2XBN

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.156 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Inhibition of the Plp-Dependent Enzyme Serine Palmitoyltransferase by Cycloserine: Evidence for a Novel Decarboxylative Mechanism of Inactivation.

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.

(2010) Mol.Biosystems 6: 1682

  • DOI: 10.1039/c003743e

  • 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 pro ...

    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.


    Organizational Affiliation

    EaStChem, School of Chemistry, The University of Edinburgh, West Mains Road, Edinburgh, EH9 3JJ, Scotland, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SERINE PALMITOYLTRANSFERASE
A
427Sphingomonas paucimobilisMutation(s): 0 
Gene Names: SPT1
Find proteins for Q93UV0 (Sphingomonas paucimobilis)
Go to UniProtKB:  Q93UV0
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
PMP
Query on PMP

Download SDF File 
Download CCD File 
A
4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE
PYRIDOXAMINE-5'-PHOSPHATE
C8 H13 N2 O5 P
ZMJGSOSNSPKHNH-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.156 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 74.141α = 90.00
b = 107.651β = 90.00
c = 90.106γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-05-19
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance