7byv - Revision history

OCA at 15:43, 29 November 2023

OCA — Wed, 29 Nov 2023 15:43:25 GMT

←Older revision		Revision as of 15:43, 29 November 2023
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	<StructureSection load='7byv' size='340' side='right'caption='[[7byv]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='7byv' size='340' side='right'caption='[[7byv]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7byv]] is a 1 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=7BYV OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=7BYV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7byv]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Phanerodontia_chrysosporium Phanerodontia chrysosporium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7BYV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7BYV 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=GAL:BETA-D-GALACTOSE'>GAL</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]] 2.5Å</td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[7bys\|7bys]], [[7byt\|7byt]], [[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=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Pc1,3Gal43A ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5306 Chrysosporium pruinosum (Gilman & Abbott) Carmich.])</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=7byv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7byv OCA], [https://pdbe.org/7byv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7byv RCSB], [https://www.ebi.ac.uk/pdbsum/7byv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7byv ProSAT]</span></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=7byv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7byv OCA], [~~http~~://pdbe.org/7byv PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=7byv RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/7byv PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=7byv ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q50KB2_PHACH Q50KB2_PHACH]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Galactan 1,3-beta-galactosidase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Fujimoto, Z]]	+	[[Category: Phanerodontia chrysosporium]]
-	[[Category: Igarashi, K]]	+	[[Category: Fujimoto Z]]
-	[[Category: Ishida, T]]	+	[[Category: Igarashi K]]
-	[[Category: Kaneko, S]]	+	[[Category: Ishida T]]
-	[[Category: Kishine, N]]	+	[[Category: Kaneko S]]
-	[[Category: Matsuyama, K]]	+	[[Category: Kishine N]]
-	~~[[Category: 3-galactanase]]~~	+	[[Category: Matsuyama K]]
-	~~[[Category: 3-galactotriose]]~~	+
-	~~[[Category: Arabinogalactan degrade]]~~	+
-	~~[[Category: Carbohydrate binding module family 35]]~~	+
-	~~[[Category: Complex with beta-1]]~~	+
-	~~[[Category: Exo-beta-1]]~~	+
-	~~[[Category: Glycoside hydrolase family 43]]~~	+
-	~~[[Category: Hydrolase~~]]	+

OCA at 06:04, 20 January 2021

OCA — Wed, 20 Jan 2021 06:04:15 GMT

←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 E208Q with beta-1,3-galactotriose==		==Crystal structure of exo-beta-1,3-galactanase from Phanerochaete chrysosporium Pc1,3Gal43A E208Q with beta-1,3-galactotriose==
-	<StructureSection load='7byv' size='340' side='right'caption='[[7byv]]' scene=''>	+	<StructureSection load='7byv' size='340' side='right'caption='[[7byv]], [[Resolution\|resolution]] 2.50Å' 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=7BYV OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=7BYV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7byv]] is a 1 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=7BYV OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=7BYV 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=7byv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7byv OCA], [http://pdbe.org/7byv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7byv RCSB], [http://www.ebi.ac.uk/pdbsum/7byv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=7byv 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=GAL:BETA-D-GALACTOSE'>GAL</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;'>[[7bys\|7bys]], [[7byt\|7byt]], [[7byx\|7byx]]</div></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Pc1,3Gal43A ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5306 Chrysosporium pruinosum (Gilman & Abbott) Carmich.])</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=7byv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7byv OCA], [http://pdbe.org/7byv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7byv RCSB], [http://www.ebi.ac.uk/pdbsum/7byv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=7byv 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 7byv" 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: 3-galactotriose]]
		+	[[Category: Arabinogalactan degrade]]
		+	[[Category: Carbohydrate binding module family 35]]
		+	[[Category: Complex with beta-1]]
		+	[[Category: Exo-beta-1]]
		+	[[Category: Glycoside hydrolase family 43]]
		+	[[Category: Hydrolase]]

OCA at 07:25, 4 November 2020

OCA — Wed, 04 Nov 2020 07:25:38 GMT

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

-	~~The entry 7byv is ON HOLD until Paper Publication~~	+	==Crystal structure of exo-beta-1,3-galactanase from Phanerochaete chrysosporium Pc1,3Gal43A E208Q with beta-1,3-galactotriose==
-		+	<StructureSection load='7byv' size='340' side='right'caption='[[7byv]]' 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=7BYV OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=7BYV FirstGlance]. <br>
-	~~Description:~~ Crystal structure of exo-beta-1,3-galactanase from Phanerochaete chrysosporium Pc1,3Gal43A E208Q with beta-1,3-galactotriose	+	</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=7byv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7byv OCA], [http://pdbe.org/7byv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7byv RCSB], [http://www.ebi.ac.uk/pdbsum/7byv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=7byv 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

OCA — Wed, 27 May 2020 05:09:35 GMT

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

-	The entry 7byv is ON HOLD	+	The entry 7byv 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.
Line 8:		Line 8:
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Ishida, T]]		[[Category: Ishida, T]]
-	[[Category: Kishine, N]]
-	[[Category: Fujimoto, Z]]
	[[Category: Kaneko, S]]		[[Category: Kaneko, S]]
	[[Category: Igarashi, K]]		[[Category: Igarashi, K]]
		+	[[Category: Kishine, N]]
		+	[[Category: Fujimoto, Z]]
	[[Category: Matsuyama, K]]		[[Category: Matsuyama, K]]

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

OCA — Wed, 29 Apr 2020 05:39:48 GMT

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

←Older revision

Revision as of 05:39, 29 April 2020

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

OCA — Wed, 29 Apr 2020 05:39:47 GMT

New page: '''Unreleased structure''' The entry 7byv 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 7byv 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 E208Q with beta-1,3-galactotriose
[[Category: Unreleased Structures]]
[[Category: Ishida, T]]
[[Category: Kishine, N]]
[[Category: Fujimoto, Z]]
[[Category: Kaneko, S]]
[[Category: Igarashi, K]]
[[Category: Matsuyama, K]]