7eis - Revision history

OCA at 16:55, 29 November 2023

2023-11-29T16:55:01Z

←Older revision		Revision as of 16:55, 29 November 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7eis]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Proteus_vulgaris Proteus vulgaris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7EIS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7EIS FirstGlance]. <br>		<table><tr><td colspan='2'>[[7eis]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Proteus_vulgaris Proteus vulgaris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7EIS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7EIS FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~"><~~scene name~~='~~pdbligand~~=MG:~~MAGNESIUM+ION'~~>MG</~~scene~~>, <scene name='pdbligand=GCD:4,5-DEHYDRO-D-GLUCURONIC+ACID'>GCD</scene>, <scene name='pdbligand=NGA:N-ACETYL-D-GALACTOSAMINE'>NGA</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~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[https://en.wikipedia.org/wiki/Chondroitin-sulfate-ABC_endolyase Chondroitin-sulfate-ABC endolyase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.2.20 4.2.2.20]~~ </~~span~~></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GCD:4,5-DEHYDRO-D-GLUCURONIC+ACID'>GCD</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NGA:N-ACETYL-D-GALACTOSAMINE'>NGA</scene>, <scene name='pdbligand=PRD_900058:UNSATURATED+CHONDROITIN+DISACCHARIDE'>PRD_900058</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=7eis FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7eis OCA], [https://pdbe.org/7eis PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7eis RCSB], [https://www.ebi.ac.uk/pdbsum/7eis PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7eis 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=7eis FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7eis OCA], [https://pdbe.org/7eis PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7eis RCSB], [https://www.ebi.ac.uk/pdbsum/7eis PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7eis ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/CABC1_PROVU CABC1_PROVU]] Endolytic, broad-specificity glycosaminoglycan lyase, which degrades the polysaccharides chondroitin, chondroitin-4-sulfate, chondroitin-6-sulfate, dermatan sulfate and to a lesser extent hyaluronan, by beta-elimination of 1,4-hexosaminidic bond to unsaturated tetrasaccharides and disaccharides. Is not active against keratan sulfate, heparan sulfate, and heparin. Is able to promote functional recovery in the injured central nervous system (CNS), via its role in the disruption of the normal organization of the extracellular matrix (ECM).<ref>PMID:15691229</ref> <ref>PMID:17572406</ref> <ref>PMID:9083041</ref>	+	[https://www.uniprot.org/uniprot/CABC1_PROVU CABC1_PROVU] Endolytic, broad-specificity glycosaminoglycan lyase, which degrades the polysaccharides chondroitin, chondroitin-4-sulfate, chondroitin-6-sulfate, dermatan sulfate and to a lesser extent hyaluronan, by beta-elimination of 1,4-hexosaminidic bond to unsaturated tetrasaccharides and disaccharides. Is not active against keratan sulfate, heparan sulfate, and heparin. Is able to promote functional recovery in the injured central nervous system (CNS), via its role in the disruption of the normal organization of the extracellular matrix (ECM).<ref>PMID:15691229</ref> <ref>PMID:17572406</ref> <ref>PMID:9083041</ref>
	<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: Chondroitin-sulfate-ABC endolyase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Proteus vulgaris]]		[[Category: Proteus vulgaris]]
-	[[Category: Eguchi, T]]	+	[[Category: Eguchi T]]
-	[[Category: Miyanaga, A]]	+	[[Category: Miyanaga A]]
-	[[Category: Takashima, M]]	+	[[Category: Takashima M]]
-	~~[[Category: Carbohydrate binding]]~~	+
-	~~[[Category: Lyase]]~~	+
-	~~[[Category: Polysaccharide lyase family 8~~]]	+

OCA at 07:37, 19 January 2022

2022-01-19T07:37:45Z

←Older revision		Revision as of 07:37, 19 January 2022
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	==Crystal structure of chondroitin ABC lyase I in complex with chondroitin disaccharide 0S==		==Crystal structure of chondroitin ABC lyase I in complex with chondroitin disaccharide 0S==
-	<StructureSection load='7eis' size='340' side='right'caption='[[7eis]]' scene=''>	+	<StructureSection load='7eis' size='340' side='right'caption='[[7eis]], [[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=7EIS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7EIS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7eis]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Proteus_vulgaris Proteus vulgaris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7EIS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7EIS FirstGlance]. <br>
-	</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=7eis FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7eis OCA], [https://pdbe.org/7eis PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7eis RCSB], [https://www.ebi.ac.uk/pdbsum/7eis PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7eis 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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=GCD:4,5-DEHYDRO-D-GLUCURONIC+ACID'>GCD</scene>, <scene name='pdbligand=NGA:N-ACETYL-D-GALACTOSAMINE'>NGA</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Chondroitin-sulfate-ABC_endolyase Chondroitin-sulfate-ABC endolyase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.2.20 4.2.2.20] </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=7eis FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7eis OCA], [https://pdbe.org/7eis PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7eis RCSB], [https://www.ebi.ac.uk/pdbsum/7eis PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7eis ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/CABC1_PROVU CABC1_PROVU]] Endolytic, broad-specificity glycosaminoglycan lyase, which degrades the polysaccharides chondroitin, chondroitin-4-sulfate, chondroitin-6-sulfate, dermatan sulfate and to a lesser extent hyaluronan, by beta-elimination of 1,4-hexosaminidic bond to unsaturated tetrasaccharides and disaccharides. Is not active against keratan sulfate, heparan sulfate, and heparin. Is able to promote functional recovery in the injured central nervous system (CNS), via its role in the disruption of the normal organization of the extracellular matrix (ECM).<ref>PMID:15691229</ref> <ref>PMID:17572406</ref> <ref>PMID:9083041</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Chondroitinase ABC I (cABC-I) is the enzyme which cleaves the beta-1,4 glycosidic linkage of chondroitin sulfate (CS) by beta-elimination. To elucidate more accurately the substrate specificity of cABC-I, we evaluated the kinetic parameters of cABC-I and its reactivity with CS isomers displaying less structural heterogeneity as substrates, e.g., approximately 90 percent of disaccharide units in Chondroitin sulfate A (CSA) or Chondroitin sulfate C (CSC) is D-glucuronic acid and 4-O-sulfated N-acetyl galactosamine (GalNAc) (A-unit) or D-glucuronic acid and 6-O-sulfated GalNAc (C-unit), respectively. cABC-I showed the highest reactivity to CSA and CSC among all CS isomers, and the kcat/Km of cABC-I was higher for CSA than for CSC. Next, we determined the crystal structures of cABC-I in complex with CS disaccharides, and analyzed the crystallographic data in combination with molecular docking data. Arg500 interacts with 4-O-sulfated and 6-O-sulfated GalNAc residues. The distance between Arg500 and the 4-O-sulfate group was 0.8 A shorter than that between Arg500 and the 6-O-sulfated group. Moreover, it is likely that the 6-O-sulfated group is electrostatically repulsed by the nearby Asp490. Thus, we demonstrated that cABC-I has the highest affinity for the CSA richest in 4-O-sulfated GalNAc residues among all CS isomers. Recently, cABC-I was used to treat lumbar disc herniation. The results provide useful information to understand the mechanism of the pharmacological action of cABC-I.
		+
		+	Substrate specificity of Chondroitinase ABC I based on analyses of biochemical reactions and crystal structures in complex with disaccharides.,Takashima M, Watanabe I, Miyanaga A, Eguchi T Glycobiology. 2021 Aug 12. pii: 6348415. doi: 10.1093/glycob/cwab086. PMID:34392362<ref>PMID:34392362</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7eis" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Chondroitin-sulfate-ABC endolyase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Eguchi T]]	+	[[Category: Proteus vulgaris]]
-	[[Category: Miyanaga A]]	+	[[Category: Eguchi, T]]
-	[[Category: Takashima M]]	+	[[Category: Miyanaga, A]]
		+	[[Category: Takashima, M]]
		+	[[Category: Carbohydrate binding]]
		+	[[Category: Lyase]]
		+	[[Category: Polysaccharide lyase family 8]]

OCA at 06:18, 25 August 2021

2021-08-25T06:18:38Z

←Older revision		Revision as of 06:18, 25 August 2021
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-	'''Unreleased structure'''

-	~~The entry~~ 7eis is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of chondroitin ABC lyase I in complex with chondroitin disaccharide 0S==
-		+	<StructureSection load='7eis' size='340' side='right'caption='[[7eis]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7EIS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7EIS FirstGlance]. <br>
-	~~Description~~:	+	</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=7eis FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7eis OCA], [https://pdbe.org/7eis PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7eis RCSB], [https://www.ebi.ac.uk/pdbsum/7eis PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7eis ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Eguchi T]]
		+	[[Category: Miyanaga A]]
		+	[[Category: Takashima M]]

OCA at 08:02, 12 May 2021

2021-05-12T08:02:27Z

←Older revision		Revision as of 08:02, 12 May 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7eis is ON HOLD	+	The entry 7eis is ON HOLD until Paper Publication

	Authors:		Authors:

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

2021-04-07T04:32:51Z

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

←Older revision

Revision as of 04:32, 7 April 2021

OCA: New page: '''Unreleased structure''' The entry 7eis is ON HOLD Authors: Description: Category: Unreleased Structures

2021-04-07T04:32:50Z

New page: '''Unreleased structure''' The entry 7eis is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7eis is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]