5k1r - Revision history

OCA at 19:18, 20 September 2023

OCA — Wed, 20 Sep 2023 19:18:14 GMT

←Older revision		Revision as of 19:18, 20 September 2023
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	==Structure of Burkholderia pseudomallei K96243 sphingosine-1-phosphate lyase Bpss2021==		==Structure of Burkholderia pseudomallei K96243 sphingosine-1-phosphate lyase Bpss2021==
-	<StructureSection load='5k1r' size='340' side='right' caption='[[5k1r]], [[Resolution\|resolution]] 2.10Å' scene=''>	+	<StructureSection load='5k1r' size='340' side='right'caption='[[5k1r]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5k1r]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Burps Burps~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K1R OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5K1R FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5k1r]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Burkholderia_pseudomallei_K96243 Burkholderia pseudomallei K96243]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K1R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5K1R FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=PLP:PYRIDOXAL~~-~~5-PHOSPHATE'>PLP</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]] 2.104Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~BPSS2021 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=5~~&id=272560 BURPS])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</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=5k1r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k1r OCA], [~~http~~://pdbe.org/5k1r PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5k1r RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5k1r PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5k1r 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=5k1r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k1r OCA], [https://pdbe.org/5k1r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5k1r RCSB], [https://www.ebi.ac.uk/pdbsum/5k1r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5k1r ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q63IP8_BURPS Q63IP8_BURPS]
	<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: ~~Burps~~]]	+	[[Category: Burkholderia pseudomallei K96243]]
-	[[Category: ~~Campopiano, D J~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Marles-Wright, J~~]]	+	[[Category: Campopiano DJ]]
-	[[Category: ~~Mclean, C~~ J]]	+	[[Category: Marles-Wright J]]
-	[[Category: ~~Lyase]]~~	+	[[Category: Mclean CJ]]
-	~~[[Category: Sphingosine-1-phosphate sphingosine-1-phosphate lyase burkholderia pseudomallei plp~~]]	+

OCA at 07:37, 6 December 2017

OCA — Wed, 06 Dec 2017 07:37:55 GMT

←Older revision		Revision as of 07:37, 6 December 2017
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	<StructureSection load='5k1r' size='340' side='right' caption='[[5k1r]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='5k1r' size='340' side='right' caption='[[5k1r]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5k1r]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K1R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5K1R FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5k1r]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Burps Burps]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K1R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5K1R FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BPSS2021 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=272560 BURPS])</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=5k1r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k1r OCA], [http://pdbe.org/5k1r PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5k1r RCSB], [http://www.ebi.ac.uk/pdbsum/5k1r PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5k1r 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=5k1r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k1r OCA], [http://pdbe.org/5k1r PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5k1r RCSB], [http://www.ebi.ac.uk/pdbsum/5k1r PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5k1r ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Sphingolipids (SLs) are ubiquitous elements in eukaryotic membranes and are also found in some bacterial and viral species. As well as playing an integral structural role, SLs also act as potent signaling molecules involved in numerous cellular pathways and have been linked to many human diseases. A central SL signaling molecule is sphingosine-1-phosphate (S1P), whose breakdown is catalyzed by S1P lyase (S1PL), a pyridoxal 5'-phosphate (PLP)-dependent enzyme that catalyzes the cleavage of S1P to (2E)-hexadecenal (2E-HEX) and phosphoethanolamine. Here, we show that the pathogenic bacterium, Burkholderia pseudomallei K96243, encodes two homologous proteins (S1PL2021 and S1PL2025) that display moderate sequence identity to known eukaryotic and prokaryotic S1PLs. Using an established MS-based methodology, we show that recombinant S1PL2021 is catalytically active. We also used recombinant human fatty aldehyde dehydrogenase to develop a spectrophotometric enzyme-coupled assay to detect 2E-HEX formation and measure the kinetic constants of the two B. pseudomallei S1PL isoforms. Furthermore, we determined the X-ray crystal structure of the PLP-bound form of S1PL2021 at 2.1 A resolution revealing that the enzyme displays a conserved structural fold and active site architecture comparable with known S1PLs. The combined data suggest that B. pseudomallei has the potential to degrade host SLs in a S1PL-dependent manner.
		+
		+	Characterization of homologous sphingosine-1-phosphate lyase isoforms in the bacterial pathogen Burkholderia pseudomallei.,McLean CJ, Marles-Wright J, Custodio R, Lowther J, Kennedy AJ, Pollock J, Clarke DJ, Brown AR, Campopiano DJ J Lipid Res. 2017 Jan;58(1):137-150. doi: 10.1194/jlr.M071258. Epub 2016 Oct 26. PMID:27784725<ref>PMID:27784725</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5k1r" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Burps]]
	[[Category: Campopiano, D J]]		[[Category: Campopiano, D J]]
	[[Category: Marles-Wright, J]]		[[Category: Marles-Wright, J]]

OCA at 18:29, 2 November 2016

OCA — Wed, 02 Nov 2016 18:29:08 GMT

←Older revision		Revision as of 18:29, 2 November 2016
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-	'''Unreleased structure'''

-	~~The entry~~ 5k1r is ~~ON HOLD until May 18 2018~~	+	==Structure of Burkholderia pseudomallei K96243 sphingosine-1-phosphate lyase Bpss2021==
-		+	<StructureSection load='5k1r' size='340' side='right' caption='[[5k1r]], [[Resolution\|resolution]] 2.10Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5k1r]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K1R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5K1R FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</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=5k1r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k1r OCA], [http://pdbe.org/5k1r PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5k1r RCSB], [http://www.ebi.ac.uk/pdbsum/5k1r PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5k1r ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Campopiano, D J]]
		+	[[Category: Marles-Wright, J]]
		+	[[Category: Mclean, C J]]
		+	[[Category: Lyase]]
		+	[[Category: Sphingosine-1-phosphate sphingosine-1-phosphate lyase burkholderia pseudomallei plp]]

OCA at 11:57, 26 July 2016

OCA — Tue, 26 Jul 2016 11:57:03 GMT

←Older revision		Revision as of 11:57, 26 July 2016
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5k1r is ON HOLD	+	The entry 5k1r is ON HOLD until May 18 2018

	Authors:		Authors:

OCA: Protected "5k1r" [edit=sysop:move=sysop]

OCA — Wed, 01 Jun 2016 14:11:58 GMT

Protected "5k1r" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:11, 1 June 2016

OCA: New page: '''Unreleased structure''' The entry 5k1r is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 01 Jun 2016 14:11:57 GMT

New page: '''Unreleased structure''' The entry 5k1r is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5k1r is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]