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

Jason J Hu; Jane K J Lee; Yun-Tao Liu; Clinton Yu; Lan Huang; Inna Aphasizheva; Ruslan Aphasizhev; Z Hong Zhou

doi:10.1016/j.str.2022.11.015

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

Structure. 2023 Jan 5;31(1):100-110.e4. doi: 10.1016/j.str.2022.11.015. Epub 2022 Dec 20.

Authors

Jason J Hu¹, Jane K J Lee², Yun-Tao Liu³, Clinton Yu⁴, Lan Huang⁴, Inna Aphasizheva⁵, Ruslan Aphasizhev⁶, Z Hong Zhou⁷

Affiliations

¹ Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA; California NanoSystems Institute, UCLA, Los Angeles, CA 90095, USA; Department of Mathematics, UCLA, Los Angeles, CA 90095, USA.
² Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA; California NanoSystems Institute, UCLA, Los Angeles, CA 90095, USA; Department of Psychology, UCLA, Los Angeles, CA 90095, USA.
³ Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA; California NanoSystems Institute, UCLA, Los Angeles, CA 90095, USA.
⁴ Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA 92697, USA.
⁵ Department of Molecular and Cell Biology, Boston University Medical Campus (BUMC), Boston, MA 02118, USA.
⁶ Department of Molecular and Cell Biology, Boston University Medical Campus (BUMC), Boston, MA 02118, USA; Department of Biochemistry, BUMC, Boston, MA 02118, USA.
⁷ Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA; California NanoSystems Institute, UCLA, Los Angeles, CA 90095, USA. Electronic address: hong.zhou@ucla.edu.

Abstract

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.

Keywords: 3-methylcrotonyl-CoA; Leishmania; atomic modeling; biotin; carboxylase; cryoEM; cryoID; filament; leucine catabolism; mitochondria.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Acyl Coenzyme A / metabolism
Biotin* / metabolism
Carboxy-Lyases*
Coenzyme A

Substances

tiglyl-coenzyme A
Biotin
Acyl Coenzyme A
Coenzyme A
Carboxy-Lyases

Abstract

Publication types

MeSH terms

Substances

Grants and funding