1G5Q: Epid H67n Complexed With Substrate Peptide Dsytc

Citation:
Abstract
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)
12
Epidermin Modifying Enzyme Epid
Molecule annotation
12
Lantibiotic Epidermin
Molecule annotation
Chemicals (16 molecules)
1
12
2
4
* Click molecule labels to explore molecular sequence information.

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