Structure of the apo PCP-E didomain of the gramicidin S synthetase A

Experimental Data Snapshot

  • Resolution: 1.75 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.170 

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Interdomain and Intermodule Organization in Epimerization Domain Containing Nonribosomal Peptide Synthetases.

Chen, W.H.Li, K.Guntaka, N.S.Bruner, S.D.

(2016) ACS Chem Biol 11: 2293-2303

  • DOI: https://doi.org/10.1021/acschembio.6b00332
  • Primary Citation of Related Structures:  
    5ISW, 5ISX

  • PubMed Abstract: 

    Nonribosomal peptide synthetases are large, complex multidomain enzymes responsible for the biosynthesis of a wide range of peptidic natural products. Inherent to synthetase chemistry is the thioester templated mechanism that relies on protein/protein interactions and interdomain dynamics. Several questions related to structure and mechanism remain to be addressed, including the incorporation of accessory domains and intermodule interactions. The inclusion of nonproteinogenic d-amino acids into peptide frameworks is a common and important modification for bioactive nonribosomal peptides. Epimerization domains, embedded in nonribosomal peptide synthetases assembly lines, catalyze the l- to d-amino acid conversion. Here we report the structure of the epimerization domain/peptidyl carrier protein didomain construct from the first module of the cyclic peptide antibiotic gramicidin synthetase. Both holo (phosphopantethiene post-translationally modified) and apo structures were determined, each representing catalytically relevant conformations of the two domains. The structures provide insight into domain-domain recognition, substrate delivery during the assembly line process, in addition to the structural organization of homologous condensation domains, canonical players in all synthetase modules.

  • Organizational Affiliation

    Department of Chemistry, University of Florida , P.O. Box 117200, Gainesville, Florida 32611, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Gramicidin S synthase 1573Brevibacillus brevisMutation(s): 0 
Gene Names: grsAgrs1
Find proteins for P0C062 (Brevibacillus brevis)
Explore P0C062 
Go to UniProtKB:  P0C062
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C062
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on GOL

Download Ideal Coordinates CCD File 
C3 H8 O3
Experimental Data & Validation

Experimental Data

  • Resolution: 1.75 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.170 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.77α = 65.72
b = 57.637β = 65.47
c = 61.384γ = 84.88
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United States1411991

Revision History  (Full details and data files)

  • Version 1.0: 2016-06-29
    Type: Initial release
  • Version 1.1: 2016-08-31
    Changes: Database references
  • Version 1.2: 2017-09-20
    Changes: Author supporting evidence, Derived calculations
  • Version 1.3: 2019-11-27
    Changes: Author supporting evidence