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Protein

Pyridoxine/pyridoxal/pyridoxamine kinase

Gene

pdxK

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

B6-vitamer kinase involved in the salvage pathway of pyridoxal 5'-phosphate (PLP). Catalyzes the phosphorylation of pyridoxine (PN), pyridoxal (PL), and pyridoxamine (PM), forming their respective 5'-phosphorylated esters, i.e. PNP, PLP and PMP.2 Publications

Catalytic activityi

ATP + pyridoxal = ADP + pyridoxal 5'-phosphate.2 Publications
ATP + pyridoxine = ADP + pyridoxine 5'-phosphate.2 Publications
ATP + pyridoxamine = ADP + pyridoxamine 5'-phosphate.1 Publication

Cofactori

Zn2+1 Publication, Mg2+1 PublicationNote: Can use both zinc and magnesium that is complexed with ATP. However, magnesium seems to be the preferred metal used under physiological conditions.1 Publication

Activity regulationi

Is activated by the monovalent cation potassium.1 Publication

Kineticsi

kcat is 140 min(-1) for the phosphorylation of PL with MgATP. kcat is 120 min(-1) for the phosphorylation of PL with ZnATP. kcat is 20 min(-1) for the phosphorylation of PN with MgATP. kcat is 40 min(-1) for the phosphorylation of PM with MgATP. kcat is 25 min(-1) for the phosphorylation of PM with ZnATP (at pH 7.3 and 37 degrees Celsius) (PubMed:15249053). kcat is 250 min(-1) for the phosphorylation of PL with MgATP (at pH 7.3 and 37 degrees Celsius) (PubMed:16740960).2 Publications
  1. KM=100 µM for pyridoxal (in the presence of MgATP, at pH 7.3 and 37 degrees Celsius)1 Publication
  2. KM=50 µM for pyridoxal (in the presence of MgATP, at pH 7.3 and 37 degrees Celsius)1 Publication
  3. KM=190 µM for pyridoxal (in the presence of ZnATP, at pH 7.3 and 37 degrees Celsius)1 Publication
  4. KM=25 µM for pyridoxine (in the presence of MgATP, at pH 7.3 and 37 degrees Celsius)1 Publication
  5. KM=30 µM for pyridoxamine (in the presence of MgATP, at pH 7.3 and 37 degrees Celsius)1 Publication
  6. KM=10 µM for pyridoxamine (in the presence of ZnATP, at pH 7.3 and 37 degrees Celsius)1 Publication
  7. KM=600 µM for MgATP (at pH 7.3 and 37 degrees Celsius)1 Publication
  8. KM=450 µM for MgATP (at pH 7.3 and 37 degrees Celsius)1 Publication
  9. KM=2100 µM for MgATP (at pH 6.1 and 37 degrees Celsius)1 Publication
  10. KM=70 µM for ZnATP (in the presence of pyridoxal, at pH 7.3 and 37 degrees Celsius)1 Publication
  11. KM=45 µM for ZnATP (in the presence of pyridoxamine, at pH 7.3 and 37 degrees Celsius)1 Publication

    Pathwayi: pyridoxal 5'-phosphate salvage

    This protein is involved in step 1 of the subpathway that synthesizes pyridoxal 5'-phosphate from pyridoxal.1 Publication
    Proteins known to be involved in this subpathway in this organism are:
    1. Pyridoxine/pyridoxal/pyridoxamine kinase (pdxK), Pyridoxal kinase PdxY (pdxY)
    This subpathway is part of the pathway pyridoxal 5'-phosphate salvage, which is itself part of Cofactor metabolism.
    View all proteins of this organism that are known to be involved in the subpathway that synthesizes pyridoxal 5'-phosphate from pyridoxal, the pathway pyridoxal 5'-phosphate salvage and in Cofactor metabolism.

    Pathwayi: pyridoxal 5'-phosphate salvage

    This protein is involved in step 1 of the subpathway that synthesizes pyridoxine 5'-phosphate from pyridoxine.1 Publication
    Proteins known to be involved in this subpathway in this organism are:
    1. Pyridoxine/pyridoxal/pyridoxamine kinase (pdxK)
    This subpathway is part of the pathway pyridoxal 5'-phosphate salvage, which is itself part of Cofactor metabolism.
    View all proteins of this organism that are known to be involved in the subpathway that synthesizes pyridoxine 5'-phosphate from pyridoxine, the pathway pyridoxal 5'-phosphate salvage and in Cofactor metabolism.

    Pathwayi: pyridoxal 5'-phosphate salvage

    This protein is involved in step 1 of the subpathway that synthesizes pyridoxamine 5'-phosphate from pyridoxamine.1 Publication
    Proteins known to be involved in this subpathway in this organism are:
    1. Pyridoxine/pyridoxal/pyridoxamine kinase (pdxK)
    This subpathway is part of the pathway pyridoxal 5'-phosphate salvage, which is itself part of Cofactor metabolism.
    View all proteins of this organism that are known to be involved in the subpathway that synthesizes pyridoxamine 5'-phosphate from pyridoxamine, the pathway pyridoxal 5'-phosphate salvage and in Cofactor metabolism.

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Binding sitei23SubstrateCombined sources1 Publication1
    Binding sitei59SubstrateCombined sources1 Publication1
    Binding sitei125ATPCombined sources1 Publication1
    Metal bindingi136Magnesium1 Publication1
    Binding sitei157ATP; via carbonyl oxygenCombined sources1 Publication1
    Metal bindingi162Magnesium1 Publication1
    Binding sitei162ATPCombined sources1 Publication1
    Binding sitei195ATPCombined sources1 Publication1
    Binding sitei231ATPCombined sources1 Publication1
    Binding sitei233SubstrateCombined sources1 Publication1

    Regions

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Nucleotide bindingi221 – 224ATPCombined sources1 Publication4

    GO - Molecular functioni

    • ATP binding Source: UniProtKB-UniRule
    • hydroxymethylpyrimidine kinase activity Source: EcoCyc
    • magnesium ion binding Source: UniProtKB-UniRule
    • metal ion binding Source: EcoCyc
    • potassium ion binding Source: EcoCyc
    • pyridoxal kinase activity Source: EcoCyc
    • pyridoxal phosphate binding Source: EcoCyc
    • zinc ion binding Source: UniProtKB-UniRule

    GO - Biological processi

    Keywordsi

    Molecular functionKinase, Transferase
    LigandATP-binding, Magnesium, Metal-binding, Nucleotide-binding, Zinc

    Enzyme and pathway databases

    BioCyciEcoCyc:PDXK-MONOMER
    MetaCyc:PDXK-MONOMER
    BRENDAi2.7.1.35 2026
    UniPathwayi
    UPA01068;UER00298

    UPA01068;UER00299

    UPA01068;UER00300

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Pyridoxine/pyridoxal/pyridoxamine kinase2 Publications (EC:2.7.1.352 Publications)
    Short name:
    PN/PL/PM kinase1 Publication
    Alternative name(s):
    B6-vitamer kinase1 Publication
    Pyridoxal kinase 11 Publication
    Short name:
    PL kinase 11 Publication
    Gene namesi
    Name:pdxK
    Synonyms:yfeI
    Ordered Locus Names:b2418, JW2411
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG12642 pdxK

    Subcellular locationi

    GO - Cellular componenti

    Pathology & Biotechi

    Disruption phenotypei

    Cells lacking this gene lack pyridoxine kinase activity but still contain pyridoxal kinase activity (PubMed:8764513). Cells lacking this gene and cells lacking both pdxY and pdxK are not auxotrophs, meaning that the de novo pathway of PLP biosynthesis is functional. For PLP salvage, the pdxY single mutant can use both pyridoxine and pyridoxal, the pdxK single mutant can use pyridoxal but not pyridoxine, and the double mutant can no longer use both compounds (PubMed:9537380).2 Publications

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00002133421 – 283Pyridoxine/pyridoxal/pyridoxamine kinaseAdd BLAST283

    Proteomic databases

    PaxDbiP40191
    PRIDEiP40191

    Interactioni

    Subunit structurei

    Homodimer.1 Publication

    Protein-protein interaction databases

    BioGridi4260568, 21 interactors
    IntActiP40191, 6 interactors
    STRINGi316385.ECDH10B_2583

    Structurei

    Secondary structure

    1283
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details

    3D structure databases

    ProteinModelPortaliP40191
    SMRiP40191
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP40191

    Family & Domainsi

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiENOG4107XGF Bacteria
    COG2240 LUCA
    HOGENOMiHOG000258173
    InParanoidiP40191
    KOiK00868
    PhylomeDBiP40191

    Family and domain databases

    CDDicd01173 pyridoxal_pyridoxamine_kinase, 1 hit
    Gene3Di3.40.1190.20, 1 hit
    HAMAPiMF_01638 PdxK, 1 hit
    InterProiView protein in InterPro
    IPR023479 PdxK
    IPR013749 PM/HMP-P_kinase-1
    IPR004625 PyrdxlKinase
    IPR029056 Ribokinase-like
    PANTHERiPTHR10534 PTHR10534, 1 hit
    PfamiView protein in Pfam
    PF08543 Phos_pyr_kin, 1 hit
    SUPFAMiSSF53613 SSF53613, 1 hit
    TIGRFAMsiTIGR00687 pyridox_kin, 1 hit

    Sequencei

    Sequence statusi: Complete.

    P40191-1 [UniParc]FASTAAdd to basket
    « Hide
            10         20         30         40         50
    MSSLLLFNDK SRALQADIVA VQSQVVYGSV GNSIAVPAIK QNGLNVFAVP
    60 70 80 90 100
    TVLLSNTPHY DTFYGGAIPD EWFSGYLRAL QERDALRQLR AVTTGYMGTA
    110 120 130 140 150
    SQIKILAEWL TALRKDHPDL LIMVDPVIGD IDSGIYVKPD LPEAYRQYLL
    160 170 180 190 200
    PLAQGITPNI FELEILTGKN CRDLDSAIAA AKSLLSDTLK WVVVTSASGN
    210 220 230 240 250
    EENQEMQVVV VTADSVNVIS HSRVKTDLKG TGDLFCAQLI SGLLKGKALT
    260 270 280
    DAVHRAGLRV LEVMRYTQQH ESDELILPPL AEA
    Length:283
    Mass (Da):30,847
    Last modified:November 1, 1997 - v2
    Checksum:i8DFEDADD2F589EA0
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U53700 Genomic DNA Translation: AAC44166.1
    U00096 Genomic DNA Translation: AAC75471.1
    AP009048 Genomic DNA Translation: BAA16292.1
    M21994 Genomic DNA No translation available.
    J02796 Genomic DNA No translation available.
    PIRiA65016
    RefSeqiNP_416913.1, NC_000913.3
    WP_000096674.1, NZ_LN832404.1

    Genome annotation databases

    EnsemblBacteriaiAAC75471; AAC75471; b2418
    BAA16292; BAA16292; BAA16292
    GeneIDi946881
    KEGGiecj:JW2411
    eco:b2418
    PATRICifig|1411691.4.peg.4313

    Similar proteinsi

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U53700 Genomic DNA Translation: AAC44166.1
    U00096 Genomic DNA Translation: AAC75471.1
    AP009048 Genomic DNA Translation: BAA16292.1
    M21994 Genomic DNA No translation available.
    J02796 Genomic DNA No translation available.
    PIRiA65016
    RefSeqiNP_416913.1, NC_000913.3
    WP_000096674.1, NZ_LN832404.1

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    2DDMX-ray2.10A/B1-283[»]
    2DDOX-ray2.60A/B1-283[»]
    2DDWX-ray3.20A/B1-283[»]
    ProteinModelPortaliP40191
    SMRiP40191
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi4260568, 21 interactors
    IntActiP40191, 6 interactors
    STRINGi316385.ECDH10B_2583

    Proteomic databases

    PaxDbiP40191
    PRIDEiP40191

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAC75471; AAC75471; b2418
    BAA16292; BAA16292; BAA16292
    GeneIDi946881
    KEGGiecj:JW2411
    eco:b2418
    PATRICifig|1411691.4.peg.4313

    Organism-specific databases

    EchoBASEiEB2519
    EcoGeneiEG12642 pdxK

    Phylogenomic databases

    eggNOGiENOG4107XGF Bacteria
    COG2240 LUCA
    HOGENOMiHOG000258173
    InParanoidiP40191
    KOiK00868
    PhylomeDBiP40191

    Enzyme and pathway databases

    UniPathwayi
    UPA01068;UER00298

    UPA01068;UER00299

    UPA01068;UER00300

    BioCyciEcoCyc:PDXK-MONOMER
    MetaCyc:PDXK-MONOMER
    BRENDAi2.7.1.35 2026

    Miscellaneous databases

    EvolutionaryTraceiP40191
    PROiPR:P40191

    Family and domain databases

    CDDicd01173 pyridoxal_pyridoxamine_kinase, 1 hit
    Gene3Di3.40.1190.20, 1 hit
    HAMAPiMF_01638 PdxK, 1 hit
    InterProiView protein in InterPro
    IPR023479 PdxK
    IPR013749 PM/HMP-P_kinase-1
    IPR004625 PyrdxlKinase
    IPR029056 Ribokinase-like
    PANTHERiPTHR10534 PTHR10534, 1 hit
    PfamiView protein in Pfam
    PF08543 Phos_pyr_kin, 1 hit
    SUPFAMiSSF53613 SSF53613, 1 hit
    TIGRFAMsiTIGR00687 pyridox_kin, 1 hit
    ProtoNetiSearch...

    Entry informationi

    Entry nameiPDXK_ECOLI
    AccessioniPrimary (citable) accession number: P40191
    Secondary accession number(s): P76964
    Entry historyiIntegrated into UniProtKB/Swiss-Prot: February 1, 1995
    Last sequence update: November 1, 1997
    Last modified: November 7, 2018
    This is version 146 of the entry and version 2 of the sequence. See complete history.
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. SIMILARITY comments
      Index of protein domains and families
    2. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    3. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    4. Escherichia coli
      Escherichia coli (strain K12): entries and cross-references to EcoGene
    UniProt is an ELIXIR core data resource
    Main funding by: National Institutes of Health

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