4BMK

Serine Palmitoyltransferase K265A from S. paucimobilis with bound PLP- Myriocin Aldimine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

The Chemical Basis of Serine Palmitoyltransferase Inhibition by Myriocin.

Wadsworth, J.M.Clarke, D.J.Mcmahon, S.A.Lowther, J.P.Beattie, A.E.Langridge-Smith, P.R.R.Broughton, H.B.Dunn, T.M.Naismith, J.H.Campopiano, D.J.

(2013) J Am Chem Soc 135: 14276

  • DOI: 10.1021/ja4059876
  • Primary Citation of Related Structures:  
    4BMK

  • PubMed Abstract: 
  • Sphingolipids (SLs) are essential components of cellular membranes formed from the condensation of L-serine and a long-chain acyl thioester. This first step is catalyzed by the pyridoxal-5'-phosphate (PLP)-dependent enzyme serine palmitoyltransferase ...

    Sphingolipids (SLs) are essential components of cellular membranes formed from the condensation of L-serine and a long-chain acyl thioester. This first step is catalyzed by the pyridoxal-5'-phosphate (PLP)-dependent enzyme serine palmitoyltransferase (SPT) which is a promising therapeutic target. The fungal natural product myriocin is a potent inhibitor of SPT and is widely used to block SL biosynthesis despite a lack of a detailed understanding of its molecular mechanism. By combining spectroscopy, mass spectrometry, X-ray crystallography, and kinetics, we have characterized the molecular details of SPT inhibition by myriocin. Myriocin initially forms an external aldimine with PLP at the active site, and a structure of the resulting co-complex explains its nanomolar affinity for the enzyme. This co-complex then catalytically degrades via an unexpected 'retro-aldol-like' cleavage mechanism to a C18 aldehyde which in turn acts as a suicide inhibitor of SPT by covalent modification of the essential catalytic lysine. This surprising dual mechanism of inhibition rationalizes the extraordinary potency and longevity of myriocin inhibition.


    Organizational Affiliation

    School of Chemistry, The University of Edinburgh , Edinburgh, Scotland, EH9 3JJ, United Kingdom.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SERINE PALMITOYLTRANSFERASEAB442Sphingomonas paucimobilisMutation(s): 1 
Gene Names: SPT1DRN02_007885
EC: 2.3.1.50
Find proteins for Q93UV0 (Sphingomonas paucimobilis)
Explore Q93UV0 
Go to UniProtKB:  Q93UV0
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MYB
Query on MYB

Download CCD File 
A, B
Decarboxylated Myriocin
C20 H39 N O4
NXVWIVNGDXWOCH-INRCJLNUSA-N
 Ligand Interaction
PLP
Query on PLP

Download CCD File 
A, B
PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.190 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.91α = 90
b = 98.71β = 90
c = 133.19γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-09-04
    Type: Initial release
  • Version 1.1: 2013-10-09
    Changes: Database references