8P5O

Proline activating adenylation domain of gramicidin S synthetase 2 - GrsB1-Acore


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.224 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Directed Evolution of Piperazic Acid Incorporation by a Nonribosomal Peptide Synthetase.

Stephan, P.Langley, C.Winkler, D.Basquin, J.Caputi, L.O'Connor, S.E.Kries, H.

(2023) Angew Chem Int Ed Engl 62: e202304843-e202304843

  • DOI: https://doi.org/10.1002/anie.202304843
  • Primary Citation of Related Structures:  
    8P5O

  • PubMed Abstract: 

    Engineering of biosynthetic enzymes is increasingly employed to synthesize structural analogues of antibiotics. Of special interest are nonribosomal peptide synthetases (NRPSs) responsible for the production of important antimicrobial peptides. Here, directed evolution of an adenylation domain of a Pro-specific NRPS module completely switched substrate specificity to the non-standard amino acid piperazic acid (Piz) bearing a labile N-N bond. This success was achieved by UPLC-MS/MS-based screening of small, rationally designed mutant libraries and can presumably be replicated with a larger number of substrates and NRPS modules. The evolved NRPS produces a Piz-derived gramicidin S analogue. Thus, we give new impetus to the too-early dismissed idea that widely accessible low-throughput methods can switch the specificity of NRPSs in a biosynthetically useful fashion.


  • Organizational Affiliation

    Junior Research Group Biosynthetic Design of Natural Products, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745, Jena, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Gramicidin S synthase 2
A, B, C, D
405Aneurinibacillus migulanusMutation(s): 0 
Gene Names: grsBgrs2
UniProt
Find proteins for P0C063 (Aneurinibacillus migulanus)
Explore P0C063 
Go to UniProtKB:  P0C063
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C063
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.224 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 195.021α = 90
b = 195.021β = 90
c = 346.46γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-05
    Type: Initial release
  • Version 1.1: 2023-08-30
    Changes: Data collection, Database references
  • Version 1.2: 2024-10-16
    Changes: Structure summary