The cryo-EM structure of trypanosome 3-methylcrotonyl-CoAcarboxylase provides mechanistic and dynamic insights into enzymatic function

Plaza-Pegueroles, A.; Aphasizheva, I.; Aphasizhev, R.; Fernandez-Tornero, C.; Ruiz, F. M.

doi:10.1101/2023.11.27.568864

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bioRxiv · 10.1101/2023.11.27.568864

The cryo-EM structure of trypanosome 3-methylcrotonyl-CoAcarboxylase provides mechanistic and dynamic insights into enzymatic function

Plaza-Pegueroles, A.·Aphasizheva, I.·Aphasizhev, R.·Fernandez-Tornero, C.·Ruiz, F. M.

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Abstract

3-methylcrotonyl-CoA carboxylase (MCC) catalyzes the two-step, biotin-dependent production of 3-methylglutaconyl-CoA, an essential intermediate in leucine catabolism. Given its critical metabolic role, deficiencies in this enzyme associate with organic aciduria, while its overexpression is linked to tumor development. MCC is a dodecameric enzyme composed of six copies of each - and {beta}-subunit. We present the cryo-EM structure of the endogenous MCC holoenzyme from Trypanosoma brucei in its soluble, non-filamentous state at 2.5 [A] resolution. We unambiguously observe the position of biotin, covalently-bound to the BBCP domain of -subunits and occupying a novel binding pocket next to the active site of a neighboring {beta}-subunit dimer. Moreover, flexibility of key residues at the /- and /{beta}-subunit interfaces enables pivoting of -subunit trimers to sequentially approach the otherwise distant active sites for the two steps in MCC catalysis. Our results provide a structural framework to understand the enzymatic mechanism of eukaryotic MCCs and assist drug discovery against trypanosome infections.

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Plaza-Pegueroles, A., Aphasizheva, I., Aphasizhev, R., Fernandez-Tornero, C., Ruiz, F. M.. 2023-11-27. The cryo-EM structure of trypanosome 3-methylcrotonyl-CoAcarboxylase provides mechanistic and dynamic insights into enzymatic function. https://doi.org/10.1101/2023.11.27.568864

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