Crystal structure of the peptidyl-cysteine decarboxylase EpiD complexed with a pentapeptide substrate.
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 A 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-Sgamma, 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.
Blaesse
M
M
Abteilung für Strukturforschung, Max-Planck-Institut für Biochemie, Am Klopferspitz 18a, 82152, Germany.
Kupke
T
T
Huber
R
R
Steinbacher
S
S
D000595:Amino Acid Sequence; D000900:Anti-Bacterial Agents / Q000737:chemistry; D001665:Binding Sites; D002262:Carboxy-Lyases; D018360:Crystallography, X-Ray; D003545:Cysteine / Q000378:metabolism; D005486:Flavin Mononucleotide / Q000378:metabolism; D005420:Flavoproteins / Q000378:metabolism; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010088:Oxidoreductases / Q000737:chemistry* / Q000378:metabolism; D010100:Oxygen / Q000378:metabolism; D010455:Peptides / Q000737:chemistry; D011499:Protein Processing, Post-Translational; D017433:Protein Structure, Secondary; D011994:Recombinant Proteins / Q000737:chemistry; D012270:Ribosomes / Q000378:metabolism; D017386:Sequence Homology, Amino Acid; D013212:Staphylococcus epidermidis / Q000737:chemistry; D014443:Tyrosine / Q000737:chemistry
D000900:Anti-Bacterial Agents; D005420:Flavoproteins; D010455:Peptides; D011994:Recombinant Proteins; D014443:Tyrosine; D005486:Flavin Mononucleotide; D010088:Oxidoreductases; C075971:epidermin decarboxylase; D002262:Carboxy-Lyases; D003545:Cysteine; D010100:Oxygen