Letter | Published:

Structure and function of a single-chain, multi-domain long-chain acyl-CoA carboxylase

Nature volume 518, pages 120124 (05 February 2015) | Download Citation

Abstract

Biotin-dependent carboxylases are widely distributed in nature and have important functions in the metabolism of fatty acids, amino acids, carbohydrates, cholesterol and other compounds1,2,3,4,5,6. Defective mutations in several of these enzymes have been linked to serious metabolic diseases in humans, and acetyl-CoA carboxylase is a target for drug discovery in the treatment of diabetes, cancer and other diseases7,8,9. Here we report the identification and biochemical, structural and functional characterizations of a novel single-chain (120 kDa), multi-domain biotin-dependent carboxylase in bacteria. It has preference for long-chain acyl-CoA substrates, although it is also active towards short-chain and medium-chain acyl-CoAs, and we have named it long-chain acyl-CoA carboxylase. The holoenzyme is a homo-hexamer with molecular mass of 720 kDa. The 3.0 Å crystal structure of the long-chain acyl-CoA carboxylase holoenzyme from Mycobacterium avium subspecies paratuberculosis revealed an architecture that is strikingly different from those of related biotin-dependent carboxylases10,11. In addition, the domains of each monomer have no direct contact with each other. They are instead extensively swapped in the holoenzyme, such that one cycle of catalysis involves the participation of four monomers. Functional studies in Pseudomonas aeruginosa suggest that the enzyme is involved in the utilization of selected carbon and nitrogen sources.

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Accessions

Primary accessions

Protein Data Bank

Data deposits

Coordinates and structure factors have been deposited in Protein Data Bank under accession number 4RCN.

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Acknowledgements

We thank C. Huang for carrying out some initial studies in this project; A. Price-Whelan for discussions on P. aeruginosa physiology; R. Jackimowicz, N. Whalen and H. Robinson for access to the X29A beamline; Z. Li for EM support; P. Penczek for help with SPARX. The in-house instrument for X-ray diffraction was purchased with a National Institutes of Health (NIH) grant to L.T. (S10OD012018). This research is supported by grants from the NIH (R01DK067238 to L.T. and R01AI103369 to L.E.P.D.) and from the Protein Structure Initiative of the NIH (U54GM094597 to L.T.). The Orchestra High Performance Compute Cluster at Harvard Medical School is a shared facility partly supported by NIH grant NCRR 1S10RR028832-01. T.W. is an investigator with the Howard Hughes Medical Institute.

Author information

Author notes

    • Yu-Shan Hsiao
    •  & Chi-Yuan Chou

    Present addresses: Department of Otolaryngology, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts 02114, USA (Y.-S.H.); Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei 112, Taiwan (C.-Y.C.).

Affiliations

  1. Department of Biological Sciences, Columbia University, New York, New York 10027, USA

    • Timothy H. Tran
    • , Jeanyoung Jo
    • , Chi-Yuan Chou
    • , Lars E. P. Dietrich
    •  & Liang Tong
  2. Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA

    • Yu-Shan Hsiao
    •  & Thomas Walz
  3. Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA

    • Thomas Walz

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Contributions

T.H.T. and C.-Y.C. performed cloning, protein expression, purification and crystallization experiments. T.H.T. and L.T. performed the crystallography experiments and calculation. Y.-S.H. and T.W. conducted the electron microscopy experiments. T.H.T. and C.-Y.C. performed the kinetic assays. J.J. and L.E.P.D. conducted the P. aeruginosa experiments. T.H.T., L.E.P.D., T.W. and L.T. wrote the paper.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Liang Tong.

Extended data

Supplementary information

Videos

  1. 1.

    Variability in the architecture of the MapLCC holoenzyme

    This animated GIF file illustrates the structural variability that results from the flexible tethering of the peripheral BC domains to the core formed by the CT domains.

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DOI

https://doi.org/10.1038/nature13912

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