2W8W

N100Y SPT with PLP-ser


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

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: 10.1074/jbc.M109.008680
  • Primary Citation of Related Structures:  

  • 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 chara ...

    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

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

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

Download SDF File 
Download CCD File 
A
[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-SERINE
PYRIDOXYL-SERINE-5-MONOPHOSPHATE
C11 H17 N2 O8 P
ODVKKQWXKRZJLG-VIFPVBQESA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
PLSKd: 7500000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.192 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 73.600α = 90.00
b = 107.130β = 90.00
c = 89.900γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-01-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance