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An unanticipated architecture of the 750-kDa α6β6 holoenzyme of 3-methylcrotonyl-CoA carboxylase


3-Methylcrotonyl-CoA carboxylase (MCC), a member of the biotin-dependent carboxylase superfamily, is essential for the metabolism of leucine, and deficient mutations in this enzyme are linked to methylcrotonylglycinuria (MCG) and other serious diseases in humans1,2,3,4,5,6,7,8. MCC has strong sequence conservation with propionyl-CoA carboxylase (PCC), and their holoenzymes are both 750-kilodalton (kDa) α6β6 dodecamers. Therefore the architecture of the MCC holoenzyme is expected to be highly similar to that of PCC9. Here we report the crystal structures of the Pseudomonas aeruginosa MCC (PaMCC) holoenzyme, alone and in complex with coenzyme A. Surprisingly, the structures show that the architecture and overall shape of PaMCC are markedly different when compared to PCC. The α-subunits show trimeric association in the PaMCC holoenzyme, whereas they have no contacts with each other in PCC. Moreover, the positions of the two domains in the β-subunit of PaMCC are swapped relative to those in PCC. This structural information establishes a foundation for understanding the disease-causing mutations of MCC and provides new insights into the catalytic mechanism and evolution of biotin-dependent carboxylases. The large structural differences between MCC and PCC also have general implications for the relationship between sequence conservation and structural similarity.

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Figure 1: The domains of MCCβ are swapped compared to PCCβ.
Figure 2: The MCC holoenzyme has a markedly different architecture compared to PCC.
Figure 3: The BT domain mediates interactions in the MCC holoenzyme.
Figure 4: Molecular basis for catalysis and disease-causing mutations in the MCC holoenzyme.

Accession codes

Primary accessions

Protein Data Bank

Data deposits

Atomic coordinates have been deposited in the Protein Data Bank under accessions 3U9R, 3U9S and 3U9T.


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We thank Y. Shen for carrying out initial studies on MCC; N. Whalen and S. Myers for setting up the X29A beamline at the National Synchrotron Light Source. This research was supported in part by National Institutes of Health (NIH) grants DK067238 (to L.T.) and GM071940 (to Z.H.Z.). C.S.H. was also supported by an NIH training program in molecular biophysics (GM08281).

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C.S.H. carried out protein expression, purification and crystallization experiments, mutagenesis and enzymatic assays. C.S.H. and L.T. carried out crystallographic data collection and processing, structure determination and refinement. P.G. and Z.H.Z. carried out electron microscopy experiments. All authors commented on the manuscript. L.T. supervised the project, analysed the data and wrote the paper.

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Correspondence to Liang Tong.

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The authors declare no competing financial interests.

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Huang, C., Ge, P., Zhou, Z. et al. An unanticipated architecture of the 750-kDa α6β6 holoenzyme of 3-methylcrotonyl-CoA carboxylase. Nature 481, 219–223 (2012).

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