6HNL

Selenomethionine derivative of IdmH 96-104 loop truncation variant

Summary for 6HNL

• Entry DOI: 10.2210/pdb6hnl/pdb
• Related: 6HNM 6HNN
• Descriptor: Putative polyketide cyclase IdmH (2 entities in total)
• Functional Keywords: polyketide synthesis, putative cyclase, biosynthetic protein
• Biological source: Streptomyces antibioticus
• Total number of polymer chains: 2
• Total formula weight: 30934.86

Authors

Drulyte, I.,Obajdin, J.,Trinh, C.,Hemsworth, G.R.,Berry, A. (deposition date: 2018-09-16, release date: 2019-11-06, Last modification date: 2024-11-06)

Primary citation

Drulyte, I.,Obajdin, J.,Trinh, C.H.,Kalverda, A.P.,van der Kamp, M.W.,Hemsworth, G.R.,Berry, A.
Crystal structure of the putative cyclase IdmH from the indanomycin nonribosomal peptide synthase/polyketide synthase.
Iucrj, 6:1120-1133, 2019

PubMed 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 [N]-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 https://proteopedia.org/w/Journal:IUCrJ:S2052252519012399.

PubMed: 31709067
DOI: 10.1107/S2052252519012399

Experimental method

X-RAY DIFFRACTION (2.2 Å)