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

Experimental Data Snapshot

  • Resolution: 1.62 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.190 

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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: https://doi.org/10.1021/ja4059876
  • Primary Citation of Related Structures:  

  • 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 (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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
442Sphingomonas paucimobilisMutation(s): 1 
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
Experimental Data & Validation

Experimental Data

  • 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
xia2data reduction
xia2data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-09-04
    Type: Initial release
  • Version 1.1: 2013-10-09
    Changes: Database references
  • Version 1.2: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description