Crystal structure of the peptidyl-cysteine decarboxylase EpiD complexed with a pentapeptide substrate

Abstract

Epidermin from Staphylococcus epidermidis Tü3298 is an antimicrobial peptide of the lantibiotic family that contains, amongst other unusual amino acids, S‐[(Z)‐ 2‐aminovinyl]‐d‐cysteine. This residue is introduced by post‐translational modification of the ribosomally synthesized precursor EpiA. Modification starts with the oxidative decarboxylation of its C‐terminal cysteine by the flavoprotein EpiD generating a reactive (Z)‐enethiol intermediate. We have determined the crystal structures of EpiD and EpiD H67N in complex with the substrate pentapeptide DSYTC at 2.5 Å resolution. Rossmann‐type monomers build up a dodecamer of 23 point symmetry with trimers disposed at the vertices of a tetrahedron. Oligomer formation is essential for binding of flavin mononucleotide and substrate, which is buried by an otherwise disordered substrate recognition clamp. A pocket for the tyrosine residue of the substrate peptide is formed by an induced fit mechanism. The substrate contacts flavin mononucleotide only via Cys‐Sγ, suggesting its oxidation as the initial step. A thioaldehyde intermediate could undergo spontaneous decarboxylation. The unusual substrate recognition mode and the type of chemical reaction performed provide insight into a novel family of flavoproteins.