PLDH_RHILO
ID PLDH_RHILO Reviewed; 248 AA.
AC Q988B7;
DT 11-JAN-2011, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2001, sequence version 1.
DT 03-AUG-2022, entry version 116.
DE RecName: Full=Pyridoxal 4-dehydrogenase {ECO:0000312|EMBL:BAF02533.1};
DE Short=tPLDH {ECO:0000303|PubMed:16824480};
DE EC=1.1.1.107;
GN Name=pldh-t {ECO:0000312|EMBL:BAF02533.1}; OrderedLocusNames=mlr6807;
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] {ECO:0000305, ECO:0000312|EMBL:BAF02533.1}
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 1-10,
RP IDENTIFICATION, FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL
RP PROPERTIES, PATHWAY, AND SUBUNIT.
RC STRAIN=LMG 29417 / CECT 9101 / MAFF 303099 {ECO:0000269|PubMed:16824480};
RX PubMed=16824480; DOI=10.1016/j.abb.2006.06.002;
RA Yokochi N., Nishimura S., Yoshikane Y., Ohnishi K., Yagi T.;
RT "Identification of a new tetrameric pyridoxal 4-dehydrogenase as the second
RT enzyme in the degradation pathway for pyridoxine in a nitrogen-fixing
RT symbiotic bacterium, Mesorhizobium loti.";
RL Arch. Biochem. Biophys. 452:1-8(2006).
RN [2] {ECO:0000312|EMBL:BAB53033.1}
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 or pyridoxamine
CC (free, phosphate-unbound, forms of vitamin B6). Oxidizes pyridoxal to
CC 4-pyridoxolactone, but does not have activity toward pyridoxal 5'-
CC phosphate, pyridoxine, pyridoxamine, pyridoxamine 5'-phosphate, 4-
CC phthalaldehyde, 2-nitrobenzaldehyde, pyridine, formaldehyde, 2-
CC carboxybenzaldehyde or sugars. {ECO:0000269|PubMed:16824480}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=NAD(+) + pyridoxal = 4-pyridoxolactone + H(+) + NADH;
CC Xref=Rhea:RHEA:21336, ChEBI:CHEBI:15378, ChEBI:CHEBI:16871,
CC ChEBI:CHEBI:17310, ChEBI:CHEBI:57540, ChEBI:CHEBI:57945;
CC EC=1.1.1.107; Evidence={ECO:0000269|PubMed:16824480};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.091 mM for pyridoxal {ECO:0000269|PubMed:16824480};
CC KM=0.28 mM for NAD(+) {ECO:0000269|PubMed:16824480};
CC pH dependence:
CC Optimum pH is 9.2. Retains 66% of maximum activity at pH 8.6 and 57%
CC of maximum activity at pH 10.0. {ECO:0000269|PubMed:16824480};
CC Temperature dependence:
CC Optimum temperature is 50 degrees Celsius. 37% and 33% of maximum
CC activity is seen at 30 and 55 degrees Celsius respectively. Stable
CC for 10 minutes at 45 degrees Celsius or lower, 76% of activity
CC remains following 10 minutes incubation at 50 degrees Celsius and
CC 1.3% of activity remains following 10 minutes incubation at 60
CC degrees Celsius. {ECO:0000269|PubMed:16824480};
CC -!- PATHWAY: Cofactor degradation; B6 vitamer degradation; 4-pyridoxate
CC from pyridoxal: step 1/2. {ECO:0000269|PubMed:16824480}.
CC -!- SUBUNIT: Homotetramer. {ECO:0000269|PubMed:16824480}.
CC -!- SIMILARITY: Belongs to the short-chain dehydrogenases/reductases (SDR)
CC family. {ECO:0000255}.
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DR EMBL; AB248363; BAF02533.1; -; Genomic_DNA.
DR EMBL; BA000012; BAB53033.1; -; Genomic_DNA.
DR RefSeq; WP_010914343.1; NC_002678.2.
DR PDB; 3NDR; X-ray; 2.88 A; A/B/C/D=2-248.
DR PDB; 3NUG; X-ray; 1.79 A; A/B/C/D=2-248.
DR PDB; 3RWB; X-ray; 1.70 A; A/B/C/D=2-248.
DR PDBsum; 3NDR; -.
DR PDBsum; 3NUG; -.
DR PDBsum; 3RWB; -.
DR AlphaFoldDB; Q988B7; -.
DR SMR; Q988B7; -.
DR STRING; 266835.14026436; -.
DR EnsemblBacteria; BAB53033; BAB53033; BAB53033.
DR KEGG; mlo:mlr6807; -.
DR PATRIC; fig|266835.9.peg.5417; -.
DR eggNOG; COG1028; Bacteria.
DR HOGENOM; CLU_010194_1_2_5; -.
DR OMA; SMRYELP; -.
DR OrthoDB; 1601931at2; -.
DR BioCyc; MetaCyc:MON-13148; -.
DR BRENDA; 1.1.1.107; 3243.
DR UniPathway; UPA00192; UER00588.
DR Proteomes; UP000000552; Chromosome.
DR GO; GO:0050235; F:pyridoxal 4-dehydrogenase activity; IDA:UniProtKB.
DR GO; GO:0042820; P:vitamin B6 catabolic process; IDA:UniProtKB.
DR InterPro; IPR036291; NAD(P)-bd_dom_sf.
DR InterPro; IPR020904; Sc_DH/Rdtase_CS.
DR InterPro; IPR002347; SDR_fam.
DR PRINTS; PR00081; GDHRDH.
DR PRINTS; PR00080; SDRFAMILY.
DR SUPFAM; SSF51735; SSF51735; 1.
DR PROSITE; PS00061; ADH_SHORT; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Direct protein sequencing; NAD; Oxidoreductase.
FT CHAIN 1..248
FT /note="Pyridoxal 4-dehydrogenase"
FT /id="PRO_0000403110"
FT ACT_SITE 154
FT /note="Proton acceptor"
FT /evidence="ECO:0000250|UniProtKB:P69167,
FT ECO:0000255|PROSITE-ProRule:PRU10001"
FT BINDING 11..35
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250|UniProtKB:P69167"
FT BINDING 141
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P69167"
FT TURN 4..7
FT /evidence="ECO:0007829|PDB:3RWB"
FT STRAND 9..13
FT /evidence="ECO:0007829|PDB:3RWB"
FT TURN 14..16
FT /evidence="ECO:0007829|PDB:3RWB"
FT HELIX 18..29
FT /evidence="ECO:0007829|PDB:3RWB"
FT STRAND 33..37
FT /evidence="ECO:0007829|PDB:3RWB"
FT HELIX 41..51
FT /evidence="ECO:0007829|PDB:3RWB"
FT STRAND 55..57
FT /evidence="ECO:0007829|PDB:3RWB"
FT HELIX 65..79
FT /evidence="ECO:0007829|PDB:3RWB"
FT STRAND 83..87
FT /evidence="ECO:0007829|PDB:3RWB"
FT HELIX 97..99
FT /evidence="ECO:0007829|PDB:3RWB"
FT HELIX 102..112
FT /evidence="ECO:0007829|PDB:3RWB"
FT HELIX 114..130
FT /evidence="ECO:0007829|PDB:3RWB"
FT STRAND 134..139
FT /evidence="ECO:0007829|PDB:3RWB"
FT HELIX 143..146
FT /evidence="ECO:0007829|PDB:3RWB"
FT HELIX 152..172
FT /evidence="ECO:0007829|PDB:3RWB"
FT HELIX 173..175
FT /evidence="ECO:0007829|PDB:3RWB"
FT STRAND 177..184
FT /evidence="ECO:0007829|PDB:3RWB"
FT HELIX 190..193
FT /evidence="ECO:0007829|PDB:3RWB"
FT HELIX 196..200
FT /evidence="ECO:0007829|PDB:3RWB"
FT HELIX 201..207
FT /evidence="ECO:0007829|PDB:3RWB"
FT STRAND 208..210
FT /evidence="ECO:0007829|PDB:3RWB"
FT HELIX 216..227
FT /evidence="ECO:0007829|PDB:3RWB"
FT HELIX 229..231
FT /evidence="ECO:0007829|PDB:3RWB"
FT STRAND 238..242
FT /evidence="ECO:0007829|PDB:3RWB"
SQ SEQUENCE 248 AA; 25531 MW; F0B299BDF2BB5D57 CRC64;
MTERLAGKTA LVTGAAQGIG KAIAARLAAD GATVIVSDIN AEGAKAAAAS IGKKARAIAA
DISDPGSVKA LFAEIQALTG GIDILVNNAS IVPFVAWDDV DLDHWRKIID VNLTGTFIVT
RAGTDQMRAA GKAGRVISIA SNTFFAGTPN MAAYVAAKGG VIGFTRALAT ELGKYNITAN
AVTPGLIESD GVKASPHNEA FGFVEMLQAM KGKGQPEHIA DVVSFLASDD ARWITGQTLN
VDAGMVRH
