1G5Q

EPID H67N COMPLEXED WITH SUBSTRATE PEPTIDE DSYTC


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.57 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.209 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

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

Blaesse, M.Kupke, T.Huber, R.Steinbacher, S.

(2000) EMBO J 19: 6299-6310

  • DOI: https://doi.org/10.1093/emboj/19.23.6299
  • Primary Citation of Related Structures:  
    1G5Q, 1G63

  • 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.


  • Organizational Affiliation

    Abteilung für Strukturforschung, Max-Planck-Institut für Biochemie, Am Klopferspitz 18a, 82152, Germany.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
EPIDERMIN MODIFYING ENZYME EPIDA,
C [auth D],
E [auth G],
G [auth L]
181Staphylococcus epidermidisMutation(s): 1 
Gene Names: EPID
UniProt
Find proteins for P30197 (Staphylococcus epidermidis)
Explore P30197 
Go to UniProtKB:  P30197
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP30197
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
LANTIBIOTIC EPIDERMINB [auth M],
D [auth N],
F [auth O],
H [auth P]
5N/AMutation(s): 0 
UniProt
Find proteins for P08136 (Staphylococcus epidermidis)
Explore P08136 
Go to UniProtKB:  P08136
Entity Groups  
UniProt GroupP08136
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.57 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.209 
  • Space Group: I 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 223.552α = 90
b = 223.552β = 90
c = 223.552γ = 90
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
MOSFLMdata reduction
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-05-02
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2021-10-27
    Changes: Database references, Derived calculations
  • Version 1.4: 2024-02-07
    Changes: Data collection