5fr0 - Revision history

OCA at 13:19, 26 July 2023

OCA — Wed, 26 Jul 2023 13:19:27 GMT

←Older revision		Revision as of 13:19, 26 July 2023
Line 3:		Line 3:
	<StructureSection load='5fr0' size='340' side='right'caption='[[5fr0]], [[Resolution\|resolution]] 1.75Å' scene=''>		<StructureSection load='5fr0' size='340' side='right'caption='[[5fr0]], [[Resolution\|resolution]] 1.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5fr0]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_perfringens"_veillon_and_zuber_1898 "bacillus~~ perfringens~~" veillon and zuber 1898~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FR0 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5FR0 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5fr0]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Clostridium_perfringens Clostridium perfringens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FR0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5FR0 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>~~, ~~<scene name='pdbligand=SIZ:N-DIFLUOROACETYL-D-GALACTOSAMINE'>SIZ</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]] 1.75Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~[[5fqe\|5fqe]]~~, ~~[[5fqf\|5fqf]], [[5fqg\|5fqg]], [[5fqh\|5fqh]]~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SIZ:N-DIFLUOROACETYL-D-GALACTOSAMINE'>SIZ</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=5fr0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fr0 OCA], [~~http~~://pdbe.org/5fr0 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5fr0 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5fr0 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5fr0 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=5fr0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fr0 OCA], [https://pdbe.org/5fr0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5fr0 RCSB], [https://www.ebi.ac.uk/pdbsum/5fr0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5fr0 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A0H2YNR7_CLOP1 A0A0H2YNR7_CLOP1]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus~~ perfringens ~~veillon and zuber 1898~~]]	+	[[Category: Clostridium perfringens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Abe~~, K T~~]]	+	[[Category: Abe KT]]
-	[[Category: Alteen, M]]	+	[[Category: Alteen M]]
-	[[Category: Boraston~~, A B~~]]	+	[[Category: Boraston AB]]
-	[[Category: Laurie, C]]	+	[[Category: Laurie C]]
-	[[Category: Noach, I]]	+	[[Category: Noach I]]
-	[[Category: Pluvinage, B]]	+	[[Category: Pluvinage B]]
-	[[Category: Vocadlo~~, D J]]~~	+	[[Category: Vocadlo DJ]]
-	~~[[Category: Ganglioside]]~~	+
-	~~[[Category: Gh123]]~~	+
-	~~[[Category: Globoside]]~~	+
-	~~[[Category: Glycoside hydrolase]]~~	+
-	~~[[Category: Glycosphingolipid]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Substrate-assisted catalysis~~]]	+

OCA at 07:32, 6 May 2020

OCA — Wed, 06 May 2020 07:32:53 GMT

←Older revision		Revision as of 07:32, 6 May 2020
Line 1:		Line 1:

	==The details of glycolipid glycan hydrolysis by the structural analysis of a family 123 glycoside hydrolase from Clostridium perfringens==		==The details of glycolipid glycan hydrolysis by the structural analysis of a family 123 glycoside hydrolase from Clostridium perfringens==
-	<StructureSection load='5fr0' size='340' side='right' caption='[[5fr0]], [[Resolution\|resolution]] 1.75Å' scene=''>	+	<StructureSection load='5fr0' size='340' side='right'caption='[[5fr0]], [[Resolution\|resolution]] 1.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5fr0]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FR0 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5FR0 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5fr0]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_perfringens"_veillon_and_zuber_1898 "bacillus perfringens" veillon and zuber 1898]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FR0 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5FR0 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SIZ:N-DIFLUOROACETYL-D-GALACTOSAMINE'>SIZ</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SIZ:N-DIFLUOROACETYL-D-GALACTOSAMINE'>SIZ</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5fqe\|5fqe]], [[5fqf\|5fqf]], [[5fqg\|5fqg]], [[5fqh\|5fqh]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5fqe\|5fqe]], [[5fqf\|5fqf]], [[5fqg\|5fqg]], [[5fqh\|5fqh]]</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=5fr0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fr0 OCA], [http://pdbe.org/5fr0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fr0 RCSB], [http://www.ebi.ac.uk/pdbsum/5fr0 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5fr0 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=5fr0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fr0 OCA], [http://pdbe.org/5fr0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fr0 RCSB], [http://www.ebi.ac.uk/pdbsum/5fr0 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5fr0 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 21:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus perfringens veillon and zuber 1898]]
		+	[[Category: Large Structures]]
	[[Category: Abe, K T]]		[[Category: Abe, K T]]
	[[Category: Alteen, M]]		[[Category: Alteen, M]]

OCA at 04:38, 9 September 2016

OCA — Fri, 09 Sep 2016 04:38:59 GMT

←Older revision		Revision as of 04:38, 9 September 2016
Line 6:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SIZ:N-DIFLUOROACETYL-D-GALACTOSAMINE'>SIZ</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SIZ:N-DIFLUOROACETYL-D-GALACTOSAMINE'>SIZ</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5fqe\|5fqe]], [[5fqf\|5fqf]], [[5fqg\|5fqg]], [[5fqh\|5fqh]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5fqe\|5fqe]], [[5fqf\|5fqf]], [[5fqg\|5fqg]], [[5fqh\|5fqh]]</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=5fr0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fr0 OCA], [http://pdbe.org/5fr0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fr0 RCSB], [http://www.ebi.ac.uk/pdbsum/5fr0 PDBsum]</span></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=5fr0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fr0 OCA], [http://pdbe.org/5fr0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fr0 RCSB], [http://www.ebi.ac.uk/pdbsum/5fr0 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5fr0 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 16:05, 10 May 2016

OCA — Tue, 10 May 2016 16:05:40 GMT

←Older revision		Revision as of 16:05, 10 May 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	The ~~entry~~ 5fr0 is ~~ON HOLD until Paper~~ Publication	+	==The details of glycolipid glycan hydrolysis by the structural analysis of a family 123 glycoside hydrolase from Clostridium perfringens==
		+	<StructureSection load='5fr0' size='340' side='right' caption='[[5fr0]], [[Resolution\|resolution]] 1.75Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5fr0]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FR0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5FR0 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SIZ:N-DIFLUOROACETYL-D-GALACTOSAMINE'>SIZ</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5fqe\|5fqe]], [[5fqf\|5fqf]], [[5fqg\|5fqg]], [[5fqh\|5fqh]]</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=5fr0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fr0 OCA], [http://pdbe.org/5fr0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fr0 RCSB], [http://www.ebi.ac.uk/pdbsum/5fr0 PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Clostridium perfringens is an opportunistic pathogen of humans and animals whose genome encodes a wide variety of putative carbohydrate-hydrolyzing enzymes that are increasingly being shown to be directed toward the cleavage of host glycans. Among these putative enzymes is a member of glycoside hydrolase family 123. Here we show that the recombinant enzyme (referred to as CpNga123) encoded by the gene cloned from C. perfringens strain ATCC 13124 (locus tag CPF_1473) is a beta-N-acetylgalactosaminidase, similar to NgaP from Paenibacillus sp. TS12. Like NgaP, CpNga123 was able to cleave the terminal beta-D-GalNAc-(1-->4)-D-Gal and beta-D-GalNAc-(1-->3)-D-Gal motifs that would be found in glycosphigolipids. The X-ray crystal structure of CpNga123 revealed it to have an N-terminal beta-sandwich domain and a (beta/alpha)8-barrel catalytic domain with a C-terminal alpha-helical elaboration. The structures determined in complex with reaction products provide details of the -1 subsite architecture, catalytic residues, and a structural change in the active site that is likely required to enable hydrolysis of the glycosidic bond by promoting engagement of the substrate by the catalytic residues. The features of the active site support the likelihood of a substrate-assisted catalytic mechanism for this enzyme. The structures of an inactive mutant of CpNga123 in complex with intact GA2 and Gb4 glycosphingolipid motifs reveal insight into aglycon recognition and suggest that the kinked or pleated conformation of GA2 caused by the beta-1,4-linkage between N-acetylgalactosamine and galactose, and the accommodation of this conformation by the enzyme active site, may be responsible for greater activity on GA2.

-	~~Authors:~~ Noach, I., Pluvinage, B., Laurie, C., Abe~~, K.T.~~, Alteen~~, M.~~, Vocadlo, D.J., ~~Boraston, A~~.B.	+	The Details of Glycolipid Glycan Hydrolysis by the Structural Analysis of a Family 123 Glycoside Hydrolase from Clostridium perfringens.,Noach I, Pluvinage B, Laurie C, Abe KT, Alteen MG, Vocadlo DJ, Boraston AB J Mol Biol. 2016 Mar 30. pii: S0022-2836(16)00206-0. doi:, 10.1016/j.jmb.2016.03.020. PMID:27038508<ref>PMID:27038508</ref>

-	~~Description: The details~~ of ~~glycolipid glycan hydrolysis by~~ the ~~structural analysis~~ of ~~a family 123 glycoside hydrolase from Clostridium perfringens~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5fr0" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Abe, K T]]
	[[Category: Alteen, M]]		[[Category: Alteen, M]]
-	[[Category: ~~Abe~~, ~~K.T~~]]	+	[[Category: Boraston, A B]]
	[[Category: Laurie, C]]		[[Category: Laurie, C]]
-	[[Category: Boraston, A.B]]
-	[[Category: Pluvinage, B]]
-	[[Category: Vocadlo, D.J]]
	[[Category: Noach, I]]		[[Category: Noach, I]]
		+	[[Category: Pluvinage, B]]
		+	[[Category: Vocadlo, D J]]
		+	[[Category: Ganglioside]]
		+	[[Category: Gh123]]
		+	[[Category: Globoside]]
		+	[[Category: Glycoside hydrolase]]
		+	[[Category: Glycosphingolipid]]
		+	[[Category: Hydrolase]]
		+	[[Category: Substrate-assisted catalysis]]

OCA at 13:19, 3 February 2016

OCA — Wed, 03 Feb 2016 13:19:44 GMT

←Older revision		Revision as of 13:19, 3 February 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5fr0 is ON HOLD	+	The entry 5fr0 is ON HOLD until Paper Publication

	Authors: Noach, I., Pluvinage, B., Laurie, C., Abe, K.T., Alteen, M., Vocadlo, D.J., Boraston, A.B.		Authors: Noach, I., Pluvinage, B., Laurie, C., Abe, K.T., Alteen, M., Vocadlo, D.J., Boraston, A.B.

OCA: Protected "5fr0" [edit=sysop:move=sysop]

OCA — Wed, 23 Dec 2015 11:49:54 GMT

Protected "5fr0" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:49, 23 December 2015

OCA: New page: '''Unreleased structure''' The entry 5fr0 is ON HOLD Authors: Noach, I., Pluvinage, B., Laurie, C., Abe, K.T., Alteen, M., Vocadlo, D.J., Boraston, A.B. Description: The details of gly...

OCA — Wed, 23 Dec 2015 11:49:53 GMT

New page: '''Unreleased structure''' The entry 5fr0 is ON HOLD Authors: Noach, I., Pluvinage, B., Laurie, C., Abe, K.T., Alteen, M., Vocadlo, D.J., Boraston, A.B. Description: The details of gly...

New page

'''Unreleased structure'''

The entry 5fr0 is ON HOLD

Authors: Noach, I., Pluvinage, B., Laurie, C., Abe, K.T., Alteen, M., Vocadlo, D.J., Boraston, A.B.

Description: The details of glycolipid glycan hydrolysis by the structural analysis of a family 123 glycoside hydrolase from Clostridium perfringens
[[Category: Unreleased Structures]]
[[Category: Alteen, M]]
[[Category: Abe, K.T]]
[[Category: Laurie, C]]
[[Category: Boraston, A.B]]
[[Category: Pluvinage, B]]
[[Category: Vocadlo, D.J]]
[[Category: Noach, I]]