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

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 struc-tures of different filament regions at 3.4, 3.9, and 7.3 A resolution using cryoEM. a6b6 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 a6b6 LtMCCs onto the exterior a-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 -swing-ing-domains model, and cast new light on the function of polymerization in the carboxylase superfamily and beyond.

Automated summary

3-methylcrotonyl-CoA carboxylase (MCC) is a biotin-dependent mitochondrial enzyme involved in leucine catabolism. We discovered that native MCC from Leishmania tarentolae (LtMCC) forms filaments and determined their structures. The filaments are composed of a6b6 LtMCCs stacked together, binding biotin non-covalently and lacking coenzyme A. The stacking immobilizes the biotin carboxylase domains, rendering the enzyme inactive. Our findings propose a new catalysis model for LtMCC and provide insights into polymerization in the carboxylase superfamily.