Crystal structure of the putative cyclase IdmH from the indanomycin nonribosomal peptide synthase/polyketide synthase

Ieva Drulyte, Jana Obajdin, Chi H Trinh, Arnout Kalverda, Marc W Van der Kamp, Glyn R Hemsworth, Alan Berry

Research output: Contribution to journalArticle (Academic Journal)peer-review

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Abstract

Indanomycin is biosynthesised by a hybrid non-ribosomal peptide synthase/polyketide synthase (NRPS/PKS) followed by a number of ‘tailoring’ steps to form the two ring systems present in the mature product. It had previously been hypothesised that the indane ring of indanomycin was formed by the action of IdmH using a Diels-Alder reaction. Here we solve the crystal structure of a selenomethionine-labelled truncated form of IdmH (D99-107 IdmH) using Single wavelength Anomalous Dispersion (SAD) phasing. This truncated variant allows consistent and easy crystallisation, but importantly, the structure was used as a search model in molecular replacement allowing us to determine the full-length IdmH structure to 2.7 Å resolution. IdmH is a homodimer with individual protomers consisting of an α + β barrel. Each protomer contains a deep hydrophobic pocket which we propose constitutes the active site of the enzyme. To investigate the reaction catalysed by IdmH, we assigned 88% of the backbone NMR resonances and demonstrated using chemical shift perturbation of the [15N]-labelled IdmH, that indanomycin binds in the active site pocket. Finally, combined quantum mechanical / molecular mechanical (QM/MM) modelling of the IdmH reaction shows that the active site of the enzyme provides an appropriate environment to promote indane ring formation, supporting the assignment of IdmH as the key Diels-Alderase catalysing the final step in the biosynthesis of indanomycin through a similar mechanism as other recently characterised Diels-Alderases involved in polyketide tailoring reactions.
Original languageEnglish
Pages (from-to)1120 - 1133
Number of pages14
JournalIUCrJ
Volume6
Issue number6
Early online date24 Oct 2019
DOIs
Publication statusE-pub ahead of print - 24 Oct 2019

Keywords

  • polyketide biosynthesis
  • antibiotics
  • Steptomyces antibioticus
  • cycloaddition
  • crystal structure
  • protein crystallography
  • QM/MM reaction modelling
  • Diels-Alder

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