Crystal structure of the PLP-bound C-S lyase in the external aldimine form from Staphylococcus hominis complexed with an inhibitor, L-cycloserine.

Experimental Data Snapshot

  • Resolution: 1.42 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.192 

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The molecular basis of thioalcohol production in human body odour.

Rudden, M.Herman, R.Rose, M.Bawdon, D.Cox, D.S.Dodson, E.Holden, M.T.G.Wilkinson, A.J.James, A.G.Thomas, G.H.

(2020) Sci Rep 10: 12500-12500

  • DOI: https://doi.org/10.1038/s41598-020-68860-z
  • Primary Citation of Related Structures:  
    6QP1, 6QP2, 6QP3

  • PubMed Abstract: 

    Body odour is a characteristic trait of Homo sapiens, however its role in human behaviour and evolution is poorly understood. Remarkably, body odour is linked to the presence of a few species of commensal microbes. Herein we discover a bacterial enzyme, limited to odour-forming staphylococci that are able to cleave odourless precursors of thioalcohols, the most pungent components of body odour. We demonstrated using phylogenetics, biochemistry and structural biology that this cysteine-thiol lyase (C-T lyase) is a PLP-dependent enzyme that moved horizontally into a unique monophyletic group of odour-forming staphylococci about 60 million years ago, and has subsequently tailored its enzymatic function to human-derived thioalcohol precursors. Significantly, transfer of this enzyme alone to non-odour producing staphylococci confers odour production, demonstrating that this C-T lyase is both necessary and sufficient for thioalcohol formation. The structure of the C-T lyase compared to that of other related enzymes reveals how the adaptation to thioalcohol precursors has evolved through changes in the binding site to create a constrained hydrophobic pocket that is selective for branched aliphatic thioalcohol ligands. The ancestral acquisition of this enzyme, and the subsequent evolution of the specificity for thioalcohol precursors implies that body odour production in humans is an ancient process.

  • Organizational Affiliation

    Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
421Staphylococcus hominisMutation(s): 0 
Gene Names: BUZ46_10400
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LCS (Subject of Investigation/LOI)
Query on LCS

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
[5-hydroxy-6-methyl-4-({[(4E)-3-oxo-1,2-oxazolidin-4-ylidene]amino}methyl)pyridin-3-yl]methyl dihydrogen phosphate
C11 H14 N3 O7 P
Experimental Data & Validation

Experimental Data

  • Resolution: 1.42 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.192 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.466α = 90
b = 115.456β = 90
c = 118.962γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/N006615/1

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-04
    Type: Initial release
  • Version 1.1: 2020-08-05
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description