6dns - Revision history

OCA at 14:36, 13 March 2024

2024-03-13T14:36:04Z

←Older revision		Revision as of 14:36, 13 March 2024
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	==Endo-fucoidan hydrolase MfFcnA9 from glycoside hydrolase family 107==		==Endo-fucoidan hydrolase MfFcnA9 from glycoside hydrolase family 107==
-	<StructureSection load='6dns' size='340' side='right' caption='[[6dns]], [[Resolution\|resolution]] 2.24Å' scene=''>	+	<StructureSection load='6dns' size='340' side='right'caption='[[6dns]], [[Resolution\|resolution]] 2.24Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6dns]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Cip_109502 Cip 109502~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DNS OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6DNS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6dns]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mariniflexile_fucanivorans Mariniflexile fucanivorans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DNS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6DNS FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=CA:CALCIUM+ION'>CA</scene~~>, ~~<scene name='pdbligand=EDO:1,~~2~~-ETHANEDIOL'>EDO</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]] 2.24Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~fcnA ([http~~:/~~/www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=264023 CIP 109502])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</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=6dns FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dns OCA], [~~http~~://pdbe.org/6dns PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6dns RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6dns PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6dns 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=6dns FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dns OCA], [https://pdbe.org/6dns PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6dns RCSB], [https://www.ebi.ac.uk/pdbsum/6dns PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6dns ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/Q08I46_9FLAO Q08I46_9FLAO]
-	Fucoidans are chemically complex and highly heterogeneous sulfated marine fucans from brown macro algae. Possessing a variety of physicochemical and biological activities, fucoidans are used as gelling and thickening agents in the food industry, and have anticoagulant, antiviral, antitumor, antibacterial, and immune activities. Although fucoidan-depolymerizing enzymes have been identified, the molecular basis of their activity on these chemically complex polysaccharides remains largely uninvestigated. In this study, we focused on three glycoside hydrolase family 107 (GH107) enzymes, MfFcnA and two newly identified members, P5AFcnA and P19DFcnA, from a bacterial species of the genus Psychromonas. Using carbohydrate-polyacrylamide gel electrophoresis, we show that P5AFcnA and P19DFcnA are active on fucoidans that differ from those depolymerized by MfFcnA, revealing differential substrate specificity within the GH107 family. Using a combination of X-ray crystallography and NMR analyses, we further show that GH107 family enzymes share features of their structures and catalytic mechanisms with GH29 alpha-L-fucosidases. However, we found that GH107 enzymes have the distinction of utilizing a histidine sidechain as the proposed acid/base catalyst in its retaining mechanism. Further interpretation of the structural data indicated that the active-site architectures within this family are highly variable, likely reflecting the specificity of GH107 enzymes for different fucoidan substructures. Together, these findings begin to illuminate the molecular details underpinning the biological processing of fucoidans.	+
-		+
-	Endo-fucoidan hydrolases from glycoside hydrolase family 107 (GH107) display structural and mechanistic similarities to alpha-L-fucosidases from GH29.,Vickers C, Liu F, Abe K, Salama-Alber O, Jenkins ML, Springate CM, Burke JE, Withers SG, Boraston AB J Biol Chem. 2018 Oct 3. pii: ~~RA118.005134. doi: 10.1074~~/~~jbc.RA118.005134. PMID:30282808<ref>PMID:30282808<~~/~~ref>~~	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 6dns" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references~~/>	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Cip 109502~~]]	+	[[Category: Large Structures]]
-	[[Category: Abe, K]]	+	[[Category: Mariniflexile fucanivorans]]
-	[[Category: Boraston~~, A B~~]]	+	[[Category: Abe K]]
-	[[Category: Salama-Alber, O]]	+	[[Category: Boraston AB]]
-	[[Category: Vickers, C]]	+	[[Category: Salama-Alber O]]
-	~~[[Category: Fucan]]~~	+	[[Category: Vickers C]]
-	~~[[Category: Fucoidan]]~~	+
-	~~[[Category: Glycoside hydrolase]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Retaining mechanism~~]]	+

OCA at 08:36, 17 October 2018

2018-10-17T08:36:47Z

←Older revision		Revision as of 08:36, 17 October 2018
Line 3:		Line 3:
	<StructureSection load='6dns' size='340' side='right' caption='[[6dns]], [[Resolution\|resolution]] 2.24Å' scene=''>		<StructureSection load='6dns' size='340' side='right' caption='[[6dns]], [[Resolution\|resolution]] 2.24Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6dns]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DNS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DNS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6dns]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Cip_109502 Cip 109502]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DNS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DNS FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">fcnA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=264023 CIP 109502])</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=6dns FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dns OCA], [http://pdbe.org/6dns PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dns RCSB], [http://www.ebi.ac.uk/pdbsum/6dns PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dns 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=6dns FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dns OCA], [http://pdbe.org/6dns PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dns RCSB], [http://www.ebi.ac.uk/pdbsum/6dns PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dns ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Fucoidans are chemically complex and highly heterogeneous sulfated marine fucans from brown macro algae. Possessing a variety of physicochemical and biological activities, fucoidans are used as gelling and thickening agents in the food industry, and have anticoagulant, antiviral, antitumor, antibacterial, and immune activities. Although fucoidan-depolymerizing enzymes have been identified, the molecular basis of their activity on these chemically complex polysaccharides remains largely uninvestigated. In this study, we focused on three glycoside hydrolase family 107 (GH107) enzymes, MfFcnA and two newly identified members, P5AFcnA and P19DFcnA, from a bacterial species of the genus Psychromonas. Using carbohydrate-polyacrylamide gel electrophoresis, we show that P5AFcnA and P19DFcnA are active on fucoidans that differ from those depolymerized by MfFcnA, revealing differential substrate specificity within the GH107 family. Using a combination of X-ray crystallography and NMR analyses, we further show that GH107 family enzymes share features of their structures and catalytic mechanisms with GH29 alpha-L-fucosidases. However, we found that GH107 enzymes have the distinction of utilizing a histidine sidechain as the proposed acid/base catalyst in its retaining mechanism. Further interpretation of the structural data indicated that the active-site architectures within this family are highly variable, likely reflecting the specificity of GH107 enzymes for different fucoidan substructures. Together, these findings begin to illuminate the molecular details underpinning the biological processing of fucoidans.
		+
		+	Endo-fucoidan hydrolases from glycoside hydrolase family 107 (GH107) display structural and mechanistic similarities to alpha-L-fucosidases from GH29.,Vickers C, Liu F, Abe K, Salama-Alber O, Jenkins ML, Springate CM, Burke JE, Withers SG, Boraston AB J Biol Chem. 2018 Oct 3. pii: RA118.005134. doi: 10.1074/jbc.RA118.005134. PMID:30282808<ref>PMID:30282808</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6dns" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Cip 109502]]
	[[Category: Abe, K]]		[[Category: Abe, K]]
	[[Category: Boraston, A B]]		[[Category: Boraston, A B]]

OCA at 07:47, 3 October 2018

2018-10-03T07:47:47Z

←Older revision		Revision as of 07:47, 3 October 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6dns is ~~ON HOLD until Paper Publication~~	+	==Endo-fucoidan hydrolase MfFcnA9 from glycoside hydrolase family 107==
-		+	<StructureSection load='6dns' size='340' side='right' caption='[[6dns]], [[Resolution\|resolution]] 2.24Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6dns]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DNS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DNS FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<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=6dns FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dns OCA], [http://pdbe.org/6dns PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dns RCSB], [http://www.ebi.ac.uk/pdbsum/6dns PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dns ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Abe, K]]
		+	[[Category: Boraston, A B]]
		+	[[Category: Salama-Alber, O]]
		+	[[Category: Vickers, C]]
		+	[[Category: Fucan]]
		+	[[Category: Fucoidan]]
		+	[[Category: Glycoside hydrolase]]
		+	[[Category: Hydrolase]]
		+	[[Category: Retaining mechanism]]

OCA at 05:39, 4 July 2018

2018-07-04T05:39:06Z

←Older revision		Revision as of 05:39, 4 July 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6dns is ON HOLD	+	The entry 6dns is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "6dns" [edit=sysop:move=sysop]

2018-06-14T05:48:33Z

Protected "6dns" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:48, 14 June 2018

OCA: New page: '''Unreleased structure''' The entry 6dns is ON HOLD Authors: Description: Category: Unreleased Structures

2018-06-14T05:48:32Z

New page: '''Unreleased structure''' The entry 6dns is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6dns is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]