{"entry": {"accession": "MF7000335", "general": {"name": "FHMPCDH", "pdb_id": "4om8", "exp_method": "X-ray", "resolution": "1.55", "assembly": "Homodimer", "source_organism": "Mesorhizobium japonicum", "publication": {"pmid": "25446130", "authors": "Mugo AN, Kobayashi J, Mikami B, Yoshikane Y, Yagi T, Ohnishi K", "title": "Crystal structure of 5-formyl-3-hydroxy-2-methylpyridine 4-carboxylic acid 5-dehydrogenase, an NAD\u207a-dependent dismutase from Mesorhizobium loti.", "journal": "Biochem. Biophys. Res. Commun.", "year": "2015", "issue": "1", "volume": "456", "pages": "35-40", "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 1.55\u00c5 (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=1.9\u00c5). 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."}}, "function": {"molecular_function": {"go": [{"accession": "GO:0050104", "name": "L-gulonate 3-dehydrogenase activity"}, {"accession": "GO:0070403", "name": "NAD+ binding"}]}, "biological_process": {"go": [{"accession": "GO:0006631", "name": "fatty acid metabolic process"}, {"accession": "GO:0042820", "name": "vitamin B6 catabolic process"}]}}, "macromolecules": {"general": {"nr_of_chains": "2", "nr_of_unique_protein_segments": "1", "class": "Homooligomeric enzymes", "subclass": "Homodimeric enzymes", "note": "All chains according to the most probable oligomerization state stored in PDBe were considered."}, "chain": [{"id": "A", "name": "5-formyl-3-hydroxy-2-methylpyridine 4-carboxylate 5-dehydrogenase", "source_organism": "Mesorhizobium japonicum", "uniprot": {"id": "Q988C8", "start": "1", "end": "309", "coverage": "100%", "sequence": "MIRNIAIIGLGTMGPGMAARLARGGLQVVAYDVAPAAIERARSMLSVAETVLDALGIALPSAGVGTVRFTDDIGDAVSGADLVIENVPENISIKADVYRTIDGLIGQDTIVASDTSGIPITKLQAHISYPERMVGMHWSNPPHIIPMIEVIAGEKTAPQTVATIRDLIRSIGLLPVVVKKDVPGFVENRVLYALLREAVDLVERGVIDPEDLDTCVSWGIGYKIAVIGPMALLDMAGLDIYKSVSSFLNADLSNRDDVAPMVLEKTSASKFGIKSGEGMFCYTPEQTKALQAERARKLVAVRRILEGRE", "length": "309"}, "regions": {"region": [{"region_type": "secondary structure", "region_name": "helix", "region_start": "13", "region_end": "24"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "34", "region_end": "55"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "72", "region_end": "78"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "90", "region_end": "103"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "119", "region_end": "124"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "125", "region_end": "127"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "129", "region_end": "131"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "157", "region_end": "171"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "186", "region_end": "204"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "208", "region_end": "220"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "220", "region_end": "227"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "228", "region_end": "237"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "237", "region_end": "252"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "259", "region_end": "268"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "283", "region_end": "306"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "4", "region_end": "8"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "27", "region_end": "31"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "66", "region_end": "70"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "82", "region_end": "85"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "110", "region_end": "113"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "133", "region_end": "137"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "147", "region_end": "151"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "174", "region_end": "178"}, {"region_type": "pfam", "region_id": "PF02737", "region_name": "3-hydroxyacyl-CoA dehydrogenase, NAD binding domain", "region_start": "4", "region_end": "181"}]}}, {"id": "A-2", "name": "5-formyl-3-hydroxy-2-methylpyridine 4-carboxylate 5-dehydrogenase", "source_organism": "Mesorhizobium japonicum", "uniprot": {"id": "Q988C8", "start": "1", "end": "309", "coverage": "100%", "sequence": "MIRNIAIIGLGTMGPGMAARLARGGLQVVAYDVAPAAIERARSMLSVAETVLDALGIALPSAGVGTVRFTDDIGDAVSGADLVIENVPENISIKADVYRTIDGLIGQDTIVASDTSGIPITKLQAHISYPERMVGMHWSNPPHIIPMIEVIAGEKTAPQTVATIRDLIRSIGLLPVVVKKDVPGFVENRVLYALLREAVDLVERGVIDPEDLDTCVSWGIGYKIAVIGPMALLDMAGLDIYKSVSSFLNADLSNRDDVAPMVLEKTSASKFGIKSGEGMFCYTPEQTKALQAERARKLVAVRRILEGRE", "length": "309"}, "regions": {"region": {"region_type": "pfam", "region_id": "PF02737", "region_name": "3-hydroxyacyl-CoA dehydrogenase, NAD binding domain", "region_start": "4", "region_end": "181"}}}]}, "evidence": {"evidence_level": "Indirect evidence", "evidence_coverage": "Only some parts of the structure participates in mutual synergistic folding.", "sequence_domain": "-", "complex_evidence": "It is a dimer. Dissociation cannot be detected by differential scanning calorimetry (PMID:35041856). The helical dimerization domain is very tightly packed.", "chain_evidence": [{"chain_id": "A", "support": "N/A"}, {"chain_id": "A-2", "support": "N/A"}]}}}