2jg2

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (08:28, 9 April 2025) (edit) (undo)
 
(19 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:2jg2.gif|left|200px]]<br /><applet load="2jg2" size="450" color="white" frame="true" align="right" spinBox="true"
 
-
caption="2jg2, resolution 1.30&Aring;" />
 
-
'''HIGH RESOLUTION STRUCTURE OF SPT WITH PLP INTERNAL ALDIMINE'''<br />
 
-
==Overview==
+
==HIGH RESOLUTION STRUCTURE OF SPT WITH PLP INTERNAL ALDIMINE==
-
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.
+
<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 [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='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='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='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>
 +
</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>
 +
<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/main_output.php?pdb_ID=2jg2 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.
-
==About this Structure==
+
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>
-
2JG2 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Sphingomonas_paucimobilis Sphingomonas paucimobilis] with MG as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [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] Known structural/functional Site: <scene name='pdbsite=AC1:Mg Binding Site For Chain Z'>AC1</scene>. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2JG2 OCA].
+
-
==Reference==
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17559874 17559874]
+
</div>
-
[[Category: Serine C-palmitoyltransferase]]
+
<div class="pdbe-citations 2jg2" style="background-color:#fffaf0;"></div>
-
[[Category: Single protein]]
+
-
[[Category: Sphingomonas paucimobilis]]
+
-
[[Category: Barton, G.J.]]
+
-
[[Category: Campopiano, D.J.]]
+
-
[[Category: Carter, L.G.]]
+
-
[[Category: Dorward, M.]]
+
-
[[Category: Johnson, K.A.]]
+
-
[[Category: Liu, H.]]
+
-
[[Category: Mcmahon, S.A.]]
+
-
[[Category: Naismith, J.H.]]
+
-
[[Category: Oke, M.]]
+
-
[[Category: Overton, I.M.]]
+
-
[[Category: Puech, D.]]
+
-
[[Category: Yard, B.A.]]
+
-
[[Category: MG]]
+
-
[[Category: plp]]
+
-
[[Category: pyridoxal phosphate]]
+
-
[[Category: serine palmitoyl transferase]]
+
-
[[Category: sphingolipid]]
+
-
[[Category: spt]]
+
-
[[Category: sspf]]
+
-
[[Category: transferase]]
+
-
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Dec 18 20:07:32 2007''
+
==See Also==
 +
*[[Serine palmitoyltransferase 3D structures|Serine palmitoyltransferase 3D structures]]
 +
== References ==
 +
<references/>
 +
__TOC__
 +
</StructureSection>
 +
[[Category: Large Structures]]
 +
[[Category: Sphingomonas paucimobilis]]
 +
[[Category: Barton GJ]]
 +
[[Category: Campopiano DJ]]
 +
[[Category: Carter LG]]
 +
[[Category: Dorward M]]
 +
[[Category: Johnson KA]]
 +
[[Category: Liu H]]
 +
[[Category: Mcmahon SA]]
 +
[[Category: Naismith JH]]
 +
[[Category: Oke M]]
 +
[[Category: Overton IM]]
 +
[[Category: Puech D]]
 +
[[Category: Yard BA]]

Current revision

HIGH RESOLUTION STRUCTURE OF SPT WITH PLP INTERNAL ALDIMINE

PDB ID 2jg2

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

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