Crystal structure of the α6β6 holoenzyme of propionyl-coenzyme A carboxylase

Abstract

Propionyl-coenzyme A carboxylase (PCC), a mitochondrial biotin-dependent enzyme, is essential for the catabolism of the amino acids Thr, Val, Ile and Met, cholesterol and fatty acids with an odd number of carbon atoms. Deficiencies in PCC activity in humans are linked to the disease propionic acidaemia, an autosomal recessive disorder that can be fatal in infants1,2,3,4. The holoenzyme of PCC is an α6β6 dodecamer, with a molecular mass of 750 kDa. The α-subunit contains the biotin carboxylase (BC) and biotin carboxyl carrier protein (BCCP) domains, whereas the β-subunit supplies the carboxyltransferase (CT) activity. Here we report the crystal structure at 3.2-Å resolution of a bacterial PCC α6β6 holoenzyme as well as cryo-electron microscopy (cryo-EM) reconstruction at 15-Å resolution demonstrating a similar structure for human PCC. The structure defines the overall architecture of PCC and reveals unexpectedly that the α-subunits are arranged as monomers in the holoenzyme, decorating a central β6 hexamer. A hitherto unrecognized domain in the α-subunit, formed by residues between the BC and BCCP domains, is crucial for interactions with the β-subunit. We have named it the BT domain. The structure reveals for the first time the relative positions of the BC and CT active sites in the holoenzyme. They are separated by approximately 55 Å, indicating that the entire BCCP domain must translocate during catalysis. The BCCP domain is located in the active site of the β-subunit in the current structure, providing insight for its involvement in the CT reaction. The structural information establishes a molecular basis for understanding the large collection of disease-causing mutations in PCC and is relevant for the holoenzymes of other biotin-dependent carboxylases, including 3-methylcrotonyl-CoA carboxylase (MCC)5,6,7 and eukaryotic acetyl-CoA carboxylase (ACC)8,9.

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Figure 1: Structure of the PCC holoenzyme.
Figure 2: Interactions between the α- and β-subunits in the PCC holoenzyme.
Figure 3: The active sites of the PCC holoenzyme.
Figure 4: Locations of disease-causing mutations in the PCC holoenzyme.

Accession codes

Primary accessions

Protein Data Bank

Data deposits

The atomic coordinates are deposited in Protein Data Bank under accession number 3N6R.

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Acknowledgements

We thank N. Whalen and H. Robinson for access to the X29A beamline at the National Synchrotron Light Source; J. Schwanof and R. Abramowitz for access to the X4A beamline; M. Sampat for help during the initial stages of the project; and W.W. Cleland for discussions. This research was supported in part by National Institutes of Health grants DK067238 (to L.T.), GM071940 and AI069015 (to Z.H.Z.). C.S.H. was also supported by a National Institutes of Health training program in molecular biophysics (GM08281).

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C.S.H., K.S.-B., Y.S. and B.D. performed the experiments, analysed the data and commented on the manuscript. L.T. and Z.H.Z. designed and performed the experiments, analysed the data and wrote the manuscript.

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Correspondence to Liang Tong.

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Huang, C., Sadre-Bazzaz, K., Shen, Y. et al. Crystal structure of the α6β6 holoenzyme of propionyl-coenzyme A carboxylase. Nature 466, 1001–1005 (2010). https://doi.org/10.1038/nature09302

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