2XBN

Inhibition of the PLP-dependent enzyme serine palmitoyltransferase by cycloserine: evidence for a novel decarboxylative mechanism of inactivation

Summary for 2XBN

• Entry DOI: 10.2210/pdb2xbn/pdb
• Related: 2JG2 2JGT 2W8J 2W8T 2W8U 2W8V 2W8W
• Descriptor: SERINE PALMITOYLTRANSFERASE, 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE, MAGNESIUM ION, ... (4 entities in total)
• Functional Keywords: transferase, pyridoxal phosphate
• Biological source: SPHINGOMONAS PAUCIMOBILIS
• Total number of polymer chains: 1
• Total formula weight: 46303.03

Authors

Lowther, J.,Yard, B.A.,Johnson, K.A.,Carter, L.G.,Bhat, V.T.,Raman, M.C.C.,Clarke, D.J.,Ramakers, B.,McMahon, S.A.,Naismith, J.H.,Campopiano, D.J. (deposition date: 2010-04-13, release date: 2010-05-19, Last modification date: 2024-05-08)

Primary citation

Lowther, J.,Yard, B.A.,Johnson, K.A.,Carter, L.G.,Bhat, V.T.,Raman, M.C.C.,Clarke, D.J.,Ramakers, B.,Mcmahon, S.A.,Naismith, J.H.,Campopiano, D.J.
Inhibition of the Plp-Dependent Enzyme Serine Palmitoyltransferase by Cycloserine: Evidence for a Novel Decarboxylative Mechanism of Inactivation.
Mol.Biosystems, 6:1682-, 2010

PubMed Abstract: Cycloserine (CS, 4-amino-3-isoxazolidone) is a cyclic amino acid mimic that is known to inhibit many essential pyridoxal 5'-phosphate (PLP)-dependent enzymes. Two CS enantiomers are known; D-cycloserine (DCS, also known as Seromycin) is a natural product that is used to treat resistant Mycobacterium tuberculosis infections as well as neurological disorders since it is a potent NMDA receptor agonist, and L-cycloserine (LCS) is a synthetic enantiomer whose usefulness as a drug has been hampered by its inherent toxicity arising through inhibition of sphingolipid metabolism. Previous studies on various PLP-dependent enzymes revealed a common mechanism of inhibition by both enantiomers of CS; the PLP cofactor is disabled by forming a stable 3-hydroxyisoxazole/pyridoxamine 5'-phosphate (PMP) adduct at the active site where the cycloserine ring remains intact. Here we describe a novel mechanism of CS inactivation of the PLP-dependent enzyme serine palmitoyltransferase (SPT) from Sphingomonas paucimobilis. SPT catalyses the condensation of l-serine and palmitoyl-CoA, the first step in the de novo sphingolipid biosynthetic pathway. We have used a range of kinetic, spectroscopic and structural techniques to postulate that both LCS and DCS inactivate SPT by transamination to form a free pyridoxamine 5'-phosphate (PMP) and beta-aminooxyacetaldehyde that remain bound at the active site. We suggest this occurs by ring opening of the cycloserine ring followed by decarboxylation. Enzyme kinetics show that inhibition is reversed by incubation with excess PLP and that LCS is a more effective SPT inhibitor than DCS. UV-visible spectroscopic data, combined with site-directed mutagenesis, suggest that a mobile Arg(378) residue is involved in cycloserine inactivation of SPT.

PubMed: 20445930
DOI: 10.1039/C003743E

Experimental method

X-RAY DIFFRACTION (1.4 Å)