Crystal Structure of Nonribosomal peptide synthetases (NRPS), FmoA3 (S1046A)

Experimental Data Snapshot

  • Resolution: 2.45 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 

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Structural and Functional Analyses of the Tridomain-Nonribosomal Peptide Synthetase FmoA3 for 4-Methyloxazoline Ring Formation.

Katsuyama, Y.Sone, K.Harada, A.Kawai, S.Urano, N.Adachi, N.Moriya, T.Kawasaki, M.Shin-Ya, K.Senda, T.Ohnishi, Y.

(2021) Angew Chem Int Ed Engl 60: 14554-14562

  • DOI: https://doi.org/10.1002/anie.202102760
  • Primary Citation of Related Structures:  
    6LTA, 6LTB, 6LTC, 6LTD

  • PubMed Abstract: 

    Nonribosomal peptide synthetases (NRPSs) are attractive targets for bioengineering to generate useful peptides. FmoA3 is a single modular NRPS composed of heterocyclization (Cy), adenylation (A), and peptidyl carrier protein (PCP) domains. It uses α-methyl-l-serine to synthesize a 4-methyloxazoline ring, probably with another Cy domain in the preceding module FmoA2. Here, we determined the head-to-tail homodimeric structures of FmoA3 by X-ray crystallography (apo-form, with adenylyl-imidodiphosphate and α-methyl-l-seryl-AMP) and cryogenic electron microscopy single particle analysis, and performed site-directed mutagenesis experiments. The data revealed that α-methyl-l-serine can be accommodated in the active site because of the extra space around Ala688. The Cy domains of FmoA2 and FmoA3 catalyze peptide bond formation and heterocyclization, respectively. FmoA3's Cy domain seems to lose its donor PCP binding activity. The collective data support a proposed catalytic cycle of FmoA3.

  • Organizational Affiliation

    Department of Biotechnology, Graduate School of Agricultural and Life science, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nonribosomal peptide synthetase1,153Streptomyces sp. Sp080513GE-23Mutation(s): 1 
Gene Names: fmoA3
Find proteins for A0A077JG85 (Streptomyces sp. Sp080513GE-23)
Explore A0A077JG85 
Go to UniProtKB:  A0A077JG85
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A077JG85
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AKR (Subject of Investigation/LOI)
Query on AKR

Download Ideal Coordinates CCD File 
C3 H4 O2
Experimental Data & Validation

Experimental Data

  • Resolution: 2.45 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.355α = 90
b = 167.65β = 90
c = 194.12γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)JapanJP17H05432
Japan Society for the Promotion of Science (JSPS)Japan17J09750
Japan Agency for Medical Research and Development (AMED)JapanBINDS1146

Revision History  (Full details and data files)

  • Version 1.0: 2021-02-24
    Type: Initial release
  • Version 1.1: 2021-04-07
    Changes: Database references
  • Version 1.2: 2021-06-30
    Changes: Database references
  • Version 1.3: 2023-11-29
    Changes: Data collection, Database references, Refinement description