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Protein

Pyridoxal 4-dehydrogenase

Gene

pldh-t

Organism
Rhizobium loti (strain MAFF303099) (Mesorhizobium loti)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Involved in the degradation of pyridoxine or pyridoxamine (free, phosphate-unbound, forms of vitamin B6). Oxidizes pyridoxal to 4-pyridoxolactone, but does not have activity toward pyridoxal 5'-phosphate, pyridoxine, pyridoxamine, pyridoxamine 5'-phosphate, 4-phthalaldehyde, 2-nitrobenzaldehyde, pyridine, formaldehyde, 2-carboxybenzaldehyde or sugars.1 Publication

Catalytic activityi

Pyridoxal + NAD+ = 4-pyridoxolactone + NADH.1 Publication

Kineticsi

  1. KM=0.091 mM for pyridoxal1 Publication
  2. KM=0.28 mM for NAD+1 Publication

    pH dependencei

    Optimum pH is 9.2. Retains 66% of maximum activity at pH 8.6 and 57% of maximum activity at pH 10.0.1 Publication

    Temperature dependencei

    Optimum temperature is 50 degrees Celsius. 37% and 33% of maximum activity is seen at 30 and 55 degrees Celsius respectively. Stable for 10 minutes at 45 degrees Celsius or lower, 76% of activity remains following 10 minutes incubation at 50 degrees Celsius and 1.3% of activity remains following 10 minutes incubation at 60 degrees Celsius.1 Publication

    Pathwayi: B6 vitamer degradation

    This protein is involved in step 1 of the subpathway that synthesizes 4-pyridoxate from pyridoxal.1 Publication
    Proteins known to be involved in the 2 steps of the subpathway in this organism are:
    1. Pyridoxal 4-dehydrogenase (pldh-t)
    2. 4-pyridoxolactonase (mlr6805)
    This subpathway is part of the pathway B6 vitamer degradation, which is itself part of Cofactor degradation.
    View all proteins of this organism that are known to be involved in the subpathway that synthesizes 4-pyridoxate from pyridoxal, the pathway B6 vitamer degradation and in Cofactor degradation.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei141 – 1411SubstrateBy similarity
    Active sitei154 – 1541Proton acceptorPROSITE-ProRule annotationBy similarity

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi11 – 3525NADBy similarityAdd
    BLAST

    GO - Molecular functioni

    • pyridoxal 4-dehydrogenase activity Source: UniProtKB

    GO - Biological processi

    • vitamin B6 catabolic process Source: UniProtKB
    Complete GO annotation...

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Ligandi

    NAD

    Enzyme and pathway databases

    BioCyciMetaCyc:MONOMER-13148.
    MLOT266835:GJ9L-5398-MONOMER.
    BRENDAi1.1.1.107. 3243.
    UniPathwayiUPA00192; UER00588.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Pyridoxal 4-dehydrogenaseImported (EC:1.1.1.107)
    Short name:
    tPLDH1 Publication
    Gene namesi
    Name:pldh-tImported
    Ordered Locus Names:mlr6807
    OrganismiRhizobium loti (strain MAFF303099) (Mesorhizobium loti)
    Taxonomic identifieri266835 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhizobialesPhyllobacteriaceaeMesorhizobium
    Proteomesi
    • UP000000552 Componenti: Chromosome

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 248248Pyridoxal 4-dehydrogenasePRO_0000403110Add
    BLAST

    Interactioni

    Subunit structurei

    Homotetramer.1 Publication

    Protein-protein interaction databases

    STRINGi266835.mlr6807.

    Structurei

    Secondary structure

    1
    248
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Turni4 – 74Combined sources
    Beta strandi9 – 135Combined sources
    Turni14 – 163Combined sources
    Helixi18 – 2912Combined sources
    Beta strandi33 – 375Combined sources
    Helixi41 – 5111Combined sources
    Beta strandi55 – 573Combined sources
    Helixi65 – 7915Combined sources
    Beta strandi83 – 875Combined sources
    Helixi97 – 993Combined sources
    Helixi102 – 11211Combined sources
    Helixi114 – 13017Combined sources
    Beta strandi134 – 1396Combined sources
    Helixi143 – 1464Combined sources
    Helixi152 – 17221Combined sources
    Helixi173 – 1753Combined sources
    Beta strandi177 – 1848Combined sources
    Helixi190 – 1934Combined sources
    Helixi196 – 2005Combined sources
    Helixi201 – 2077Combined sources
    Beta strandi208 – 2103Combined sources
    Helixi216 – 22712Combined sources
    Helixi229 – 2313Combined sources
    Beta strandi238 – 2425Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    3NDRX-ray2.88A/B/C/D2-248[»]
    3NUGX-ray1.79A/B/C/D2-248[»]
    3RWBX-ray1.70A/B/C/D2-248[»]
    ProteinModelPortaliQ988B7.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Compositional bias

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Compositional biasi6 – 6055Ala-richSequence analysisAdd
    BLAST

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiENOG4108KEZ. Bacteria.
    ENOG410XRY7. LUCA.
    KOiK18609.
    OMAiIASNTFF.
    OrthoDBiPOG091H085B.

    Family and domain databases

    Gene3Di3.40.50.720. 1 hit.
    InterProiIPR016040. NAD(P)-bd_dom.
    IPR020904. Sc_DH/Rdtase_CS.
    IPR002347. SDR_fam.
    [Graphical view]
    PANTHERiPTHR24322. PTHR24322. 2 hits.
    PRINTSiPR00081. GDHRDH.
    PR00080. SDRFAMILY.
    SUPFAMiSSF51735. SSF51735. 1 hit.
    PROSITEiPS00061. ADH_SHORT. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Q988B7-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MTERLAGKTA LVTGAAQGIG KAIAARLAAD GATVIVSDIN AEGAKAAAAS
    60 70 80 90 100
    IGKKARAIAA DISDPGSVKA LFAEIQALTG GIDILVNNAS IVPFVAWDDV
    110 120 130 140 150
    DLDHWRKIID VNLTGTFIVT RAGTDQMRAA GKAGRVISIA SNTFFAGTPN
    160 170 180 190 200
    MAAYVAAKGG VIGFTRALAT ELGKYNITAN AVTPGLIESD GVKASPHNEA
    210 220 230 240
    FGFVEMLQAM KGKGQPEHIA DVVSFLASDD ARWITGQTLN VDAGMVRH
    Length:248
    Mass (Da):25,531
    Last modified:October 1, 2001 - v1
    Checksum:iF0B299BDF2BB5D57
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AB248363 Genomic DNA. Translation: BAF02533.1.
    BA000012 Genomic DNA. Translation: BAB53033.1.
    RefSeqiWP_010914343.1. NC_002678.2.

    Genome annotation databases

    EnsemblBacteriaiBAB53033; BAB53033; BAB53033.
    GeneIDi1229902.
    KEGGimlo:mlr6807.
    PATRICi22485075. VBIMesLot2464_5417.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AB248363 Genomic DNA. Translation: BAF02533.1.
    BA000012 Genomic DNA. Translation: BAB53033.1.
    RefSeqiWP_010914343.1. NC_002678.2.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    3NDRX-ray2.88A/B/C/D2-248[»]
    3NUGX-ray1.79A/B/C/D2-248[»]
    3RWBX-ray1.70A/B/C/D2-248[»]
    ProteinModelPortaliQ988B7.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi266835.mlr6807.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiBAB53033; BAB53033; BAB53033.
    GeneIDi1229902.
    KEGGimlo:mlr6807.
    PATRICi22485075. VBIMesLot2464_5417.

    Phylogenomic databases

    eggNOGiENOG4108KEZ. Bacteria.
    ENOG410XRY7. LUCA.
    KOiK18609.
    OMAiIASNTFF.
    OrthoDBiPOG091H085B.

    Enzyme and pathway databases

    UniPathwayiUPA00192; UER00588.
    BioCyciMetaCyc:MONOMER-13148.
    MLOT266835:GJ9L-5398-MONOMER.
    BRENDAi1.1.1.107. 3243.

    Family and domain databases

    Gene3Di3.40.50.720. 1 hit.
    InterProiIPR016040. NAD(P)-bd_dom.
    IPR020904. Sc_DH/Rdtase_CS.
    IPR002347. SDR_fam.
    [Graphical view]
    PANTHERiPTHR24322. PTHR24322. 2 hits.
    PRINTSiPR00081. GDHRDH.
    PR00080. SDRFAMILY.
    SUPFAMiSSF51735. SSF51735. 1 hit.
    PROSITEiPS00061. ADH_SHORT. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Entry informationi

    Entry nameiPLDH_RHILO
    AccessioniPrimary (citable) accession number: Q988B7
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: January 11, 2011
    Last sequence update: October 1, 2001
    Last modified: September 7, 2016
    This is version 87 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

    Documents

    1. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. SIMILARITY comments
      Index of protein domains and families

    Similar proteinsi

    Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
    100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
    90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
    50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.