7byx]]</div></td></tr>
			<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Galactan_1,3-beta-galactosidase Galactan 1,3-beta-galactosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.145 3.2.1.145] </span></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=7bys FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7bys OCA], [http://pdbe.org/7bys PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7bys RCSB], [http://www.ebi.ac.uk/pdbsum/7bys PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=7bys ProSAT]</span></td></tr>
	</table>		</table>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Arabinogalactan proteins (AGPs) are plant proteoglycans with functions in growth and development. However, these functions are largely unexplored, mainly because of the complexity of the sugar moieties. These carbohydrate sequences are generally analyzed with the aid of glycoside hydrolases. The exo-beta-1,3-galactanase is a glycoside hydrolase from the basidiomycete Phanerochaete chrysosporium (Pc1,3Gal43A), which specifically cleaves AGPs. However, its structure is not known in relation to its mechanism bypassing side chains. In this study, we solved the apo and liganded structures of Pc1,3Gal43A, which reveal a glycoside hydrolase family 43 subfamily 24 (GH43_sub24) catalytic domain together with a carbohydrate-binding module family (CBM) 35 binding domain. GH43_sub24 is known to lack the catalytic base Asp conserved among other GH43 subfamilies. Our structure in combination with kinetic analyses reveal that the tautomerized imidic acid group of Gln263 serves as the catalytic base residue instead. Pc1,3Gal43A has three subsites that continue from the bottom of the catalytic pocket to the solvent. Subsite -1 contains a space that can accommodate the C-6 methylol of Gal, enabling the enzyme to bypass the beta-1,6-linked galactan side chains of AGPs. Furthermore, the galactan-binding domain in CBM35 has a different ligand interaction mechanism from other sugar-binding CBM35s, including those that bind galactomannan. Specifically, we noted a Gly->Trp substitution, which affects pyranose stacking, and an Asp->Asn substitution in the binding pocket, which recognizes beta-linked rather than alpha-linked Gal residues. These findings should facilitate further structural analysis of AGPs and may also be helpful in engineering designer enzymes for efficient biomass utilization.

			Unique active site and subsite features in the arabinogalactan-degrading GH43 exo-beta-1,3-galactanase from Phanerochaete chrysosporium.,Matsuyama K, Kishine N, Fujimoto Z, Sunagawa N, Kotake T, Tsumuraya Y, Samejima M, Igarashi K, Kaneko S J Biol Chem. 2020 Oct 22. pii: RA120.016149. doi: 10.1074/jbc.RA120.016149. PMID:33093171<ref>PMID:33093171</ref>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			<div class="pdbe-citations 7bys" style="background-color:#fffaf0;"></div>
			== References ==
			<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Galactan 1,3-beta-galactosidase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Fujimoto Z]]		[[Category: Fujimoto, Z]]
	[[Category: Igarashi K]]		[[Category: Igarashi, K]]
	[[Category: Ishida T]]		[[Category: Ishida, T]]
	[[Category: Kaneko S]]		[[Category: Kaneko, S]]
	[[Category: Kishine N]]		[[Category: Kishine, N]]
	[[Category: Matsuyama K]]		[[Category: Matsuyama, K]]
			[[Category: 3-galactanase]]
			[[Category: Apo form]]
			[[Category: Arabinogalactan degrade]]
			[[Category: Carbohydrate binding module family 35]]
			[[Category: Exo-beta-1]]
			[[Category: Glycoside hydrolase family 43]]
			[[Category: Hydrolase]]

OCA at 07:25, 4 November 2020

2020-11-04T07:25:36Z

← Older revision		Revision as of 07:25, 4 November 2020
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	~~'''Unreleased structure'''~~

	~~The entry 7bys is ON HOLD until Paper Publication~~		==Crystal structure of exo-beta-1,3-galactanase from Phanerochaete chrysosporium Pc1,3Gal43A apo form==
			<StructureSection load='7bys' size='340' side='right'caption='[[7bys]]' scene=''>
	~~Authors: Matsuyama, K., Ishida, T., Kishine, N., Fujimoto, Z., Igarashi, K., Kaneko, S.~~		== Structural highlights ==
			<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7BYS OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=7BYS FirstGlance]. <br>
	~~Description:~~ Crystal structure of exo-beta-1,3-galactanase from Phanerochaete chrysosporium Pc1,3Gal43A apo form		</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=7bys FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7bys OCA], [http://pdbe.org/7bys PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7bys RCSB], [http://www.ebi.ac.uk/pdbsum/7bys PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=7bys ProSAT]</span></td></tr>
	[[Category: ~~Unreleased~~ Structures]]		</table>
	[[Category: ~~Ishida, T~~]]		__TOC__
	[[Category: ~~Kaneko, S~~]]		</StructureSection>
	[[Category: ~~Igarashi, K~~]]		[[Category: Large Structures]]
	[[Category: ~~Kishine, N~~]]		[[Category: Fujimoto Z]]
	[[Category: ~~Fujimoto, Z~~]]		[[Category: Igarashi K]]
	[[Category: Matsuyama, K]]		[[Category: Ishida T]]
			[[Category: Kaneko S]]
			[[Category: Kishine N]]
			[[Category: Matsuyama K]]

OCA at 05:09, 27 May 2020

2020-05-27T05:09:22Z

← Older revision		Revision as of 05:09, 27 May 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 7bys is ON HOLD		The entry 7bys is ON HOLD until Paper Publication

	Authors: Matsuyama, K., Ishida, T., Kishine, N., Fujimoto, Z., Igarashi, K., Kaneko, S.		Authors: Matsuyama, K., Ishida, T., Kishine, N., Fujimoto, Z., Igarashi, K., Kaneko, S.

	Description: Crystal structure of exo-beta-1,3-galactanase from ~~phanerochaete~~ chrysosporium Pc1,3Gal43A apo form		Description: Crystal structure of exo-beta-1,3-galactanase from Phanerochaete chrysosporium Pc1,3Gal43A apo form
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Ishida, T]]		[[Category: Ishida, T]]
			[[Category: Kaneko, S]]
			[[Category: Igarashi, K]]
	[[Category: Kishine, N]]		[[Category: Kishine, N]]
	[[Category: Fujimoto, Z]]		[[Category: Fujimoto, Z]]
	~~[[Category: Kaneko, S]]~~
	~~[[Category: Igarashi, K]]~~
	[[Category: Matsuyama, K]]		[[Category: Matsuyama, K]]

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

2020-04-29T05:39:33Z

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

← Older revision	Revision as of 05:39, 29 April 2020
(No difference)

OCA: New page: '''Unreleased structure''' The entry 7bys is ON HOLD Authors: Matsuyama, K., Ishida, T., Kishine, N., Fujimoto, Z., Igarashi, K., Kaneko, S. Description: Crystal structure of exo-beta-...

2020-04-29T05:39:32Z

New page: '''Unreleased structure''' The entry 7bys is ON HOLD Authors: Matsuyama, K., Ishida, T., Kishine, N., Fujimoto, Z., Igarashi, K., Kaneko, S. Description: Crystal structure of exo-beta-...

New page

'''Unreleased structure'''

The entry 7bys is ON HOLD

Authors: Matsuyama, K., Ishida, T., Kishine, N., Fujimoto, Z., Igarashi, K., Kaneko, S.

Description: Crystal structure of exo-beta-1,3-galactanase from phanerochaete chrysosporium Pc1,3Gal43A apo form
[[Category: Unreleased Structures]]
[[Category: Ishida, T]]
[[Category: Kishine, N]]
[[Category: Fujimoto, Z]]
[[Category: Kaneko, S]]
[[Category: Igarashi, K]]
[[Category: Matsuyama, K]]