4OM8
Crystal structure of 5-formly-3-hydroxy-2-methylpyridine 4-carboxylic acid (FHMPC) 5-dehydrogenase, an NAD+ dependent dismutase.
Summary for 4OM8
| Entry DOI | 10.2210/pdb4om8/pdb |
| Descriptor | 5-formyl-3-hydroxy-2-methylpyridine 4-carboxylate 5-dehydrogenase, NICOTINAMIDE-ADENINE-DINUCLEOTIDE, ACETATE ION, ... (5 entities in total) |
| Functional Keywords | dehydrogenase, dismutase, structural genomics, enzyme function initiative, rossmann fold, nad-binding, oxidoreductase |
| Biological source | Mesorhizobium japonicum MAFF 303099 |
| Total number of polymer chains | 2 |
| Total formula weight | 67939.04 |
| Authors | Mugo, A.N.,Kobayashi, J.,Mikami, B.,Yagi, T.,Ohnishi, K. (deposition date: 2014-01-27, release date: 2015-01-28, Last modification date: 2024-12-25) |
| Primary citation | Mugo, A.N.,Kobayashi, J.,Mikami, B.,Yoshikane, Y.,Yagi, T.,Ohnishi, K. Crystal structure of 5-formyl-3-hydroxy-2-methylpyridine 4-carboxylic acid 5-dehydrogenase, an NAD(+)-dependent dismutase from Mesorhizobium loti Biochem.Biophys.Res.Commun., 456:35-40, 2015 Cited by PubMed 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. PubMed: 25446130DOI: 10.1016/j.bbrc.2014.11.028 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.55 Å) |
Structure validation
Download full validation report
