2W8J

SPT with PLP-ser

Summary for 2W8J

• Entry DOI: 10.2210/pdb2w8j/pdb
• Related: 2JG2 2JGT
• Descriptor: SERINE PALMITOYLTRANSFERASE, [3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-SERINE (3 entities in total)
• Functional Keywords: transferase
• Biological source: SPHINGOMONAS PAUCIMOBILIS
• Total number of polymer chains: 1
• Total formula weight: 46366.79

Authors

Carter, L.G.,Raman, M.C.C.,Johnson, K.A.,Campopiano, D.J.,Naismith, J.H. (deposition date: 2009-01-16, release date: 2009-01-27, Last modification date: 2024-05-08)

Primary citation

Raman, M.C.C.,Johnson, K.A.,Yard, B.A.,Lowther, J.,Carter, L.G.,Naismith, J.H.,Campopiano, D.J.
The External-Aldimine Form of Serine Palmitoyltranserase; Structural, Kinetic and Spectroscopic Analysis of the Wild-Type Enzyme and Hsan1 Mutant Mimics.
J.Biol.Chem., 284:17328-, 2009

PubMed Abstract: Sphingolipid biosynthesis begins with the condensation of L-serine and palmitoyl-CoA catalyzed by the PLP-dependent enzyme serine palmitoyltransferase (SPT). Mutations in human SPT cause hereditary sensory autonomic neuropathy type 1, a disease characterized by loss of feeling in extremities and severe pain. The human enzyme is a membrane-bound hetereodimer, and the most common mutations are located in the enzymatically incompetent monomer, suggesting a "dominant" or regulatory effect. The molecular basis of how these mutations perturb SPT activity is subtle and is not simply loss of activity. To further explore the structure and mechanism of SPT, we have studied the homodimeric bacterial enzyme from Sphingomonas paucimobilis. We have analyzed two mutants (N100Y and N100W) engineered to mimic the mutations seen in hereditary sensory autonomic neuropathy type 1 as well as a third mutant N100C designed to mimic the wild-type human SPT. The N100C mutant appears fully active, whereas both N100Y and N100W are significantly compromised. The structures of the holoenzymes reveal differences around the active site and in neighboring secondary structure that transmit across the dimeric interface in both N100Y and N100W. Comparison of the l-Ser external aldimine structures of both native and N100Y reveals significant differences that hinder the movement of a catalytically important Arg(378) residue into the active site. Spectroscopic analysis confirms that both N100Y and N100W mutants subtly affect the chemistry of the PLP. Furthermore, the N100Y and R378A mutants appear less able to stabilize a quinonoid intermediate. These data provide the first experimental insight into how the most common disease-associated mutations of human SPT may lead to perturbation of enzyme activity.

PubMed: 19376777
DOI: 10.1074/JBC.M109.008680

Experimental method

X-RAY DIFFRACTION (1.5 Å)