2jgt

From Proteopedia

(Difference between revisions)

Current revision

Low resolution structure of SPT

Structural highlights

2jgt is a 2 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 3Å
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/2jgt"

@@ Line 1: / Line 1: @@
-{{Seed}}
-[[Image:2jgt.png|left|200px]]
-<!--
+==Low resolution structure of SPT==
-The line below this paragraph, containing "STRUCTURE_2jgt", creates the "Structure Box" on the page.
+<StructureSection load='2jgt' size='340' side='right'caption='[[2jgt]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[2jgt]] is a 2 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=2JGT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2JGT FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3&#8491;</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=2jgt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jgt OCA], [https://pdbe.org/2jgt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2jgt RCSB], [https://www.ebi.ac.uk/pdbsum/2jgt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2jgt ProSAT]</span></td></tr>
-{{STRUCTURE_2jgt|  PDB=2jgt  |  SCENE=  }}
+</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/2jgt_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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/main_output.php?pdb_ID=2jgt ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== 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.
-===LOW RESOLUTION STRUCTURE OF SPT===
+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<ref>PMID:17559874</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2jgt" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_17559874}}, adds the Publication Abstract to the page
+*[[Serine palmitoyltransferase 3D structures|Serine palmitoyltransferase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 17559874 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_17559874}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-JGT is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Sphingomonas_paucimobilis Sphingomonas paucimobilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JGT OCA].
-==Reference==
-<ref group="xtra">PMID:17559874</ref><references group="xtra"/>
-[[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]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 16:52:10 2009''

2jgt

From Proteopedia

Current revision

Low resolution structure of SPT

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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