PDBsum entry 2jg2

Transferase

PDB id: 2jg2

Contents

Protein chain

399 a.a. *

Ligands

PLP

Metals

_MG

Waters ×409

* Residue conservation analysis

PDB id:

2jg2

Name:

Transferase

Title:

High resolution structure of spt with plp internal aldimine

Structure:

Serine palmitoyltransferase. Chain: a. Engineered: yes. Other_details: plp forming internal aldimine with lys265

Source:

Pseudomonas paucimobilis. Organism_taxid: 13689. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.30Å R-factor: 0.155 R-free: 0.185

Authors:

B.A.Yard,L.G.Carter,K.A.Johnson,I.M.Overton,S.A.Mcmahon,M.Dorward, H.Liu,D.Puech,M.Oke,G.J.Barton,J.H.Naismith,D.J.Campopiano

Key ref:

B.A.Yard et al. (2007). The structure of serine palmitoyltransferase; gateway to sphingolipid biosynthesis. J Mol Biol, 370, 870-886. PubMed id: 17559874 DOI: 10.1016/j.jmb.2007.04.086

Date:

07-Feb-07 Release date: 01-May-07

Protein chain

Q93UV0  (SPT_SPHPI) -  Serine palmitoyltransferase from Sphingomonas paucimobilis

Seq: 420 a.a.

Struc: 399 a.a.

Enzyme reactions

• Enzyme class: E.C.2.3.1.50 - serine C-palmitoyltransferase.
• Reaction: L-serine + hexadecanoyl-CoA + H⁺ = 3-oxosphinganine + CO2 + CoA
• Cofactor: Pyridoxal 5'-phosphate

Pyridoxal 5'-phosphate (Bound ligand (Het Group name = PLP) matches with 93.75% similarity)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1016/j.jmb.2007.04.086

J Mol Biol 370:870-886 (2007)

PubMed id: 17559874

The structure of serine palmitoyltransferase; gateway to sphingolipid biosynthesis.

B.A.Yard, L.G.Carter, K.A.Johnson, I.M.Overton, M.Dorward, H.Liu, S.A.McMahon, M.Oke, D.Puech, G.J.Barton, J.H.Naismith, D.J.Campopiano.

ABSTRACT

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.

Selected figure(s)

Figure 2.
Figure 2. Proposed reaction mechanism of SPT. (a) Transaldimination of internal aldimine (holo-SPT), I with L-serine to form external aldimine, II; (b) deprotonation of C^α by base to form quinonoid, III; (c) Claisen condensation to form putative β-ketoacid-aldimine complex, IV; (d) decarboxylation to form product quinonoid, V; (e) reprotonation of quinonoid to form product external aldimine, VI (f) release of product 3-ketodihydrosphingosine (KDS) and regeneration of I.

Figure 7.
Figure 7. Stereo view showing the proximity of the Asn100 residue of monomer B to the PLP cofactor of monomer A in the S. paucimobilis SPT homodimer. Monomer A is drawn in green and monomer B is drawn in blue. Asn100 of monomer B is shown in CPK. Using the sequence alignment in Figure 9, the S. paucimobilis SPT Asn100 residue maps to residue Cys133 on the SPT1 subunit of human SPT. Mutations at this residue C133W and C133Y are known to cause the autosomal disease hereditary sensory and autonomic neuropathy type I (HSAN1). The conserved residues His159 and His234 which interact directly with the PLP cofactor are also highlighted.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2007, 370, 870-886) copyright 2007.

Figures were selected by the author.