Crystal Structure of the Epimerization Domain from the Initiation Module of Tyrocidine Biosynthesis

Experimental Data Snapshot

  • Resolution: 1.50 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.160 

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Structure of the Epimerization Domain of Tyrocidine Synthetase A

Samel, S.-A.Czodrowski, P.Essen, L.-O.

(2014) Acta Crystallogr D Biol Crystallogr 70: 1442

  • DOI: https://doi.org/10.1107/S1399004714004398
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Tyrocidine, a macrocyclic decapeptide from Bacillus brevis, is nonribosomally assembled by a set of multimodular peptide synthetases, which condense two D-amino acids and eight L-amino acids to produce this membrane-disturbing antibiotic. D-Phenylalanine, the first amino acid incorporated into tyrocidine, is catalytically derived from enzyme-bound L-Phe by the C-terminal epimerization (E) domain of tyrocidine synthetase A (TycA). The 1.5 Å resolution structure of the cofactor-independent TycA E domain reveals an intimate relationship to the condensation (C) domains of peptide synthetases. In contrast to the latter, the TycA E domain uses an enlarged bridge region to plug the active-site canyon from the acceptor side, whereas at the donor side a latch-like floor loop is suitably extended to accommodate the αIII helix of the preceding peptide-carrier domain. Additionally, E domains exclusively harbour a conserved glutamate residue, Glu882, that is opposite the active-site residue His743. This active-site topology implies Glu882 as a candidate acid-base catalyst, whereas His743 stabilizes in the protonated state a transient enolate intermediate of the L↔D isomerization.

  • Organizational Affiliation

    Computational Chemistry, Merck KGaA, Frankfurter Strasse 250, 64293 Darmstadt, Germany.

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
TYROCIDINE SYNTHETASE A466Brevibacillus brevisMutation(s): 0 
Find proteins for G1K3P2 (Brevibacillus brevis)
Explore G1K3P2 
Go to UniProtKB:  G1K3P2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG1K3P2
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.50 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.160 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.71α = 90
b = 74.59β = 90
c = 124.75γ = 90
Software Package:
Software NamePurpose

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-07-06
    Type: Initial release
  • Version 1.1: 2014-05-14
    Changes: Database references, Non-polymer description, Source and taxonomy, Version format compliance
  • Version 1.2: 2014-10-22
    Changes: Database references