Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
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)DescriptionActionsGraphical viewLength
    Binding sitei141SubstrateBy similarity1
    Active sitei154Proton acceptorPROSITE-ProRule annotationBy similarity1

    Regions

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Nucleotide bindingi11 – 35NADBy similarityAdd BLAST25

    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.
    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)DescriptionActionsGraphical viewLength
    ChainiPRO_00004031101 – 248Pyridoxal 4-dehydrogenaseAdd BLAST248

    Interactioni

    Subunit structurei

    Homotetramer.1 Publication

    Protein-protein interaction databases

    STRINGi266835.mlr6807.

    Structurei

    Secondary structure

    1248
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Turni4 – 7Combined sources4
    Beta strandi9 – 13Combined sources5
    Turni14 – 16Combined sources3
    Helixi18 – 29Combined sources12
    Beta strandi33 – 37Combined sources5
    Helixi41 – 51Combined sources11
    Beta strandi55 – 57Combined sources3
    Helixi65 – 79Combined sources15
    Beta strandi83 – 87Combined sources5
    Helixi97 – 99Combined sources3
    Helixi102 – 112Combined sources11
    Helixi114 – 130Combined sources17
    Beta strandi134 – 139Combined sources6
    Helixi143 – 146Combined sources4
    Helixi152 – 172Combined sources21
    Helixi173 – 175Combined sources3
    Beta strandi177 – 184Combined sources8
    Helixi190 – 193Combined sources4
    Helixi196 – 200Combined sources5
    Helixi201 – 207Combined sources7
    Beta strandi208 – 210Combined sources3
    Helixi216 – 227Combined sources12
    Helixi229 – 231Combined sources3
    Beta strandi238 – 242Combined sources5

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB 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.
    SMRiQ988B7.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Compositional bias

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Compositional biasi6 – 60Ala-richSequence analysisAdd BLAST55

    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
    PDB 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.
    SMRiQ988B7.
    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.
    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: November 2, 2016
    This is version 88 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.