Determinants of substrate specificity in D-3-phosphoglycerate dehydrogenase. Conversion of the M. tuberculosis enzyme from one that does not use α-ketoglutarate as a substrate to one that does

Structural insights into the catalytic mechanism of the microcystin tailoring enzyme McyI

The most common cyanotoxin microcystin is a cyclic heptapeptide produced by non-ribosomal peptide-polyketide synthetases and tailoring enzymes. The tailoring enzyme McyI, a 2-hydroxyacid dehydrogenase, converts (3-methyl)malate into (3-methyl)oxaloacetate to produce the non-proteinogenic amino acid (3-methyl)aspartate. The reaction is NAD(P)-dependent but the catalytic mechanism remains unclear. Here we describe the crystal structures of McyI at three states: bound with copurified NAD, cocrystallized with NAD/NADP, and cocrystallized with malate or the substrate analogue citrate. An McyI protomer has unusual three nicotinamide cofactor-binding sites, named the NAD-prebound, NADP specific, and non-specific sites. Biochemical studies confirmed the NADP preference during oxidoreductase reaction. Molecular basis for McyI catalysis was revealed by the structures of McyI-NAD binary complex, McyI-NAD-NADP and McyI-NAD-malate ternary complexes, which demonstrate different opening angles between the substrate-binding domain and the nucleotide-binding domain. These findings indicate that McyI is a unique member of the 2-hydroxyacid dehydrogenase superfamily and provide detailed structural insights into its catalytic mechanism. In addition, the structural ensemble representing various binding states offers clues for designing enzyme for bioengineering applications.

Revealing a New Family of D-2-Hydroxyglutarate Dehydrogenases in Escherichia coli and Pantoea ananatis Encoded by ydiJ

In E. coli and P. ananatis, L-serine biosynthesis is initiated by the action of D-3-phosphoglycerate dehydrogenase (SerA), which converts D-3-phosphoglycerate into 3-phosphohydroxypyruvate. SerA can concomitantly catalyze the production of D-2-hydroxyglutarate (D-2-HGA) from 2-ketoglutarate by oxidizing NADH to NAD⁺. Several bacterial D-2-hydroxyglutarate dehydrogenases (D2HGDHs) have recently been identified, which convert D-2-HGA back to 2-ketoglutarate. However, knowledge about the enzymes that can metabolize D-2-HGA is lacking in bacteria belonging to the Enterobacteriaceae family. We found that ydiJ encodes novel D2HGDHs in P. ananatis and E. coli, which were assigned as D2HGDHPa and D2HGDHEc, respectively. Inactivation of ydiJ in P. ananatis and E. coli led to the significant accumulation of D-2-HGA. Recombinant D2HGDHEc and D2HGDHPa were purified to homogeneity and characterized. D2HGDHEc and D2HGDHPa are homotetrameric with a subunit molecular mass of 110 kDa. The pH optimum was 7.5 for D2HGDHPa and 8.0 for D2HGDHEc. The Km for D-2-HGA was 208 μM for D2HGDHPa and 83 μM for D2HGDHEc. The enzymes have strict substrate specificity towards D-2-HGA and displayed maximal activity at 45 °C. Their activity was completely inhibited by 0.5 mM Mn²⁺, Ni²⁺ or Co²⁺. The discovery of a novel family of D2HGDHs may provide fundamental information for the metabolic engineering of microbial chassis with desired properties.