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

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Abstract
The crystal structure of Pseudomonas aeruginosa 3-methylcrotonyl-CoA carboxylase is determined and found to be markedly different from that of propionyl-CoA carboxylase. The biotin-dependent enzyme 3-methylcrotonyl-CoA carboxylase (MCC), essential for the metabolism of leucine, is highly homologous to propionyl-CoA carboxylase (PCC). The structures of MCC and PCC were therefore expected to be very similar. But Liang Tong et al. find that the architecture of MCC differs considerably from that of PCC. The structure of MCC also reveals why known disease-causing mutations lead to enzyme dysfunction, as they are at amino-acid positions critical to substrate binding and/or catalysis. The extensive structural differences between MCC and PCC also have general implications for the relationship between sequence conservation and structural similarity. 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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