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Protein

Pyridoxine/pyridoxal/pyridoxamine kinase

Gene

pdxK

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-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

Enzyme 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. Pyridoxal kinase PdxY (pdxY), 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 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)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei23 – 231SubstrateCombined sources1 Publication
    Binding sitei59 – 591SubstrateCombined sources1 Publication
    Binding sitei125 – 1251ATPCombined sources1 Publication
    Metal bindingi136 – 1361Magnesium1 Publication
    Binding sitei157 – 1571ATP; via carbonyl oxygenCombined sources1 Publication
    Metal bindingi162 – 1621Magnesium1 Publication
    Binding sitei162 – 1621ATPCombined sources1 Publication
    Binding sitei195 – 1951ATPCombined sources1 Publication
    Binding sitei231 – 2311ATPCombined sources1 Publication
    Binding sitei233 – 2331SubstrateCombined sources1 Publication

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi221 – 2244ATPCombined sources1 Publication

    GO - Molecular functioni

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

    GO - Biological processi

    • phosphorylation Source: EcoCyc
    • pyridoxal 5'-phosphate salvage Source: EcoCyc
    • pyridoxine biosynthetic process Source: EcoCyc
    Complete GO annotation...

    Keywords - Molecular functioni

    Kinase, Transferase

    Keywords - Ligandi

    ATP-binding, Magnesium, Metal-binding, Nucleotide-binding, Zinc

    Enzyme and pathway databases

    BioCyciEcoCyc:PDXK-MONOMER.
    ECOL316407:JW2411-MONOMER.
    MetaCyc:PDXK-MONOMER.
    BRENDAi2.7.1.35. 2026.
    UniPathwayiUPA01068; 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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG12642. pdxK.

    Subcellular locationi

    GO - Cellular componenti

    • cytosol Source: EcoCyc
    Complete GO annotation...

    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)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 283283Pyridoxine/pyridoxal/pyridoxamine kinasePRO_0000213342Add
    BLAST

    Proteomic databases

    PaxDbiP40191.
    PRIDEiP40191.

    Interactioni

    Subunit structurei

    Homodimer.1 Publication

    Protein-protein interaction databases

    BioGridi4260568. 17 interactions.
    IntActiP40191. 6 interactions.
    STRINGi511145.b2418.

    Structurei

    Secondary structure

    1
    283
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi17 – 3014Combined sources
    Helixi32 – 4110Combined sources
    Beta strandi46 – 5611Combined sources
    Beta strandi65 – 673Combined sources
    Helixi70 – 8213Combined sources
    Beta strandi91 – 944Combined sources
    Helixi100 – 11415Combined sources
    Beta strandi121 – 1244Combined sources
    Turni131 – 1333Combined sources
    Helixi141 – 1477Combined sources
    Helixi150 – 1523Combined sources
    Beta strandi154 – 1563Combined sources
    Helixi160 – 1678Combined sources
    Helixi174 – 18411Combined sources
    Beta strandi191 – 1988Combined sources
    Beta strandi205 – 2128Combined sources
    Beta strandi215 – 2228Combined sources
    Helixi231 – 24414Combined sources
    Helixi249 – 26921Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2DDMX-ray2.10A/B1-283[»]
    2DDOX-ray2.60A/B1-283[»]
    2DDWX-ray3.20A/B1-283[»]
    ProteinModelPortaliP40191.
    SMRiP40191. Positions 2-280.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP40191.

    Family & Domainsi

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiENOG4107XGF. Bacteria.
    COG2240. LUCA.
    HOGENOMiHOG000258173.
    InParanoidiP40191.
    KOiK00868.
    OMAiRIRMEMH.
    OrthoDBiEOG69PQ1X.
    PhylomeDBiP40191.

    Family and domain databases

    Gene3Di3.40.1190.20. 1 hit.
    HAMAPiMF_01638. PdxK.
    InterProiIPR023479. PdxK.
    IPR013749. PM/HMP-P_kinase-1.
    IPR004625. PyrdxlKinase.
    IPR029056. Ribokinase-like.
    [Graphical view]
    PANTHERiPTHR10534. PTHR10534. 1 hit.
    PfamiPF08543. Phos_pyr_kin. 1 hit.
    [Graphical view]
    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.
    PATRICi32120219. VBIEscCol129921_2512.

    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
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2DDMX-ray2.10A/B1-283[»]
    2DDOX-ray2.60A/B1-283[»]
    2DDWX-ray3.20A/B1-283[»]
    ProteinModelPortaliP40191.
    SMRiP40191. Positions 2-280.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi4260568. 17 interactions.
    IntActiP40191. 6 interactions.
    STRINGi511145.b2418.

    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.
    PATRICi32120219. VBIEscCol129921_2512.

    Organism-specific databases

    EchoBASEiEB2519.
    EcoGeneiEG12642. pdxK.

    Phylogenomic databases

    eggNOGiENOG4107XGF. Bacteria.
    COG2240. LUCA.
    HOGENOMiHOG000258173.
    InParanoidiP40191.
    KOiK00868.
    OMAiRIRMEMH.
    OrthoDBiEOG69PQ1X.
    PhylomeDBiP40191.

    Enzyme and pathway databases

    UniPathwayiUPA01068; UER00298.
    UPA01068; UER00299.
    UPA01068; UER00300.
    BioCyciEcoCyc:PDXK-MONOMER.
    ECOL316407:JW2411-MONOMER.
    MetaCyc:PDXK-MONOMER.
    BRENDAi2.7.1.35. 2026.

    Miscellaneous databases

    EvolutionaryTraceiP40191.
    PROiP40191.

    Family and domain databases

    Gene3Di3.40.1190.20. 1 hit.
    HAMAPiMF_01638. PdxK.
    InterProiIPR023479. PdxK.
    IPR013749. PM/HMP-P_kinase-1.
    IPR004625. PyrdxlKinase.
    IPR029056. Ribokinase-like.
    [Graphical view]
    PANTHERiPTHR10534. PTHR10534. 1 hit.
    PfamiPF08543. Phos_pyr_kin. 1 hit.
    [Graphical view]
    SUPFAMiSSF53613. SSF53613. 1 hit.
    TIGRFAMsiTIGR00687. pyridox_kin. 1 hit.
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. "Identification of the pdxK gene that encodes pyridoxine (vitamin B6) kinase in Escherichia coli K-12."
      Yang Y., Zhao G., Winkler M.E.
      FEMS Microbiol. Lett. 141:89-95(1996) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, DISRUPTION PHENOTYPE.
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    2. "Construction of a contiguous 874-kb sequence of the Escherichia coli-K12 genome corresponding to 50.0-68.8 min on the linkage map and analysis of its sequence features."
      Yamamoto Y., Aiba H., Baba T., Hayashi K., Inada T., Isono K., Itoh T., Kimura S., Kitagawa M., Makino K., Miki T., Mitsuhashi N., Mizobuchi K., Mori H., Nakade S., Nakamura Y., Nashimoto H., Oshima T.
      , Oyama S., Saito N., Sampei G., Satoh Y., Sivasundaram S., Tagami H., Takahashi H., Takeda J., Takemoto K., Uehara K., Wada C., Yamagata S., Horiuchi T.
      DNA Res. 4:91-113(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / MG1655 / ATCC 47076.
    4. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
      Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
      Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    5. "The ptsH, ptsI, and crr genes of the Escherichia coli phosphoenolpyruvate-dependent phosphotransferase system: a complex operon with several modes of transcription."
      de Reuse H., Danchin A.
      J. Bacteriol. 170:3827-3837(1988) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 250-283.
    6. "Sugar transport by the bacterial phosphotransferase system. Molecular cloning and structural analysis of the Escherichia coli ptsH, ptsI, and crr genes."
      Saffen D.W., Presper K.A., Doering T.L., Roseman S.
      J. Biol. Chem. 262:16241-16253(1987) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 280-283.
    7. "Identification and function of the pdxY gene, which encodes a novel pyridoxal kinase involved in the salvage pathway of pyridoxal 5'-phosphate biosynthesis in Escherichia coli K-12."
      Yang Y., Tsui H.C., Man T.K., Winkler M.E.
      J. Bacteriol. 180:1814-1821(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, CATALYTIC ACTIVITY, DISRUPTION PHENOTYPE, PATHWAY.
      Strain: K12.
    8. "Expression, purification, and kinetic constants for human and Escherichia coli pyridoxal kinases."
      di Salvo M.L., Hunt S., Schirch V.
      Protein Expr. Purif. 36:300-306(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, COFACTOR.
    9. "Crystal structure of pyridoxal kinase from the Escherichia coli pdxK gene: implications for the classification of pyridoxal kinases."
      Safo M.K., Musayev F.N., di Salvo M.L., Hunt S., Claude J.B., Schirch V.
      J. Bacteriol. 188:4542-4552(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.10 ANGSTROMS) OF APOENZYME AND IN COMPLEXES WITH MG-ATP AND PYRIDOXAL, BIOPHYSICOCHEMICAL PROPERTIES, ENZYME REGULATION, SUBUNIT.

    Entry informationi

    Entry nameiPDXK_ECOLI
    AccessioniPrimary (citable) accession number: P40191
    Secondary accession number(s): P76964
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: February 1, 1995
    Last sequence update: November 1, 1997
    Last modified: May 11, 2016
    This is version 134 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. Escherichia coli
      Escherichia coli (strain K12): entries and cross-references to EcoGene
    2. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    3. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    4. 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.