9C5K
Trypanosoma cruzi R19T/K20S/C64Y mutant D-3-hydroxybutyrate dehydrogenase in complex with NADPH and malonate
Summary for 9C5K
| Entry DOI | 10.2210/pdb9c5k/pdb |
| Descriptor | Hydroxybutyrate dehydrogenase, NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE, 1,2-ETHANEDIOL, ... (7 entities in total) |
| Functional Keywords | trypanosoma cruzi, nadph, malonate, 3-hydroxybutyrate dehydrogenase, beta-hydroxybutyrate dehydrogenase, short-chain dehydrogenase/reductase (sdr) family, nad(p) specificity, oxidoreductase |
| Biological source | Trypanosoma cruzi |
| Total number of polymer chains | 4 |
| Total formula weight | 118995.28 |
| Authors | Hashimoto, H.,Debler, E.W. (deposition date: 2024-06-06, release date: 2025-08-27, Last modification date: 2026-08-12) |
| Primary citation | Hashimoto, H.,Mawn, I.H.,Escobar-Arrillaga, W.,Nguyen, L.,Madigan, L.A.,Antuono, G.,Rossy, T.,Sojati, J.,Mienko, A.,Debler, E.W.,Palenchar, J.B. The beta 2 alpha B loop determines NAD(P) cofactor specificity and kinetics in trypanosomal D-3-hydroxybutyrate dehydrogenases. J.Mol.Biol., 438:169946-169946, 2026 Cited by PubMed Abstract: Bacterial d-3-hydroxybutyrate dehydrogenases (HBDHs) catalyze the conversion between d-3-hydroxybutyrate and acetoacetate with NAD as the cofactor but not with NAD 2'-phosphate (NADP). However, HBDHs of the early-branched eukaryotic genus Trypanosoma utilize both NAD and NADP (T. brucei) or exclusively NADP (T. cruzi). Here we reveal that NADP specificity of T. cruzi HBDH arises from stabilization of the flexible β2αB loop by the 2'-phosphate interaction. Stabilization of this loop by a nearby C64Y mutation enables T. cruzi HBDH to use NAD in addition to NADP; thus, the Cys/Tyr residue is critical for determining cofactor specificity in trypanosomal HBDHs, suggesting that most trypanosomal HBDHs use both NAD and NADP except for T. cruzi HBDH. Furthermore, Arg42 within the β2αB loop interacts with the adenine ring of NADP by ideal CH-π interactions, while the R42F mutant switches to non-ideal π-π interactions, increasing k ∼10-fold and K ∼40-fold. Collectively, we identified the β2αB loop stability and sequence as key determinants of NAD(P) co-factor specificity and kinetics in HBDHs. PubMed: 42456964DOI: 10.1016/j.jmb.2026.169946 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.79 Å) |
Structure validation
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