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 1.2 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: 10.1093/emboj/19.23.6299
  • Primary Citation of Related Structures:  

  • 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 ...

    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.


    Related Citations: 
    • Molecular characterization of lantibiotic synthesizing enzyme EpiD reveals a function for bacterial Dfp proteins in coenzyme A biosynthesis
      Kupke, T.,Uebele, M.,Schmid, D.,Jung, G.,Blaesse, M.,Steinbacher, S.
      (2000) J.Biol.Chem. 275: 31838


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
EPIDERMIN MODIFYING ENZYME EPID
A, D, G, L
181Staphylococcus epidermidisMutation(s): 1 
Gene Names: epiD
EC: 4.1.1.-
Find proteins for P30197 (Staphylococcus epidermidis)
Go to UniProtKB:  P30197
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
LANTIBIOTIC EPIDERMIN
M, N, O, P
5Staphylococcus epidermidisMutation(s): 0 
Gene Names: epiA
Find proteins for P08136 (Staphylococcus epidermidis)
Go to UniProtKB:  P08136
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMN
Query on FMN

Download SDF File 
Download CCD File 
A, D, G, L
FLAVIN MONONUCLEOTIDE
RIBOFLAVIN MONOPHOSPHATE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
TRS
Query on TRS

Download SDF File 
Download CCD File 
A, G
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
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 = 90.00
b = 223.552β = 90.00
c = 223.552γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
MOSFLMdata reduction
AMoREphasing
CCP4data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-05-02
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance