6U3J

Structure of the 2-oxoadipate dehydrogenase DHTKD1

Summary for 6U3J

• Entry DOI: 10.2210/pdb6u3j/pdb
• Descriptor: 2-oxoglutarate dehydrogenase E1 component DHKTD1, mitochondrial, THIAMINE DIPHOSPHATE, MAGNESIUM ION, ... (4 entities in total)
• Functional Keywords: lysine metabolism mitochondrial dehydrogenase, oxidoreductase
• Biological source: Homo sapiens (Human)
• Total number of polymer chains: 2
• Total formula weight: 204599.84

Authors

Khamrui, S.,Lazarus, M.B. (deposition date: 2019-08-21, release date: 2020-07-22, Last modification date: 2023-10-11)

Primary citation

Leandro, J.,Khamrui, S.,Wang, H.,Suebsuwong, C.,Nemeria, N.S.,Huynh, K.,Moustakim, M.,Secor, C.,Wang, M.,Dodatko, T.,Stauffer, B.,Wilson, C.G.,Yu, C.,Arkin, M.R.,Jordan, F.,Sanchez, R.,DeVita, R.J.,Lazarus, M.B.,Houten, S.M.
Inhibition and Crystal Structure of the Human DHTKD1-Thiamin Diphosphate Complex.
Acs Chem.Biol., 15:2041-2047, 2020

PubMed Abstract: DHTKD1 is the E1 component of the 2-oxoadipate dehydrogenase complex, which is an enzyme involved in the catabolism of (hydroxy-)lysine and tryptophan. Mutations in DHTKD1 have been associated with 2-aminoadipic and 2-oxoadipic aciduria, Charcot-Marie-Tooth disease type 2Q and eosinophilic esophagitis, but the pathophysiology of these clinically distinct disorders remains elusive. Here, we report the identification of adipoylphosphonic acid and tenatoprazole as DHTKD1 inhibitors using targeted and high throughput screening, respectively. We furthermore elucidate the DHTKD1 crystal structure with thiamin diphosphate bound at 2.25 Å. We also report the impact of 10 disease-associated missense mutations on DHTKD1. Whereas the majority of the DHTKD1 variants displayed impaired folding or reduced thermal stability in combination with absent or reduced enzyme activity, three variants showed no abnormalities. Our work provides chemical and structural tools for further understanding of the function of DHTKD1 and its role in several human pathologies.

PubMed: 32633484
DOI: 10.1021/acschembio.0c00114

Experimental method

X-RAY DIFFRACTION (2.25 Å)