The mll6786 gene encodes a repressor protein controlling the degradation pathway for vitamin B6 in Mesorhizobium loti

Role of the Tyr270 residue in 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase from Mesorhizobium loti

The flavoenzyme 2-Methyl-3-hydroxypyridine-5-carboxylic acid oxygenase (MHPCO) catalyzes the cleavage of the pyridine ring of 2-methyl-3-hydroxypyridine-5-carboxylic acid (MHPC) in the presence of NADH, molecular oxygen, and water. MHPCO also catalyzes the NADH oxidation reaction uncoupled with ring opening in the absence of MHPC (the basal activity). The enzyme shows activity toward not only MHPC but also 5-hydroxynicotinic acid (5HN) and 5-pyridoxic acid (5PA). The reaction rate toward 5PA is extremely low (5% of the activity toward MHPC or 5HN). We determined the crystal structures of MHPCO without substrate and the MHPCO/5HN and MHPCO/5PA complexes, together with a Y270F mutant without substrate and its 5HN complex. The Tyr270 residue was located in the active site and formed hydrogen bonds between the Oη and water molecules to make the active site hydrophilic. Although Tyr270 took a fixed conformation in the structures of the MHPCO and MHPCO/5HN complex, it took two conformations in its 5PA complex, accompanied by two conformations of the bound 5PA. In the wild-type (WT) enzyme, the turnover number of the ring-opening activity was 6800 times that of the basal activity (1300 and 0.19 s^-1, respectively), whereas no such difference was observed in the Y270F (19 and 7.4 s^-1) or Y270A (0.05 and 0.84 s^-1) mutants. In the Y270F/5HN complex, the substrate bound ∼1 Å farther away than in the WT enzyme. These results revealed that Tyr270 is essential to maintain the WT conformation, which in turn enhances the coupling of the NADH oxidation with the ring-opening reaction.

Crystal structure of 5-formyl-3-hydroxy-2-methylpyridine 4-carboxylic acid 5-dehydrogenase, an NAD⁺-dependent dismutase from Mesorhizobium loti

5-Formyl-3-hydroxy-2-methylpyridine 4-carboxylic acid 5-dehydrogenase (FHMPCDH) from Mesorhizobium loti is the fifth enzyme in degradation pathway I for pyridoxine. The enzyme catalyzes a dismutation reaction: the oxidation of 5-formyl-3-hydroxy-2-methylpyridine 4-carboxylic acid (FHMPC) to 3-hydroxy-2-methylpyridine 4,5-dicarboxylic acid with NAD(+) and reduction of FHMPC to 4-pyridoxic acid with NADH. FHMPCDH belongs to the l-3-hydroxyacyl-CoA dehydrogenase (HAD) family. The crystal structure was determined by molecular replacement and refined to a resolution of 1.55Å (R-factor of 16.4%, Rfree=19.4%). There were two monomers in the asymmetric unit. The overall structure of the monomer consisted of N- and C-terminal domains connected by a short linker loop. The monomer was similar to members of the HAD family (RMSD=1.9Å). The active site was located between the domains and highly conserved to that of human heart l-3-hydroxyacyl-CoA dehydrogenase (HhHAD). His-Glu catalytic dyad, a serine and two asparagine residues of HhHAD were conserved. Ser116, His137 and Glu149 in FHMPCDH are connected by a hydrogen bonding network forming a catalytic triad. The functions of the active site residues in the reaction mechanism are discussed.

Crystal structure of pyridoxine 4-oxidase from Mesorhizobium loti

Pyridoxine 4-oxidase (PNOX) from Mesorhizobium loti is a monomeric glucose-methanol-choline (GMC) oxidoreductase family enzyme, catalyzes FAD-dependent oxidation of pyridoxine (PN) into pyridoxal, and is the first enzyme in pathway I for the degradation of PN. The tertiary structures of PNOX with a C-terminal His6-tag and PNOX-pyridoxamine (PM) complex were determined at 2.2Å and at 2.1Å resolutions, respectively. The overall structure consisted of FAD-binding and substrate-binding domains. In the active site, His460, His462, and Pro504 were located on the re-face of the isoalloxazine ring of FAD. PM binds to the active site through several hydrogen bonds. The side chains of His462 and His460 are located at 2.7 and 3.1Å from the N4' atom of PM. The activities of His460Ala and His462Ala mutant PNOXs were very low, and 460Ala/His462Ala double mutant PNOX exhibited no activity. His462 may act as a general base for the abstraction of a proton from the 4'-hydroxyl of PN. His460 may play a role in the binding and positioning of PN. The C4' atom in PM is located at 3.2Å, and the hydride ion from the C4' atom may be transferred to the N5 atom of the isoalloxazine ring. The comparison of active site residues in GMC oxidoreductase shows that Pro504 in PNOX corresponds to Asn or His of the conserved His-Asn or His-His pair in other GMC oxidoreductases. The function of the novel proline residue was discussed.