1G5Q: Epid H67n Complexed With Substrate Peptide Dsytc

Epidermin from Staphylococcus epidermidis Tu3298 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.
PDB ID: 1G5QDownload
MMDB ID: 16150
PDB Deposition Date: 2000/11/2
Updated in MMDB: 2012/11
Experimental Method:
x-ray diffraction
Resolution: 2.57  Å
Source Organism:
synthetic construct
Similar Structures:
Biological Unit for 1G5Q: 24-meric; determined by author and by software (PISA,PQS)
Molecular Components in 1G5Q
Label Count Molecule
Proteins (24 molecules)
Epidermin Modifying Enzyme Epid
Molecule annotation
Lantibiotic Epidermin
Molecule annotation
Chemicals (16 molecules)
* Click molecule labels to explore molecular sequence information.

Citing MMDB