1G63

PEPTIDYL-CYSTEINE DECARBOXYLASE EPID

Summary for 1G63

• Entry DOI: 10.2210/pdb1g63/pdb
• Related: 1G5Q
• Descriptor: EPIDERMIN MODIFYING ENZYME EPID, FLAVIN MONONUCLEOTIDE (3 entities in total)
• Functional Keywords: alpha, beta protein, rossmann like fold, oxidoreductase
• Biological source: Staphylococcus epidermidis
• Total number of polymer chains: 12
• Total formula weight: 255616.50

Authors

Blaesse, M.,Kupke, T.,Huber, R.,Steinbac, S. (deposition date: 2000-11-03, release date: 2001-05-03, Last modification date: 2024-02-07)

Primary citation

Blaesse, M.,Kupke, T.,Huber, R.,Steinbacher, S.
Crystal structure of the peptidyl-cysteine decarboxylase EpiD complexed with a pentapeptide substrate.
EMBO J., 19:6299-6310, 2000

PubMed 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 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.

PubMed: 11101502
DOI: 10.1093/emboj/19.23.6299

Experimental method

X-RAY DIFFRACTION (2.5 Å)