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TitleCrystal structure and interaction studies of human DHTKD1 provide insight into a mitochondrial megacomplex in lysine catabolism.
Journal, issue, pagesIUCrJ, Vol. 7, Issue Pt 4, Page 693-706, Year 2020
Publish dateJul 1, 2020
AuthorsGustavo A Bezerra / William R Foster / Henry J Bailey / Kevin G Hicks / Sven W Sauer / Bianca Dimitrov / Thomas J McCorvie / Jürgen G Okun / Jared Rutter / Stefan Kölker / Wyatt W Yue /
PubMed AbstractDHTKD1 is a lesser-studied E1 enzyme among the family of 2-oxoacid de-hydrogenases. In complex with E2 (di-hydro-lipo-amide succinyltransferase, DLST) and E3 (dihydrolipo-amide de-hydrogenase, DLD) ...DHTKD1 is a lesser-studied E1 enzyme among the family of 2-oxoacid de-hydrogenases. In complex with E2 (di-hydro-lipo-amide succinyltransferase, DLST) and E3 (dihydrolipo-amide de-hydrogenase, DLD) components, DHTKD1 is involved in lysine and tryptophan catabolism by catalysing the oxidative de-carboxyl-ation of 2-oxoadipate (2OA) in mitochondria. Here, the 1.9 Å resolution crystal structure of human DHTKD1 is solved in complex with the thi-amine diphosphate co-factor. The structure reveals how the DHTKD1 active site is modelled upon the well characterized homologue 2-oxoglutarate (2OG) de-hydrogenase but engineered specifically to accommodate its preference for the longer substrate of 2OA over 2OG. A 4.7 Å resolution reconstruction of the human DLST catalytic core is also generated by single-particle electron microscopy, revealing a 24-mer cubic scaffold for assembling DHTKD1 and DLD protomers into a megacomplex. It is further demonstrated that missense DHTKD1 variants causing the inborn error of 2-amino-adipic and 2-oxoadipic aciduria impact on the complex formation, either directly by disrupting the interaction with DLST, or indirectly through destabilizing the DHTKD1 protein. This study provides the starting framework for developing DHTKD1 modulators to probe the intricate mitochondrial energy metabolism.
External linksIUCrJ / PubMed:32695416 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution1.87 - 4.7 Å
Structure data

EMDB-11014:
Cryo-EM map of human dihydrolipoamide succinyltransferase catalytic domain (DLST)
Method: EM (single particle) / Resolution: 4.7 Å

PDB-6sy1:
Crystal structure of the human 2-oxoadipate dehydrogenase DHTKD1 (E1)
Method: X-RAY DIFFRACTION / Resolution: 1.87 Å

Chemicals

ChemComp-TPP:
THIAMINE DIPHOSPHATE / Thiamine pyrophosphate

ChemComp-MG:
Unknown entry

ChemComp-HOH:
WATER / Water

Source
  • homo sapiens (human)
KeywordsSTRUCTURAL GENOMICS / Dehydrogenase / transketolase / thiamine pyrophosphate / Mg / Structural Genomics Consortium / SGC

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