Subdomain dynamics enable chemical chain reactions in non-ribosomal peptide synthetases

Xun Sun, Jonas Alfermann, Hao Li, Maxwell B. Watkins, Yi Tsao Chen, Thomas E. Morrell, Florian Mayerthaler, Chia Ying Wang, Tamiki Komatsuzaki, Jhih Wei Chu, Nozomi Ando, Henning D. Mootz, Haw Yang

Research output: Contribution to journalArticlepeer-review

2 Scopus citations


Many peptide-derived natural products are produced by non-ribosomal peptide synthetases (NRPSs) in an assembly-line fashion. Each amino acid is coupled to a designated peptidyl carrier protein (PCP) through two distinct reactions catalysed sequentially by the single active site of the adenylation domain (A-domain). Accumulating evidence suggests that large-amplitude structural changes occur in different NRPS states; yet how these molecular machines orchestrate such biochemical sequences has remained elusive. Here, using single-molecule Förster resonance energy transfer, we show that the A-domain of gramicidin S synthetase I adopts structurally extended and functionally obligatory conformations for alternating between adenylation and thioester-formation structures during enzymatic cycles. Complementary biochemical, computational and small-angle X-ray scattering studies reveal interconversion among these three conformations as intrinsic and hierarchical where intra-A-domain organizations propagate to remodel inter-A–PCP didomain configurations during catalysis. The tight kinetic coupling between structural transitions and enzymatic transformations is quantified, and how the gramicidin S synthetase I A-domain utilizes its inherent conformational dynamics to drive directional biosynthesis with a flexibly linked PCP domain is revealed. (Figure presented.)

Original languageEnglish (US)
Pages (from-to)259-268
Number of pages10
JournalNature chemistry
Issue number2
StatePublished - Feb 2024

All Science Journal Classification (ASJC) codes

  • General Chemistry
  • General Chemical Engineering


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