Discovery, structure, and function of filamentous 3-methylcrotonyl-CoA carboxylase

• Published in: Structure (London) 2023-01, Vol.31 (1), p.100-110.e4
• Main Authors: Hu, Jason J., Lee, Jane K.J., Liu, Yun-Tao, Yu, Clinton, Huang, Lan, Aphasizheva, Inna, Aphasizhev, Ruslan, Zhou, Z. Hong
• Format: Article
• Language: English
• Subjects: 3-methylcrotonyl-CoA; Acyl Coenzyme A - metabolism; atomic modeling; biotin; Biotin - metabolism; Carboxy-Lyases; carboxylase; Coenzyme A; cryoEM; cryoID; filament; Leishmania; leucine catabolism; mitochondria
• ISSN: 0969-2126; 1878-4186; 1878-4186
• DOI: 10.1016/j.str.2022.11.015

3-methylcrotonyl-CoA carboxylase (MCC) is a biotin-dependent mitochondrial enzyme necessary for leucine catabolism in most organisms. While the crystal structure of recombinant bacterial MCC has been characterized, the structure and potential polymerization of native MCC remain elusive. Here, we discovered that native MCC from Leishmania tarentolae (LtMCC) forms filaments, and determined the structures of different filament regions at 3.4, 3.9, and 7.3 Å resolution using cryoEM. α6β6 LtMCCs assemble in a twisted-stacks architecture, manifesting as supramolecular rods up to 400 nm. Filamentous LtMCCs bind biotin non-covalently and lack coenzyme A. Filaments elongate by stacking α6β6 LtMCCs onto the exterior α-trimer of the terminal LtMCC. This stacking immobilizes the biotin carboxylase domains, sequestering the enzyme in an inactive state. Our results support a new model for LtMCC catalysis, termed the dual-swinging-domains model, and cast new light on the function of polymerization in the carboxylase superfamily and beyond. [Display omitted] •Native 3-methylcrotonyl-CoA carboxylase from Leishmania tarentolae forms filaments•The structure of filamentous LtMCC was resolved up to 3.4 Å resolution•Filamentation sequesters LtMCC in an inactive state•A new model of LtMCC catalysis, termed the dual-swinging-domains model, is proposed Hu et al. serendipitously discover that 3-methylcrotonyl-CoA carboxylase (MCC), an enzyme involved in leucine catabolism, forms filaments using cryogenic electron microscopy. Their work supports a new model of MCC catalysis and casts new light on the unusual structural and functional diversity of enzymatic polymerization.