title: Crystal structure of 5-formyl-3-hydroxy-2-methylpyridine 4-carboxylic acid 5-dehydrogenase, an NAD⁺-dependent dismutase from Mesorhizobium loti.
abstract: 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.
authors.affiliation: Research Institute of Molecular Genetics, Kochi University, Nankoku, Kochi 783-8502, Japan.
authors.forename: Andrew Njagi
authors.initials: AN
authors.lastname: Mugo
authors.affiliation: Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan.
authors.forename: Jun
authors.initials: J
authors.lastname: Kobayashi
authors.affiliation: Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan.
authors.forename: Bunzo
authors.initials: B
authors.lastname: Mikami
authors.affiliation: Faculty of Agriculture and Agricultural Science Program, Graduate School of Integrated Arts and Science, Kochi University, Nankoku, Kochi 783-8502, Japan.
authors.forename: Yu
authors.initials: Y
authors.lastname: Yoshikane
authors.affiliation: Faculty of Agriculture and Agricultural Science Program, Graduate School of Integrated Arts and Science, Kochi University, Nankoku, Kochi 783-8502, Japan.
authors.forename: Toshiharu
authors.initials: T
authors.lastname: Yagi
authors.affiliation: Research Institute of Molecular Genetics, Kochi University, Nankoku, Kochi 783-8502, Japan. Electronic address: kouheio@kochi-u.ac.jp.
authors.forename: Kouhei
authors.initials: K
authors.lastname: Ohnishi
mesh_terms: D063988:3-Hydroxyacyl-CoA Dehydrogenase / Q000737:chemistry; D000429:Alcohol Oxidoreductases / Q000737:chemistry*; D001426:Bacterial Proteins / Q000737:chemistry*; D002384:Catalysis; D020134:Catalytic Domain; D017124:Conserved Sequence; D018360:Crystallography, X-Ray; D015971:Gene Expression Regulation, Enzymologic; D006801:Humans; D006860:Hydrogen Bonding; D059128:Mesorhizobium / Q000201:enzymology*; D008958:Models, Molecular; D009206:Myocardium / Q000201:enzymology; D009243:NAD / Q000737:chemistry; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D025101:Vitamin B 6 / Q000737:chemistry
chemical_list: D001426:Bacterial Proteins; D009243:NAD; D025101:Vitamin B 6; D000429:Alcohol Oxidoreductases; C050710:5-formyl-3-hydroxy-2-methylpyridine-4-carboxylic acid dehydrogenase; D063988:3-Hydroxyacyl-CoA Dehydrogenase
keywords: 3-Hydroxyacyl-CoA dehydrogenase; 5-Formyl-3-hydroxy-2-methylpyridine 4-carboxylic acid 5-dehydrogenase; Dismutase; Mesorhizobium loti; Nicotinamide adenine dinucleotide; Vitamin B(6)-degradation pathway