3maf: Difference between revisions

Latest revision as of 08:50, 6 September 2023

Crystal structure of StSPL (asymmetric form)

Structural highlights

3maf is a 2 chain structure with sequence from Symbiobacterium thermophilum. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.971Å
Ligands:	CL, LLP, PO4
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

Q67PY4_SYMTH

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

Sphingosine-1-phosphate lyase (SPL), a key enzyme of sphingolipid metabolism, catalyzes the irreversible degradation of sphingoid base phosphates. Its main substrate sphingosine-1-phosphate (S1P) acts both extracellularly, by binding G protein-coupled receptors of the lysophospholipid receptor family, and inside the cell, as a second messenger. There, S1P takes part in regulating various cellular processes and its levels are tightly regulated. SPL is a pivotal enzyme regulating S1P intracellular concentrations and a promising drug target for the design of immunosuppressants. We structurally and functionally characterized yeast SPL (Dpl1p) and its first prokaryotic homolog, from Symbiobacterium thermophilum. The Dpl1p structure served as a basis for a very reliable model of Homo sapiens SPL. The above results, together with in vitro and in vivo studies of SPL mutants, reveal which residues are involved in activity and substrate binding and pave the way to studies aimed at controlling the activity of this pivotal enzyme.

Structure and function of sphingosine-1-phosphate lyase, a key enzyme of sphingolipid metabolism.,Bourquin F, Riezman H, Capitani G, Grutter MG Structure. 2010 Aug 11;18(8):1054-65. PMID:20696404^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Bourquin F, Riezman H, Capitani G, Grutter MG. Structure and function of sphingosine-1-phosphate lyase, a key enzyme of sphingolipid metabolism. Structure. 2010 Aug 11;18(8):1054-65. PMID:20696404 doi:10.1016/j.str.2010.05.011

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OCA

[1] Bourquin F, Riezman H, Capitani G, Grutter MG. Structure and function of sphingosine-1-phosphate lyase, a key enzyme of sphingolipid metabolism. Structure. 2010 Aug 11;18(8):1054-65. PMID:20696404 doi:10.1016/j.str.2010.05.011

[1]

@@ Line 1: / Line 1: @@
 ==Crystal structure of StSPL (asymmetric form)==
-<StructureSection load='3maf' size='340' side='right' caption='[[3maf]], [[Resolution|resolution]] 2.97&Aring;' scene=''>
+<StructureSection load='3maf' size='340' side='right'caption='[[3maf]], [[Resolution|resolution]] 2.97&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3maf]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Dsm_24528 Dsm 24528]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3MAF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3MAF FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3maf]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Symbiobacterium_thermophilum Symbiobacterium thermophilum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3MAF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3MAF FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 2.971&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3mad|3mad]], [[3mau|3mau]], [[3mbb|3mbb]], [[3mc6|3mc6]]</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=3maf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3maf OCA], [https://pdbe.org/3maf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3maf RCSB], [https://www.ebi.ac.uk/pdbsum/3maf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3maf ProSAT]</span></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">STH1274 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2734 DSM 24528])</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Sphinganine-1-phosphate_aldolase Sphinganine-1-phosphate aldolase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.2.27 4.1.2.27] </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=3maf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3maf OCA], [http://pdbe.org/3maf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3maf RCSB], [http://www.ebi.ac.uk/pdbsum/3maf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3maf ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q67PY4_SYMTH Q67PY4_SYMTH]
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 34: / Line 33: @@
 __TOC__
 </StructureSection>
-[[Category: Dsm 24528]]
+[[Category: Large Structures]]
-[[Category: Sphinganine-1-phosphate aldolase]]
+[[Category: Symbiobacterium thermophilum]]
-[[Category: Bourquin, F]]
+[[Category: Bourquin F]]
-[[Category: Capitani, G]]
+[[Category: Capitani G]]
-[[Category: Grutter, M G]]
+[[Category: Grutter MG]]
-[[Category: Carboxy-lyase activity]]
-[[Category: Lyase]]
-[[Category: Pyridoxal phosphate]]

3maf: Difference between revisions

Latest revision as of 08:50, 6 September 2023

Crystal structure of StSPL (asymmetric form)

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

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