Crystal structure and interaction studies of human DHTKD1 provide insight into a mitochondrial megacomplex in lysine catabolism

Bezerra, G. A.; Foster, W. R.; Bailey, H. J.; Hicks, K. G.; Sauer, S. W.; Dimitrov, B.; Okun, J. G.; Rutter, J.; Koelker, S.; Yue, W. W.

doi:10.1101/2020.01.20.912931

bioRxiv · 10.1101/2020.01.20.912931

Crystal structure and interaction studies of human DHTKD1 provide insight into a mitochondrial megacomplex in lysine catabolism

Bezerra, G. A.·Foster, W. R.·Bailey, H. J.·Hicks, K. G.·Sauer, S. W.·Dimitrov, B.·Okun, J. G.·Rutter, J.·Koelker, S.·Yue, W. W.

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Abstract

DHTKD1 is a lesser-studied E1 enzyme belonging to the family of 2-oxoacid dehydrogenases. DHTKD1, in complex with the E2 (dihydrolipoamide succinyltransferase, DLST) and E3 (lipoamide dehydrogenase, DLD) components, is implicated in lysine and tryptophan catabolism by catalysing the oxidative decarboxylation of 2-oxoadipate (2OA) in the mitochondria. Here, we solved the crystal structure of human DHTKD1 at 1.9 [A] resolution in binary complex with the thiamine diphosphate (ThDP) cofactor. Our structure explains the evolutionary divergence of DHTKD1 from the well-characterized homologue 2-oxoglutarate (2OG) dehydrogenase, in its preference for the larger 2OA substrate than 2OG. Inherited DHTKD1 missense mutations cause the lysine metabolic condition 2-aminoadipic and 2-oxoadipic aciduria. Reconstruction of the missense variant proteins reveal their underlying molecular defects, which include protein destabilisation, disruption of protein-protein interactions, and alterations in the protein surface. We further generated a 5.0 [A] reconstruction of the human DLST inner core by single-particle electron microscopy, revealing a 24-mer cubic architecture that serves as a scaffold for assembly of DHTKD1 and DLD. This structural study provides a starting point to develop small molecule DHTKD1 inhibitors for probing mitochondrial energy metabolism.

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Bezerra, G. A., Foster, W. R., Bailey, H. J., Hicks, K. G., Sauer, S. W., Dimitrov, B., Okun, J. G., Rutter, J., Koelker, S., Yue, W. W.. 2020-01-20. Crystal structure and interaction studies of human DHTKD1 provide insight into a mitochondrial megacomplex in lysine catabolism. https://doi.org/10.1101/2020.01.20.912931

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