SPT with PLP-ser

Experimental Data Snapshot

  • Resolution: 1.50 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.159 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


The External-Aldimine Form of Serine Palmitoyltranserase; Structural, Kinetic and Spectroscopic Analysis of the Wild-Type Enzyme and Hsan1 Mutant Mimics.

Raman, M.C.C.Johnson, K.A.Yard, B.A.Lowther, J.Carter, L.G.Naismith, J.H.Campopiano, D.J.

(2009) J Biol Chem 284: 17328

  • DOI: https://doi.org/10.1074/jbc.M109.008680
  • Primary Citation of Related Structures:  
    2W8J, 2W8T, 2W8U, 2W8V, 2W8W

  • 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.

  • Organizational Affiliation

    From EaStChem, School of Chemistry, University of Edinburgh, Edinburgh EH9 3JJ.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SERINE PALMITOYLTRANSFERASE427Sphingomonas paucimobilisMutation(s): 0 
Find proteins for Q93UV0 (Sphingomonas paucimobilis)
Explore Q93UV0 
Go to UniProtKB:  Q93UV0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ93UV0
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on PLS

Download Ideal Coordinates CCD File 
C11 H17 N2 O8 P
Binding Affinity Annotations 
IDSourceBinding Affinity
PLS PDBBind:  2W8J Kd: 1.10e+6 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.50 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.159 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.248α = 90
b = 108.375β = 90
c = 91.213γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-01-27
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-05-08
    Changes: Data collection, Database references, Derived calculations, Other