5ccu - Revision history

OCA at 16:08, 8 November 2023

2023-11-08T16:08:15Z

←Older revision		Revision as of 16:08, 8 November 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5ccu]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodococcus_hoagii_103S Rhodococcus hoagii 103S]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5CCU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5CCU FirstGlance]. <br>		<table><tr><td colspan='2'>[[5ccu]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodococcus_hoagii_103S Rhodococcus hoagii 103S]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5CCU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5CCU FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 2.11Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></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=5ccu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ccu OCA], [https://pdbe.org/5ccu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ccu RCSB], [https://www.ebi.ac.uk/pdbsum/5ccu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ccu 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=5ccu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ccu OCA], [https://pdbe.org/5ccu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ccu RCSB], [https://www.ebi.ac.uk/pdbsum/5ccu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ccu ProSAT]</span></td></tr>
	</table>		</table>

OCA at 11:59, 14 June 2023

2023-06-14T11:59:18Z

←Older revision		Revision as of 11:59, 14 June 2023
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	<StructureSection load='5ccu' size='340' side='right'caption='[[5ccu]], [[Resolution\|resolution]] 2.11Å' scene=''>		<StructureSection load='5ccu' size='340' side='right'caption='[[5ccu]], [[Resolution\|resolution]] 2.11Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ccu]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Rhoh1 Rhoh1~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5CCU OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5CCU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ccu]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodococcus_hoagii_103S Rhodococcus hoagii 103S]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5CCU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5CCU FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">REQ_38260 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=685727 RHOH1])~~</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=5ccu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ccu OCA], [https://pdbe.org/5ccu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ccu RCSB], [https://www.ebi.ac.uk/pdbsum/5ccu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ccu ProSAT]</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=5ccu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ccu OCA], [~~http~~://pdbe.org/5ccu PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5ccu RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5ccu PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5ccu ProSAT]</span></td></tr>	+
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Rhoh1~~]]	+	[[Category: Rhodococcus hoagii 103S]]
-	[[Category: Chen, L]]	+	[[Category: Chen L]]
-	~~[[Category: Apo]]~~	+
-	~~[[Category: Hydrolase~~]]	+

OCA at 11:32, 27 March 2020

2020-03-27T11:32:49Z

←Older revision		Revision as of 11:32, 27 March 2020
Line 1:		Line 1:

	==Crystal structure of endoglycoceramidase I from Rhodococ-cus equi==		==Crystal structure of endoglycoceramidase I from Rhodococ-cus equi==
-	<StructureSection load='5ccu' size='340' side='right' caption='[[5ccu]], [[Resolution\|resolution]] 2.11Å' scene=''>	+	<StructureSection load='5ccu' size='340' side='right'caption='[[5ccu]], [[Resolution\|resolution]] 2.11Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ccu]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5CCU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5CCU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ccu]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhoh1 Rhoh1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5CCU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5CCU FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">REQ_38260 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=685727 RHOH1])</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=5ccu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ccu OCA], [http://pdbe.org/5ccu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ccu RCSB], [http://www.ebi.ac.uk/pdbsum/5ccu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ccu ProSAT]</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=5ccu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ccu OCA], [http://pdbe.org/5ccu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ccu RCSB], [http://www.ebi.ac.uk/pdbsum/5ccu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ccu ProSAT]</span></td></tr>
	</table>		</table>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Rhoh1]]
	[[Category: Chen, L]]		[[Category: Chen, L]]
	[[Category: Apo]]		[[Category: Apo]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]

OCA at 06:33, 5 April 2017

2017-04-05T06:33:16Z

←Older revision		Revision as of 06:33, 5 April 2017
Line 1:		Line 1:
		+
	==Crystal structure of endoglycoceramidase I from Rhodococ-cus equi==		==Crystal structure of endoglycoceramidase I from Rhodococ-cus equi==
	<StructureSection load='5ccu' size='340' side='right' caption='[[5ccu]], [[Resolution\|resolution]] 2.11Å' scene=''>		<StructureSection load='5ccu' size='340' side='right' caption='[[5ccu]], [[Resolution\|resolution]] 2.11Å' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[5ccu]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5CCU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5CCU FirstGlance]. <br>		<table><tr><td colspan='2'>[[5ccu]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5CCU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5CCU FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=5ccu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ccu OCA], [http://www.rcsb.org/pdb/explore.do?structureId=5ccu RCSB], [http://www.ebi.ac.uk/pdbsum/5ccu 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=5ccu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ccu OCA], [http://pdbe.org/5ccu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ccu RCSB], [http://www.ebi.ac.uk/pdbsum/5ccu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ccu ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Endoglycoceramidases (EGCases) specifically hydrolyze the glycosidic linkage between the oligosaccharide and the ceramide moieties of various glycosphingolipids, and they have received substantial attention in the emerging field of glycosphingolipidology. However, the mechanism regulating the strict substrate specificity of these GH5 glycosidases has not been identified. In this study, we report a novel EGCase I from Rhodococcus equi 103S (103S_EGCase I) with remarkably broad substrate specificity. Based on phylogenetic analyses, the enzyme may represent a new subfamily of GH5 glycosidases. The X-ray crystal structures of 103S_EGCase I alone and in complex with its substrates monosialodihexosylganglioside (GM3) and monosialotetrahexosylganglioside (GM1) enabled us to identify several structural features that may account for its broad specificity. Compared with EGCase II from Rhodococcus sp. M-777 (M777_EGCase II), which possesses strict substrate specificity, 103S_EGCase I possesses a longer alpha7-helix and a shorter loop 4, which forms a larger substrate-binding pocket that could accommodate more extended oligosaccharides. In addition, loop 2 and loop 8 of the enzyme adopt a more open conformation, which also enlarges the oligosaccharide-binding cavity. Based on this knowledge, a rationally designed experiment was performed to examine the substrate specificity of EGCase II. The truncation of loop 4 in M777_EGCase II increased its activity toward GM1 (163%). Remarkably, the S63G mutant of M777_EGCase II showed a broader substrate spectra and significantly increased activity toward bulky substrates (up to >1370-fold for fucosyl-GM1). Collectively, the results presented here reveal the exquisite substrate recognition mechanism of EGCases and provide an opportunity for further engineering of these enzymes.
		+
		+	Structural Insights into the Broad Substrate Specificity of a Novel Endoglycoceramidase I Belonging to a New Subfamily of GH5 Glycosidases.,Han YB, Chen LQ, Li Z, Tan YM, Feng Y, Yang GY J Biol Chem. 2017 Mar 24;292(12):4789-4800. doi: 10.1074/jbc.M116.763821. Epub, 2017 Feb 8. PMID:28179425<ref>PMID:28179425</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5ccu" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 12:35, 2 September 2015

2015-09-02T12:35:20Z

←Older revision		Revision as of 12:35, 2 September 2015
Line 1:		Line 1:
-	'''~~Unreleased structure~~'''	+	==Crystal structure of endoglycoceramidase I from Rhodococ-cus equi==
-		+	<StructureSection load='5ccu' size='340' side='right' caption='[[5ccu]], [[Resolution\|resolution]] 2.11Å' scene=''>
-	~~The entry~~ 5ccu is ~~ON HOLD until Aug 27 2016~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5ccu]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5CCU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5CCU FirstGlance]. <br>
-	~~Authors~~: ~~Chen, L~~.	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=5ccu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ccu OCA], [http://www.rcsb.org/pdb/explore.do?structureId=5ccu RCSB], [http://www.ebi.ac.uk/pdbsum/5ccu PDBsum]</span></td></tr>
-	~~Description~~: ~~Crystal structure of endoglycoceramidase I from Rhodococ~~-~~cus equi~~	+	</table>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	__TOC__
		+	</StructureSection>
	[[Category: Chen, L]]		[[Category: Chen, L]]
		+	[[Category: Apo]]
		+	[[Category: Hydrolase]]

OCA at 10:38, 20 August 2015

2015-08-20T10:38:29Z

←Older revision		Revision as of 10:38, 20 August 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5ccu is ON HOLD	+	The entry 5ccu is ON HOLD until Aug 27 2016

	Authors: Chen, L.		Authors: Chen, L.

OCA at 13:00, 22 July 2015

2015-07-22T13:00:03Z

←Older revision		Revision as of 13:00, 22 July 2015
Line 3:		Line 3:
	The entry 5ccu is ON HOLD		The entry 5ccu is ON HOLD

-	Authors: ~~Liuqing~~ Chen	+	Authors: Chen, L.

	Description: Crystal structure of endoglycoceramidase I from Rhodococ-cus equi		Description: Crystal structure of endoglycoceramidase I from Rhodococ-cus equi
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: ~~Liuqing~~ Chen]]	+	[[Category: Chen, L]]

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

2015-07-15T12:23:18Z

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

←Older revision

Revision as of 12:23, 15 July 2015

OCA: New page: '''Unreleased structure''' The entry 5ccu is ON HOLD Authors: Liuqing Chen Description: Crystal structure of endoglycoceramidase I from Rhodococ-cus equi [[Category: Unreleased Structu...

2015-07-15T12:23:17Z

New page: '''Unreleased structure''' The entry 5ccu is ON HOLD Authors: Liuqing Chen Description: Crystal structure of endoglycoceramidase I from Rhodococ-cus equi [[Category: Unreleased Structu...

New page

'''Unreleased structure'''

The entry 5ccu is ON HOLD

Authors: Liuqing Chen

Description: Crystal structure of endoglycoceramidase I from Rhodococ-cus equi
[[Category: Unreleased Structures]]
[[Category: Liuqing Chen]]