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

DOI: 10.1107/S2052252519012399 DOI Help

Authors: Ieva Drulyte (University of Leeds) , Jana Obajdin (University of Leeds) , Chi H. Trinh (University of Leeds) , Arnout P. Kalverda (University of Leeds) , Marc W. Van Der Kamp (University of Bristol) , Glyn R. Hemsworth (University of Leeds) , Alan Berry (University of Leeds)
Co-authored by industrial partner: No

Type: Journal Paper
Journal: Iucrj , VOL 6

State: Published (Approved)
Published: November 2019
Diamond Proposal Number(s): 15378

Open Access Open Access

Abstract: Indanomycin is biosynthesized by a hybrid nonribosomal peptide synthase/polyketide synthase (NRPS/PKS) followed by a number of `tailoring' steps to form the two ring systems that are present in the mature product. It had previously been hypothesized that the indane ring of indanomycin was formed by the action of IdmH using a Diels–Alder reaction. Here, the crystal structure of a selenomethionine-labelled truncated form of IdmH (IdmH-Δ99–107) was solved using single-wavelength anomalous dispersion (SAD) phasing. This truncated variant allows consistent and easy crystallization, but importantly the structure was used as a search model in molecular replacement, allowing the full-length IdmH structure to be determined to 2.7 Å resolution. IdmH is a homodimer, with the individual protomers consisting of an α+β barrel. Each protomer contains a deep hydrophobic pocket which is proposed to constitute the active site of the enzyme. To investigate the reaction catalysed by IdmH, 88% of the backbone NMR resonances were assigned, and using chemical shift perturbation of [15N]-labelled IdmH it was demonstrated 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 to other recently characterized Diels–Alderases involved in polyketide-tailoring reactions. An animated Interactive 3D Complement (I3DC) is available in Proteopedia at

Journal Keywords: polyketide biosynthesis; antibiotics; Steptomyces antibioticus; cycloaddition; crystal structure; protein crystallography; QM/MM reaction modelling; Diels–Alder reaction

Diamond Keywords: Bacteria; Enzymes

Subject Areas: Biology and Bio-materials, Chemistry

Instruments: I03-Macromolecular Crystallography , I04-Macromolecular Crystallography

Other Facilities: European Synchrotron Radiation Facility

Added On: 29/10/2019 10:56


Discipline Tags:

Biochemistry Catalysis Chemistry Structural biology Life Sciences & Biotech

Technical Tags:

Diffraction Macromolecular Crystallography (MX)