Substrate selection of adenylation domains for nonribosomal peptide synthetase (NRPS) in bacillamide C biosynthesis by marine Bacillus atrophaeus C89

  • Fengli Zhang
  • Yukun Wang
  • Qun Jiang
  • Qihua Chen
  • Loganathan Karthik
  • Yi-Lei Zhao
  • Zhiyong Li
Biotechnology Methods - Original Paper


Nonribosomal peptide synthetases (NRPSs) are multi-modular enzymes involved in the biosynthesis of natural products. Bacillamide C was synthesized by Bacillus atrophaeus C89. A nonribosomal peptide synthetase (NRPS) cluster found in the genome of B. atrophaeus C89 was hypothesized to be responsible for the biosynthesis of bacillamide C using alanine and cysteine as substrates. Here, the structure analysis of adenylation domains based on homologous proteins with known crystal structures indicated locations of the substrate-binding pockets. Molecular docking suggested alanine and cysteine as the potential substrates for the two adenylation domains in the NRPS cluster. Furthermore, biochemical characterization of the purified recombinant adenylation domains proved that alanine and cysteine were the optimum substrates for the two adenylation domains. The results provided the in vitro evidence for the hypothesis that the two adenylation domains in the NRPS of B. atrophaeus C89 preferentially select alanine and cysteine, respectively, as a substrate to synthesize bacillamide C. Furthermore, this study on substrates selectivity of adenylation domains provided basis for rational design of bacillamide analogs.


Adenylation domain Bacillamide C Bacillus atrophaeus Nonribosomal peptide synthetases (NRPS) Substrates selection 



This work was supported by the National Natural Science Foundation of China (NSFC) (31300104).

Supplementary material

10295_2018_2028_MOESM1_ESM.docx (63 kb)
Fig. S1 The structures of bacillamide A, bacillamide B, bacillamide C, bacillamide D and bacillamide E
10295_2018_2028_MOESM2_ESM.docx (68 kb)
Fig. S2 NRPSpredictor2 prediction report for the A1 and A2 domains. Location of the A domain within the sequence and the bit score of the PFAM-HMM are provided. The green checkmark signals indicate that the signature sequence lies within the applicability domain. The list of predictions is provided along with the scores of the respective SVM predictors. The final row provides the nearest sequence neighbor in the NRPSpredictor2 database (based on the Stachelhaus code) and the respective sequence identity (%)
10295_2018_2028_MOESM3_ESM.pdf (164 kb)
Fig. S3 Ramachandran plot atlas of the A-domain structure model (a) and Ramachandran plot atlas of the A-domain structure model after energy minimization (b). (1) A1 domain; (2) A2 domain. The figure is plotted using Discovery Studio


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Copyright information

© Society for Industrial Microbiology and Biotechnology 2018

Authors and Affiliations

  1. 1.Marine Biotechnology Laboratory, State Key Laboratory of Microbial Metabolism and School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
  2. 2.Computational Chemistry and Molecular Bioinformatics Laboratory, State Key Laboratory of Microbial Metabolism and School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiChina

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