7o7t - Revision history

OCA at 12:46, 1 February 2024

2024-02-01T12:46:13Z

← Older revision		Revision as of 12:46, 1 February 2024
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	<StructureSection load='7o7t' size='340' side='right'caption='[[7o7t]], [[Resolution\|resolution]] 2.05Å' scene=''>		<StructureSection load='7o7t' size='340' side='right'caption='[[7o7t]], [[Resolution\|resolution]] 2.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7o7t]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Psea6 Psea6~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7O7T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7O7T FirstGlance]. <br>		<table><tr><td colspan='2'>[[7o7t]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudoalteromonas_atlantica_T6c Pseudoalteromonas atlantica T6c]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7O7T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7O7T 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=GOL:GLYCEROL'>GOL</scene>~~, ~~<scene name='pdbligand=V4W:4-deoxy-L-erythro-hex-5-ulosuronic+acid'>V4W</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]] 2.05Å</td></tr>
	~~<tr id='related'><td class="sblockLbl"><b>~~[[~~Related_structure~~\|~~Related:~~]]~~</b></td><td class="sblockDat"><div style='overflow: auto~~; ~~max-height: 3em;'>[[7o77\|7o77]]</div>~~</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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=V4W:4-deoxy-L-erythro-hex-5-ulosuronic+acid'>V4W</scene></td></tr>
	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~Patl_3640 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=342610 PSEA6])</td~~></tr>
	<~~tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks'>[https~~:~~//en.wikipedia.org/wiki/Poly(beta~~-D-~~mannuronate)_lyase Poly(beta~~-D-~~mannuronate) lyase], with EC number [https://www.brenda~~-~~enzymes.info/php/result_flat.php4?ecno=4.2.2.3 4.2.2.3]~~ </~~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=7o7t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7o7t OCA], [https://pdbe.org/7o7t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7o7t RCSB], [https://www.ebi.ac.uk/pdbsum/7o7t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7o7t 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=7o7t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7o7t OCA], [https://pdbe.org/7o7t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7o7t RCSB], [https://www.ebi.ac.uk/pdbsum/7o7t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7o7t ProSAT]</span></td></tr>
	</table>		</table>
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: ~~Psea6~~]]		[[Category: Pseudoalteromonas atlantica T6c]]
	[[Category: Aghajari, N]]		[[Category: Aghajari N]]
	[[Category: Ballut, L]]		[[Category: Ballut L]]
	[[Category: Carrique, L]]		[[Category: Carrique L]]
	[[Category: Violot, S]]		[[Category: Violot S]]
	~~[[Category: Beta helix]]~~
	~~[[Category: Complex]]~~
	~~[[Category: Lyase~~]]

OCA at 14:17, 29 December 2021

2021-12-29T14:17:49Z

← Older revision		Revision as of 14:17, 29 December 2021
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	==Structure of the PL6 family alginate lyase Patl3640 from Pseudoalteromonas atlantica T6c in complex with 4-deoxy-L-erythro-5-hexoseulose uronic acid==		==Structure of the PL6 family alginate lyase Patl3640 from Pseudoalteromonas atlantica T6c in complex with 4-deoxy-L-erythro-5-hexoseulose uronic acid==
	<StructureSection load='7o7t' size='340' side='right'caption='[[7o7t]]' scene=''>		<StructureSection load='7o7t' size='340' side='right'caption='[[7o7t]], [[Resolution\|resolution]] 2.05Å' 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=7O7T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7O7T FirstGlance]. <br>		<table><tr><td colspan='2'>[[7o7t]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Psea6 Psea6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7O7T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7O7T 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=7o7t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7o7t OCA], [https://pdbe.org/7o7t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7o7t RCSB], [https://www.ebi.ac.uk/pdbsum/7o7t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7o7t 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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=V4W:4-deoxy-L-erythro-hex-5-ulosuronic+acid'>V4W</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;'>[[7o77\|7o77]]</div></td></tr>
			<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Patl_3640 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=342610 PSEA6])</td></tr>
			<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Poly(beta-D-mannuronate)_lyase Poly(beta-D-mannuronate) lyase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.2.3 4.2.2.3] </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=7o7t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7o7t OCA], [https://pdbe.org/7o7t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7o7t RCSB], [https://www.ebi.ac.uk/pdbsum/7o7t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7o7t ProSAT]</span></td></tr>
	</table>		</table>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			The Polysaccharide Lyase Family 6 (PL6) represents one of the 41 polysaccharide lyase families classified in the CAZy database with the vast majority of its members being alginate lyases grouped into three subfamilies, PL6_1-3. To decipher the mode of recognition and action of the enzymes belonging to subfamily PL6_1, we solved the crystal structures of Pedsa0632, Patl3640, Pedsa3628 and Pedsa3807, which all show different substrate specificities and mode of action (endo-/exo-lyase). Thorough exploration of the structures of Pedsa0632 and Patl3640 in complex with their substrates as well as docking experiments confirm that the conserved residues in subsites -1 to +3 of the catalytic site form a common platform which can accommodate various types of alginate in a very similar manner but with a series of original adaptations bringing them their specificities of action. From comparative studies with existing structures of PL6_1 alginate lyases, we observe that in the right-handed parallel beta-helix fold shared by all these enzymes, the substrate binding site harbors the same overall conserved structures and organization. Despite this apparent similarity, it appears that members of the PL6_1 subfamily specifically accommodate and catalyze the degradation of different alginates suggesting that this common platform is actually a highly adaptable and specific tool.

			Exploring molecular determinants of polysaccharide Lyase family 6-1 enzyme activity.,Violot S, Galisson F, Carrique L, Jugnarain V, Conchou L, Robert X, Thureau A, Helbert W, Aghajari N, Ballut L Glycobiology. 2021 Jul 10. pii: 6318796. doi: 10.1093/glycob/cwab073. PMID:34245266<ref>PMID:34245266</ref>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			<div class="pdbe-citations 7o7t" style="background-color:#fffaf0;"></div>
			== References ==
			<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Aghajari N]]		[[Category: Psea6]]
	[[Category: Ballut L]]		[[Category: Aghajari, N]]
	[[Category: Carrique L]]		[[Category: Ballut, L]]
	[[Category: Violot S]]		[[Category: Carrique, L]]
			[[Category: Violot, S]]
			[[Category: Beta helix]]
			[[Category: Complex]]
			[[Category: Lyase]]

OCA at 10:35, 28 July 2021

2021-07-28T10:35:48Z

← Older revision		Revision as of 10:35, 28 July 2021
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	~~'''Unreleased structure'''~~

	~~The entry 7o7t is ON HOLD until Paper Publication~~		==Structure of the PL6 family alginate lyase Patl3640 from Pseudoalteromonas atlantica T6c in complex with 4-deoxy-L-erythro-5-hexoseulose uronic acid==
			<StructureSection load='7o7t' size='340' side='right'caption='[[7o7t]]' scene=''>
	~~Authors: Ballut, L., Violot, S., Carrique, L., Aghajari, N.~~		== Structural highlights ==
			<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7O7T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7O7T FirstGlance]. <br>
	~~Description:~~ Structure of the PL6 family alginate lyase Patl3640 from Pseudoalteromonas atlantica T6c in complex with 4-deoxy-L-erythro-5-hexoseulose uronic acid		</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=7o7t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7o7t OCA], [https://pdbe.org/7o7t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7o7t RCSB], [https://www.ebi.ac.uk/pdbsum/7o7t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7o7t ProSAT]</span></td></tr>
	[[~~Category~~: ~~Unreleased Structures~~]]		</table>
	[[~~Category~~: ~~Carrique~~, L]]		__TOC__
	[[Category: ~~Violot, S~~]]		</StructureSection>
	[[Category: Aghajari, N]]		[[Category: Large Structures]]
	[[Category: Ballut, L]]		[[Category: Aghajari N]]
			[[Category: Ballut L]]
			[[Category: Carrique L]]
			[[Category: Violot S]]

OCA at 08:20, 12 May 2021

2021-05-12T08:20:44Z

← Older revision		Revision as of 08:20, 12 May 2021
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	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 7o7t is ON HOLD		The entry 7o7t is ON HOLD until Paper Publication

	Authors: Ballut, L., Violot, S., Carrique, L., Aghajari, N.		Authors: Ballut, L., Violot, S., Carrique, L., Aghajari, N.

OCA: Protected "7o7t" [edit=sysop:move=sysop]

2021-04-21T06:42:10Z

Protected "7o7t" [edit=sysop:move=sysop]

← Older revision	Revision as of 06:42, 21 April 2021
(No difference)

OCA: New page: '''Unreleased structure''' The entry 7o7t is ON HOLD Authors: Ballut, L., Violot, S., Carrique, L., Aghajari, N. Description: Structure of the PL6 family alginate lyase Patl3640 from P...

2021-04-21T06:42:08Z

New page: '''Unreleased structure''' The entry 7o7t is ON HOLD Authors: Ballut, L., Violot, S., Carrique, L., Aghajari, N. Description: Structure of the PL6 family alginate lyase Patl3640 from P...

New page

'''Unreleased structure'''

The entry 7o7t is ON HOLD

Authors: Ballut, L., Violot, S., Carrique, L., Aghajari, N.

Description: Structure of the PL6 family alginate lyase Patl3640 from Pseudoalteromonas atlantica T6c in complex with 4-deoxy-L-erythro-5-hexoseulose uronic acid
[[Category: Unreleased Structures]]
[[Category: Carrique, L]]
[[Category: Violot, S]]
[[Category: Aghajari, N]]
[[Category: Ballut, L]]