4PADH_RHILO
ID 4PADH_RHILO Reviewed; 543 AA.
AC Q988C9; B3IWB4;
DT 17-JUN-2020, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2001, sequence version 1.
DT 03-AUG-2022, entry version 111.
DE RecName: Full=4-pyridoxate dehydrogenase {ECO:0000305};
DE EC=1.1.99.42 {ECO:0000269|PubMed:18216065};
DE AltName: Full=4-pyridoxic acid dehydrogenase {ECO:0000303|PubMed:18216065};
DE Short=4-PADH {ECO:0000303|PubMed:18216065};
GN Name=padh1 {ECO:0000312|EMBL:BAG49092.1};
GN OrderedLocusNames=mlr6792 {ECO:0000312|EMBL:BAB53021.1};
OS Mesorhizobium japonicum (strain LMG 29417 / CECT 9101 / MAFF 303099)
OS (Mesorhizobium loti (strain MAFF 303099)).
OC Bacteria; Proteobacteria; Alphaproteobacteria; Hyphomicrobiales;
OC Phyllobacteriaceae; Mesorhizobium.
OX NCBI_TaxID=266835;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 406-415, FUNCTION,
RP CATALYTIC ACTIVITY, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES, PATHWAY,
RP SUBUNIT, AND SUBCELLULAR LOCATION.
RC STRAIN=LMG 29417 / CECT 9101 / MAFF 303099;
RX PubMed=18216065; DOI=10.1093/jb/mvn010;
RA Ge F., Yokochi N., Yoshikane Y., Ohnishi K., Yagi T.;
RT "Gene identification and characterization of the pyridoxine degradative
RT enzyme 4-pyridoxic acid dehydrogenase from the nitrogen-fixing symbiotic
RT bacterium Mesorhizobium loti MAFF303099.";
RL J. Biochem. 143:603-609(2008).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=LMG 29417 / CECT 9101 / MAFF 303099;
RX PubMed=11214968; DOI=10.1093/dnares/7.6.331;
RA Kaneko T., Nakamura Y., Sato S., Asamizu E., Kato T., Sasamoto S.,
RA Watanabe A., Idesawa K., Ishikawa A., Kawashima K., Kimura T., Kishida Y.,
RA Kiyokawa C., Kohara M., Matsumoto M., Matsuno A., Mochizuki Y.,
RA Nakayama S., Nakazaki N., Shimpo S., Sugimoto M., Takeuchi C., Yamada M.,
RA Tabata S.;
RT "Complete genome structure of the nitrogen-fixing symbiotic bacterium
RT Mesorhizobium loti.";
RL DNA Res. 7:331-338(2000).
CC -!- FUNCTION: Involved in the degradation of pyridoxine (vitamin B(6)).
CC Catalyzes the oxidation of 4-pyridoxic acid to 5-formyl-3-hydroxy-2-
CC methylpyridine-4-carboxylate. {ECO:0000269|PubMed:18216065}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=4-pyridoxate + A = 5-formyl-3-hydroxy-2-methylpyridine-4-
CC carboxylate + AH2; Xref=Rhea:RHEA:17085, ChEBI:CHEBI:13193,
CC ChEBI:CHEBI:17499, ChEBI:CHEBI:30959, ChEBI:CHEBI:140633;
CC EC=1.1.99.42; Evidence={ECO:0000269|PubMed:18216065};
CC -!- COFACTOR:
CC Name=FAD; Xref=ChEBI:CHEBI:57692;
CC Evidence={ECO:0000269|PubMed:18216065};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=29 uM for 4-pyridoxic acid {ECO:0000269|PubMed:18216065};
CC Note=kcat is 11 sec(-1). {ECO:0000269|PubMed:18216065};
CC pH dependence:
CC Optimum pH is 8.5. {ECO:0000269|PubMed:18216065};
CC Temperature dependence:
CC Optimum temperature is 30-35 degrees Celsius.
CC {ECO:0000269|PubMed:18216065};
CC -!- PATHWAY: Cofactor degradation; B6 vitamer degradation.
CC {ECO:0000305|PubMed:18216065}.
CC -!- SUBUNIT: Monomer. {ECO:0000269|PubMed:18216065}.
CC -!- SUBCELLULAR LOCATION: Cell inner membrane
CC {ECO:0000269|PubMed:18216065}; Peripheral membrane protein
CC {ECO:0000269|PubMed:18216065}. Note=Membrane-bound.
CC {ECO:0000269|PubMed:18216065}.
CC -!- PTM: The N-terminus is blocked. {ECO:0000269|PubMed:18216065}.
CC -!- SIMILARITY: Belongs to the GMC oxidoreductase family. {ECO:0000305}.
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DR EMBL; AB362509; BAG49092.1; -; Genomic_DNA.
DR EMBL; BA000012; BAB53021.1; -; Genomic_DNA.
DR RefSeq; WP_010914331.1; NC_002678.2.
DR AlphaFoldDB; Q988C9; -.
DR SMR; Q988C9; -.
DR STRING; 266835.14026424; -.
DR EnsemblBacteria; BAB53021; BAB53021; BAB53021.
DR KEGG; mlo:mlr6792; -.
DR PATRIC; fig|266835.9.peg.5405; -.
DR eggNOG; COG2303; Bacteria.
DR HOGENOM; CLU_002865_7_2_5; -.
DR OMA; WPKIDPK; -.
DR OrthoDB; 543793at2; -.
DR BioCyc; MetaCyc:MON-20509; -.
DR BRENDA; 1.1.99.42; 3243.
DR UniPathway; UPA00192; -.
DR Proteomes; UP000000552; Chromosome.
DR GO; GO:0005886; C:plasma membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0050660; F:flavin adenine dinucleotide binding; IEA:InterPro.
DR GO; GO:0016614; F:oxidoreductase activity, acting on CH-OH group of donors; IEA:InterPro.
DR GO; GO:0042820; P:vitamin B6 catabolic process; IEA:UniProtKB-UniPathway.
DR Gene3D; 3.50.50.60; -; 1.
DR InterPro; IPR036188; FAD/NAD-bd_sf.
DR InterPro; IPR012132; GMC_OxRdtase.
DR InterPro; IPR000172; GMC_OxRdtase_N.
DR InterPro; IPR007867; GMC_OxRtase_C.
DR PANTHER; PTHR11552; PTHR11552; 1.
DR Pfam; PF05199; GMC_oxred_C; 1.
DR Pfam; PF00732; GMC_oxred_N; 1.
DR PIRSF; PIRSF000137; Alcohol_oxidase; 1.
DR SUPFAM; SSF51905; SSF51905; 1.
PE 1: Evidence at protein level;
KW Cell inner membrane; Cell membrane; Direct protein sequencing; FAD;
KW Flavoprotein; Membrane; Oxidoreductase.
FT CHAIN 1..543
FT /note="4-pyridoxate dehydrogenase"
FT /id="PRO_0000450076"
FT ACT_SITE 475
FT /note="Proton acceptor"
FT /evidence="ECO:0000250|UniProtKB:E4QP00"
FT BINDING 16..17
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250|UniProtKB:E4QP00"
FT BINDING 37..38
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250|UniProtKB:E4QP00"
SQ SEQUENCE 543 AA; 58988 MW; 451E6C5FD7A5D2DE CRC64;
MPHAESYDYI IVGAGSAGCV LANRLSADPR CSVLLLEAGG WDRDPMIHIP LGWGKILTER
RHDWMYFCEP EDNVGGRRVE CARGKVIGGS SSTNAMAYVR GNRGDYDRWA ATGLSEWSYD
KVLPYFRKQE SWEGGANQYR GGNGPVSTQF CRYKDTLIDA FAQASVQAGY AQTKDYNGER
QEGFGRLQMT ISKGRRASTA SAYLRPVLKR PNLTVLTEAS ATRIVLEGAR ATGVTINHRG
GERTVLARKE VLLAGGVINT PQLMMLSGIG AQDELAAHGV QTRVNLPAVG KNLQDHVSVI
LMYRRRAPGG PFLRNMRADR IGFDFVKTYL TGRGFSGDVP GGVVAFLKSG PARPLPDVQL
LFTAAPLAAW PYFKPFKAPF ADGFATRIVA TQPESRGAVK LASADPSAAP LIHQNFLASP
KDWESLRAGF RVARDLAAQP SMQPFIEAEF FPGPKCQSDD EIDEHIRKTS ITVHHPAGTC
RMGADAASVV DPQLRVRGVD RLRVVDASVM PDLVCGNINA AVIMIAEKAA DLIASSKEGR
AVQ
