2jg2

From Proteopedia

(Difference between revisions)

Current revision

HIGH RESOLUTION STRUCTURE OF SPT WITH PLP INTERNAL ALDIMINE

Structural highlights

2jg2 is a 1 chain structure with sequence from Sphingomonas paucimobilis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.3Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

SPT_SPHPI Catalyzes the condensation of L-serine with palmitoyl-CoA (hexadecanoyl-CoA) to produce 3-oxosphinganine (PubMed:11279212, PubMed:17557831, PubMed:17559874, PubMed:19376777). Exhibits a broad substrate specificity concerning the chain length and the degree of unsaturation of acyl-CoA (PubMed:11279212, PubMed:19376777).^[1] ^[2] ^[3] ^[4]

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

Sphingolipid biosynthesis commences with the condensation of L-serine and palmitoyl-CoA to produce 3-ketodihydrosphingosine (KDS). This reaction is catalysed by the PLP-dependent enzyme serine palmitoyltransferase (SPT; EC 2.3.1.50), which is a membrane-bound heterodimer (SPT1/SPT2) in eukaryotes such as humans and yeast and a cytoplasmic homodimer in the Gram-negative bacterium Sphingomonas paucimobilis. Unusually, the outer membrane of S. paucimobilis contains glycosphingolipid (GSL) instead of lipopolysaccharide (LPS), and SPT catalyses the first step of the GSL biosynthetic pathway in this organism. We report here the crystal structure of the holo-form of S. paucimobilis SPT at 1.3 A resolution. The enzyme is a symmetrical homodimer with two active sites and a monomeric tertiary structure consisting of three domains. The PLP cofactor is bound covalently to a lysine residue (Lys265) as an internal aldimine/Schiff base and the active site is composed of residues from both subunits, located at the bottom of a deep cleft. Models of the human SPT1/SPT2 heterodimer were generated from the bacterial structure by bioinformatics analysis. Mutations in the human SPT1-encoding subunit have been shown to cause a neuropathological disease known as hereditary sensory and autonomic neuropathy type I (HSAN1). Our models provide an understanding of how these mutations may affect the activity of the enzyme.

The structure of serine palmitoyltransferase; gateway to sphingolipid biosynthesis.,Yard BA, Carter LG, Johnson KA, Overton IM, Dorward M, Liu H, McMahon SA, Oke M, Puech D, Barton GJ, Naismith JH, Campopiano DJ J Mol Biol. 2007 Jul 27;370(5):870-86. Epub 2007 May 10. PMID:17559874^[5]

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

References

↑ Ikushiro H, Hayashi H, Kagamiyama H. A water-soluble homodimeric serine palmitoyltransferase from Sphingomonas paucimobilis EY2395T strain. Purification, characterization, cloning, and overproduction. J Biol Chem. 2001 May 25;276(21):18249-56. PMID:11279212 doi:10.1074/jbc.M101550200
↑ Ikushiro H, Islam MM, Tojo H, Hayashi H. Molecular characterization of membrane-associated soluble serine palmitoyltransferases from Sphingobacterium multivorum and Bdellovibrio stolpii. J Bacteriol. 2007 Aug;189(15):5749-61. PMID:17557831 doi:10.1128/JB.00194-07
↑ Yard BA, Carter LG, Johnson KA, Overton IM, Dorward M, Liu H, McMahon SA, Oke M, Puech D, Barton GJ, Naismith JH, Campopiano DJ. The structure of serine palmitoyltransferase; gateway to sphingolipid biosynthesis. J Mol Biol. 2007 Jul 27;370(5):870-86. Epub 2007 May 10. PMID:17559874 doi:10.1016/j.jmb.2007.04.086
↑ Raman MC, Johnson KA, Yard BA, Lowther J, Carter LG, Naismith JH, Campopiano DJ. The external aldimine form of serine palmitoyltransferase: structural, kinetic, and spectroscopic analysis of the wild-type enzyme and HSAN1 mutant mimics. J Biol Chem. 2009 Jun 19;284(25):17328-39. Epub 2009 Apr 17. PMID:19376777 doi:10.1074/jbc.M109.008680
↑ Yard BA, Carter LG, Johnson KA, Overton IM, Dorward M, Liu H, McMahon SA, Oke M, Puech D, Barton GJ, Naismith JH, Campopiano DJ. The structure of serine palmitoyltransferase; gateway to sphingolipid biosynthesis. J Mol Biol. 2007 Jul 27;370(5):870-86. Epub 2007 May 10. PMID:17559874 doi:10.1016/j.jmb.2007.04.086

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2jg2"

@@ Line 1: / Line 1: @@
 ==HIGH RESOLUTION STRUCTURE OF SPT WITH PLP INTERNAL ALDIMINE==
-<StructureSection load='2jg2' size='340' side='right' caption='[[2jg2]], [[Resolution|resolution]] 1.30&Aring;' scene=''>
+<StructureSection load='2jg2' size='340' side='right'caption='[[2jg2]], [[Resolution|resolution]] 1.30&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2jg2]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_devorans"_zimmermann_1890 "bacillus devorans" zimmermann 1890]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JG2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2JG2 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2jg2]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Sphingomonas_paucimobilis Sphingomonas paucimobilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JG2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2JG2 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 1.3&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=LLP:2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)'>LLP</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Serine_C-palmitoyltransferase Serine C-palmitoyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.50 2.3.1.50] </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=2jg2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jg2 OCA], [https://pdbe.org/2jg2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2jg2 RCSB], [https://www.ebi.ac.uk/pdbsum/2jg2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2jg2 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=2jg2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jg2 OCA], [http://pdbe.org/2jg2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2jg2 RCSB], [http://www.ebi.ac.uk/pdbsum/2jg2 PDBsum]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/SPT_SPHPI SPT_SPHPI] Catalyzes the condensation of L-serine with palmitoyl-CoA (hexadecanoyl-CoA) to produce 3-oxosphinganine (PubMed:11279212, PubMed:17557831, PubMed:17559874, PubMed:19376777). Exhibits a broad substrate specificity concerning the chain length and the degree of unsaturation of acyl-CoA (PubMed:11279212, PubMed:19376777).<ref>PMID:11279212</ref> <ref>PMID:17557831</ref> <ref>PMID:17559874</ref> <ref>PMID:19376777</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/jg/2jg2_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/jg/2jg2_consurf.spt"</scriptWhenChecked>
-    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
-</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2jg2 ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 29: / Line 31: @@
 ==See Also==
-*[[Serine palmitoyltransferase|Serine palmitoyltransferase]]
+*[[Serine palmitoyltransferase 3D structures|Serine palmitoyltransferase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Bacillus devorans zimmermann 1890]]
+[[Category: Large Structures]]
-[[Category: Serine C-palmitoyltransferase]]
+[[Category: Sphingomonas paucimobilis]]
-[[Category: Barton, G J]]
+[[Category: Barton GJ]]
-[[Category: Campopiano, D J]]
+[[Category: Campopiano DJ]]
-[[Category: Carter, L G]]
+[[Category: Carter LG]]
-[[Category: Dorward, M]]
+[[Category: Dorward M]]
-[[Category: Johnson, K A]]
+[[Category: Johnson KA]]
-[[Category: Liu, H]]
+[[Category: Liu H]]
-[[Category: Mcmahon, S A]]
+[[Category: Mcmahon SA]]
-[[Category: Naismith, J H]]
+[[Category: Naismith JH]]
-[[Category: Oke, M]]
+[[Category: Oke M]]
-[[Category: Overton, I M]]
+[[Category: Overton IM]]
-[[Category: Puech, D]]
+[[Category: Puech D]]
-[[Category: Yard, B A]]
+[[Category: Yard BA]]
-[[Category: Plp]]
-[[Category: Pyridoxal phosphate]]
-[[Category: Serine palmitoyl transferase]]
-[[Category: Sphingolipid]]
-[[Category: Spt]]
-[[Category: Sspf]]
-[[Category: Transferase]]

2jg2

From Proteopedia

Current revision

HIGH RESOLUTION STRUCTURE OF SPT WITH PLP INTERNAL ALDIMINE

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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