Database accession: MF7000335
Name: FHMPCDH
PDB ID: 4om8
Experimental method: X-ray (1.55 Å)
Assembly: Homodimer
Source organism: Mesorhizobium japonicum
Primary publication of the structure:
Mugo AN, 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.
(2015) Biochem. Biophys. Res. Commun. 456: 35-40
PMID: 25446130
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.
Annotations from the GeneOntology database. Only terms that fit at least two of the interacting proteins are shown. Molecular function:
L-gulonate 3-dehydrogenase activity L-gulonate 3-dehydrogenase activity
NAD+ binding NAD+ binding
Biological process:
fatty acid metabolic process fatty acid metabolic process
vitamin B6 catabolic process vitamin B6 catabolic process
Cellular component: not assigned
Structural annotations of the participating protein chains.Entry contents: 2 distinct polypeptide molecules
Chains: A, A-2
Notes: All chains according to the most probable oligomerization state stored in PDBe were considered.
Number of unique protein segments: 1
Name: 5-formyl-3-hydroxy-2-methylpyridine 4-carboxylate 5-dehydrogenase
Source organism: Mesorhizobium japonicum
Length: 309 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMIRNIAIIGLGTMGPGMAARLARGGLQVVAYDVAPAAIERARSMLSVAETVLDALGIALPSAGVGTVRFTDDIGDAVSGADLVIENVPENISIKADVYRTIDGLIGQDTIVASDTSGIPITKLQAHISYPERMVGMHWSNPPHIIPMIEVIAGEKTAPQTVATIRDLIRSIGLLPVVVKKDVPGFVENRVLYALLREAVDLVERGVIDPEDLDTCVSWGIGYKIAVIGPMALLDMAGLDIYKSVSSFLNADLSNRDDVAPMVLEKTSASKFGIKSGEGMFCYTPEQTKALQAERARKLVAVRRILEGRE
UniProtKB AC: Q988C8 (positions: 1-309)
Coverage: 100%
Name: 5-formyl-3-hydroxy-2-methylpyridine 4-carboxylate 5-dehydrogenase
Source organism: Mesorhizobium japonicum
Length: 309 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMIRNIAIIGLGTMGPGMAARLARGGLQVVAYDVAPAAIERARSMLSVAETVLDALGIALPSAGVGTVRFTDDIGDAVSGADLVIENVPENISIKADVYRTIDGLIGQDTIVASDTSGIPITKLQAHISYPERMVGMHWSNPPHIIPMIEVIAGEKTAPQTVATIRDLIRSIGLLPVVVKKDVPGFVENRVLYALLREAVDLVERGVIDPEDLDTCVSWGIGYKIAVIGPMALLDMAGLDIYKSVSSFLNADLSNRDDVAPMVLEKTSASKFGIKSGEGMFCYTPEQTKALQAERARKLVAVRRILEGRE
UniProtKB AC: Q988C8 (positions: 1-309)
Coverage: 100%
Evidence demonstrating that the participating proteins are unstructured prior to the interaction and their folding is coupled to binding. Representative domain in related structures: -
Evidence level: Indirect evidence
Evidence coverage: Only some parts of the structure participates in mutual synergistic folding.
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 A:
N/A
Chain A-2:
N/A
Surface and contacts features:
Structures from the PDB that contain the same number of proteins, and the proteins from the two structures show a sufficient degree of pairwise similarity, i.e. they belong to the same UniRef90 cluster (the full proteins exhibit at least 90% sequence identity) and convey roughly the same region to their respective interactions (the two regions from the two proteins share a minimum of 70% overlap). No related structure was found in the MFIB database.
Download the CIF file (.cif)
Download this entry's XML file (.xml)
Download this entry's JSON file (.json)
