6jph - Revision history

OCA at 10:39, 27 March 2024

2024-03-27T10:39:03Z

←Older revision		Revision as of 10:39, 27 March 2024
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	<StructureSection load='6jph' size='340' side='right'caption='[[6jph]], [[Resolution\|resolution]] 2.76Å' scene=''>		<StructureSection load='6jph' size='340' side='right'caption='[[6jph]], [[Resolution\|resolution]] 2.76Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6jph]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Defluviitalea_phaphyphila Defluviitalea phaphyphila]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JPH OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6JPH FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6jph]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Defluviitalea_phaphyphila Defluviitalea phaphyphila]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JPH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6JPH FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=BEM:BETA-D-MANNURONIC+ACID'>BEM</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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]] 2.759Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6jp4\|6jp4]]~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=BEM:BETA-D-MANNURONIC+ACID'>BEM</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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=6jph FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jph OCA], [~~http~~://pdbe.org/6jph PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6jph RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6jph PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6jph 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=6jph FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jph OCA], [https://pdbe.org/6jph PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6jph RCSB], [https://www.ebi.ac.uk/pdbsum/6jph PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6jph ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/A0A4Y5UXE1_9FIRM A0A4Y5UXE1_9FIRM]
-	Alginate is a polymer containing two uronic acid epimers, beta-d-mannuronate (M) and alpha-l-guluronate (G), and is a major component of brown seaweed that is depolymerized by alginate lyases. These enzymes have diverse specificity, cleaving the chain with endo- or exotype activity and with differential selectivity for the sequence of M or G at the cleavage site. Dp0100 is a 201-kDa multi-modular, broad-specificity endotype alginate lyase from the marine thermophile Defluviitalea phaphyphila, which uses brown algae as a carbon source, converting it to ethanol, and bioinformatics analysis suggested that its catalytic domain represents a new polysaccharide lyase family, PLxx. The structure of the Dp0100 catalytic domain, determined at 2.07 A resolution, revealed that it comprises three regions strongly resembling those of the exotype lyase families PL15 and PL17. The conservation of key catalytic histidine and tyrosine residues belonging to the latter suggest these enzymes share mechanistic similarities. A complex of Dp0100 with a pentasaccharide, M5, showed that the oligosaccharide is located in subsites -2, -1, +1, +2, and +3 in a long, deep canyon open at both ends, explaining the endotype activity of this lyase. This contrasted with the hindered binding sites of the exotype enzymes, which are blocked such that only one sugar moiety can be accommodated at the -1 position in the catalytic site. The biochemical and structural analyses of Dp0100, the first for this new class of endotype alginate lyases, has furthered our understanding of the structure-function and evolutionary relationships within this important class of enzymes.	+
-		+
-	The molecular basis of endolytic activity of a multidomain alginate lyase from Defluviitalea phaphyphila, a representative of a new lyase family, PLxx.,Ji S, Dix SR, Aziz AA, Sedelnikova SE, Baker PJ, Rafferty JB, Bullough PA, Tzokov SB, Agirre J, Li FL, Rice DW J Biol Chem. 2019 Oct 17. pii: ~~RA119.010716. doi: 10.1074~~/~~jbc.RA119.010716. PMID:31624143<ref>PMID:31624143<~~/~~ref>~~	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 6jph" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references~~/>	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Defluviitalea phaphyphila]]		[[Category: Defluviitalea phaphyphila]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Aziz, A]]	+	[[Category: Aziz A]]
-	[[Category: Dix~~, S R~~]]	+	[[Category: Dix SR]]
-	[[Category: Ji~~, S Q~~]]	+	[[Category: Ji SQ]]
-	[[Category: Li~~, F L~~]]	+	[[Category: Li FL]]
-	[[Category: Rice~~, D W~~]]	+	[[Category: Rice DW]]
-	[[Category: Sedelnikova~~, S E]]~~	+	[[Category: Sedelnikova SE]]
-	~~[[Category: Alpha barrel+beta sandwich]]~~	+
-	~~[[Category: Lyase~~]]	+

OCA at 09:03, 30 October 2019

2019-10-30T09:03:16Z

←Older revision		Revision as of 09:03, 30 October 2019
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-	'''Unreleased structure'''

-	~~The entry~~ 6jph is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of the catalytic domain of a multi-domain alginate lyase Dp0100 from thermophilic bacterium Defluviitalea phaphyphila==
		+	<StructureSection load='6jph' size='340' side='right'caption='[[6jph]], [[Resolution\|resolution]] 2.76Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6jph]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Defluviitalea_phaphyphila Defluviitalea phaphyphila]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JPH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6JPH FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=BEM:BETA-D-MANNURONIC+ACID'>BEM</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6jp4\|6jp4]]</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=6jph FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jph OCA], [http://pdbe.org/6jph PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6jph RCSB], [http://www.ebi.ac.uk/pdbsum/6jph PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6jph ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Alginate is a polymer containing two uronic acid epimers, beta-d-mannuronate (M) and alpha-l-guluronate (G), and is a major component of brown seaweed that is depolymerized by alginate lyases. These enzymes have diverse specificity, cleaving the chain with endo- or exotype activity and with differential selectivity for the sequence of M or G at the cleavage site. Dp0100 is a 201-kDa multi-modular, broad-specificity endotype alginate lyase from the marine thermophile Defluviitalea phaphyphila, which uses brown algae as a carbon source, converting it to ethanol, and bioinformatics analysis suggested that its catalytic domain represents a new polysaccharide lyase family, PLxx. The structure of the Dp0100 catalytic domain, determined at 2.07 A resolution, revealed that it comprises three regions strongly resembling those of the exotype lyase families PL15 and PL17. The conservation of key catalytic histidine and tyrosine residues belonging to the latter suggest these enzymes share mechanistic similarities. A complex of Dp0100 with a pentasaccharide, M5, showed that the oligosaccharide is located in subsites -2, -1, +1, +2, and +3 in a long, deep canyon open at both ends, explaining the endotype activity of this lyase. This contrasted with the hindered binding sites of the exotype enzymes, which are blocked such that only one sugar moiety can be accommodated at the -1 position in the catalytic site. The biochemical and structural analyses of Dp0100, the first for this new class of endotype alginate lyases, has furthered our understanding of the structure-function and evolutionary relationships within this important class of enzymes.

-	~~Authors: Ji~~, ~~S.Q~~., ~~Dix,~~ S~~.R.~~, Aziz~~, A.~~, Sedelnikova, ~~S.E.~~, Li, F.L.~~, Rice, D~~.W.	+	The molecular basis of endolytic activity of a multidomain alginate lyase from Defluviitalea phaphyphila, a representative of a new lyase family, PLxx.,Ji S, Dix SR, Aziz AA, Sedelnikova SE, Baker PJ, Rafferty JB, Bullough PA, Tzokov SB, Agirre J, Li FL, Rice DW J Biol Chem. 2019 Oct 17. pii: RA119.010716. doi: 10.1074/jbc.RA119.010716. PMID:31624143<ref>PMID:31624143</ref>

-	~~Description: Crystal structure~~ of the ~~catalytic domain~~ of ~~a multi-domain alginate lyase Dp0100 from thermophilic bacterium Defluviitalea phaphyphila~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	~~[[Category~~: ~~Rice, D.W]]~~	+	<div class="pdbe-citations 6jph" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Li, F.L~~]]	+	== References ==
-	[[Category: ~~Sedelnikova, S.E~~]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Defluviitalea phaphyphila]]
		+	[[Category: Large Structures]]
	[[Category: Aziz, A]]		[[Category: Aziz, A]]
-	[[Category: Dix, S.R]]	+	[[Category: Dix, S R]]
-	[[Category: Ji, S.Q]]	+	[[Category: Ji, S Q]]
		+	[[Category: Li, F L]]
		+	[[Category: Rice, D W]]
		+	[[Category: Sedelnikova, S E]]
		+	[[Category: Alpha barrel+beta sandwich]]
		+	[[Category: Lyase]]

OCA at 04:47, 23 October 2019

2019-10-23T04:47:28Z

←Older revision		Revision as of 04:47, 23 October 2019
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	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Ji, S.Q., Dix, S.R., Aziz, A., Sedelnikova, S.E., Li, F.L., Rice, D.W.		Authors: Ji, S.Q., Dix, S.R., Aziz, A., Sedelnikova, S.E., Li, F.L., Rice, D.W.
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	Description: Crystal structure of the catalytic domain of a multi-domain alginate lyase Dp0100 from thermophilic bacterium Defluviitalea phaphyphila		Description: Crystal structure of the catalytic domain of a multi-domain alginate lyase Dp0100 from thermophilic bacterium Defluviitalea phaphyphila
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Li, F.L]]
-	[[Category: Dix, S.R]]
-	[[Category: Ji, S.Q]]
	[[Category: Rice, D.W]]		[[Category: Rice, D.W]]
		+	[[Category: Li, F.L]]
	[[Category: Sedelnikova, S.E]]		[[Category: Sedelnikova, S.E]]
	[[Category: Aziz, A]]		[[Category: Aziz, A]]
		+	[[Category: Dix, S.R]]
		+	[[Category: Ji, S.Q]]

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

2019-04-03T04:28:06Z

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

←Older revision

Revision as of 04:28, 3 April 2019

OCA: New page: '''Unreleased structure''' The entry 6jph is ON HOLD Authors: Ji, S.Q., Dix, S.R., Aziz, A., Sedelnikova, S.E., Li, F.L., Rice, D.W. Description: Crystal structure of the catalytic dom...

2019-04-03T04:28:05Z

New page: '''Unreleased structure''' The entry 6jph is ON HOLD Authors: Ji, S.Q., Dix, S.R., Aziz, A., Sedelnikova, S.E., Li, F.L., Rice, D.W. Description: Crystal structure of the catalytic dom...

New page

'''Unreleased structure'''

The entry 6jph is ON HOLD

Authors: Ji, S.Q., Dix, S.R., Aziz, A., Sedelnikova, S.E., Li, F.L., Rice, D.W.

Description: Crystal structure of the catalytic domain of a multi-domain alginate lyase Dp0100 from thermophilic bacterium Defluviitalea phaphyphila
[[Category: Unreleased Structures]]
[[Category: Li, F.L]]
[[Category: Dix, S.R]]
[[Category: Ji, S.Q]]
[[Category: Rice, D.W]]
[[Category: Sedelnikova, S.E]]
[[Category: Aziz, A]]