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Protein

Pyridoxine kinase

Gene

pdxK

Organism
Bacillus subtilis (strain 168)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Phosphorylates B6 vitamers; functions in a salvage pathway. Uses pyridoxal, pyridoxine, and pyridoxamine as substrates. Can also use hydroxymethylpyrimidine (HMP) as substrate.1 Publication

Catalytic activityi

ATP + pyridoxal = ADP + pyridoxal 5'-phosphate.1 Publication

Kineticsi

  1. KM=2 mM for HMP1 Publication
  2. KM=46.6 µM for pyridoxal1 Publication

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei141 – 1411ATP
    Metal bindingi144 – 1441MagnesiumBy similarity
    Binding sitei190 – 1901ATP
    Binding sitei206 – 2061ATP; via amide nitrogen and carbonyl oxygen
    Binding sitei215 – 2151ATP; via amide nitrogen
    Binding sitei240 – 2401ATP

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi178 – 1825ATP

    GO - Molecular functioni

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Kinase, Transferase

    Keywords - Ligandi

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

    Enzyme and pathway databases

    BioCyciBSUB:BSU38020-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Pyridoxine kinase (EC:2.7.1.35)
    Alternative name(s):
    PN/PL/PM kinase
    Pyridoxal kinase
    Pyridoxamine kinase
    Vitamin B6 kinase
    Gene namesi
    Name:pdxK
    Synonyms:ywdB
    Ordered Locus Names:BSU38020
    ORF Names:ipa-52r
    OrganismiBacillus subtilis (strain 168)
    Taxonomic identifieri224308 [NCBI]
    Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
    Proteomesi
    • UP000001570 Componenti: Chromosome

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 271271Pyridoxine kinasePRO_0000192017Add
    BLAST

    Proteomic databases

    PaxDbiP39610.

    Interactioni

    Subunit structurei

    Homodimer.1 Publication

    Protein-protein interaction databases

    STRINGi224308.Bsubs1_010100020531.

    Structurei

    Secondary structure

    1
    271
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi5 – 139Combined sources
    Beta strandi16 – 183Combined sources
    Helixi19 – 2911Combined sources
    Beta strandi33 – 4412Combined sources
    Turni46 – 505Combined sources
    Beta strandi52 – 565Combined sources
    Helixi59 – 7214Combined sources
    Beta strandi76 – 805Combined sources
    Helixi86 – 9813Combined sources
    Beta strandi102 – 1065Combined sources
    Beta strandi111 – 1133Combined sources
    Beta strandi115 – 1206Combined sources
    Helixi121 – 13010Combined sources
    Helixi132 – 1343Combined sources
    Beta strandi136 – 1383Combined sources
    Helixi142 – 1498Combined sources
    Helixi157 – 16812Combined sources
    Turni169 – 1713Combined sources
    Beta strandi173 – 1786Combined sources
    Helixi180 – 1823Combined sources
    Beta strandi185 – 1939Combined sources
    Beta strandi198 – 2036Combined sources
    Helixi214 – 22714Combined sources
    Helixi232 – 24817Combined sources
    Beta strandi253 – 2564Combined sources
    Helixi264 – 2685Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2I5BX-ray2.80A/B/C/D/E1-271[»]
    ProteinModelPortaliP39610.
    SMRiP39610. Positions 3-271.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP39610.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the ThiD family.Curated

    Phylogenomic databases

    eggNOGiENOG4105DWF. Bacteria.
    COG0351. LUCA.
    HOGENOMiHOG000225273.
    InParanoidiP39610.
    KOiK00868.
    OMAiCLTAMTD.
    OrthoDBiEOG6XWV53.
    PhylomeDBiP39610.

    Family and domain databases

    Gene3Di3.40.1190.20. 1 hit.
    InterProiIPR004399. HMP/HMP-P_kinase.
    IPR013749. PM/HMP-P_kinase-1.
    IPR029056. Ribokinase-like.
    [Graphical view]
    PfamiPF08543. Phos_pyr_kin. 1 hit.
    [Graphical view]
    SUPFAMiSSF53613. SSF53613. 1 hit.
    TIGRFAMsiTIGR00097. HMP-P_kinase. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    P39610-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MSMHKALTIA GSDSSGGAGI QADLKTFQEK NVYGMTALTV IVAMDPNNSW
    60 70 80 90 100
    NHQVFPIDTD TIRAQLATIT DGIGVDAMKT GMLPTVDIIE LAAKTIKEKQ
    110 120 130 140 150
    LKNVVIDPVM VCKGANEVLY PEHAQALREQ LAPLATVITP NLFEASQLSG
    160 170 180 190 200
    MDELKTVDDM IEAAKKIHAL GAQYVVITGG GKLKHEKAVD VLYDGETAEV
    210 220 230 240 250
    LESEMIDTPY THGAGCTFSA AVTAELAKGA EVKEAIYAAK EFITAAIKES
    260 270
    FPLNQYVGPT KHSALRLNQQ S
    Length:271
    Mass (Da):29,017
    Last modified:February 1, 1995 - v1
    Checksum:iCCC0DA345DA3724F
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    X73124 Genomic DNA. Translation: CAA51608.1.
    AL009126 Genomic DNA. Translation: CAB15828.1.
    PIRiS39707.
    RefSeqiNP_391681.1. NC_000964.3.
    WP_003242645.1. NZ_JNCM01000034.1.

    Genome annotation databases

    EnsemblBacteriaiCAB15828; CAB15828; BSU38020.
    GeneIDi937262.
    KEGGibsu:BSU38020.
    PATRICi18979648. VBIBacSub10457_3986.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    X73124 Genomic DNA. Translation: CAA51608.1.
    AL009126 Genomic DNA. Translation: CAB15828.1.
    PIRiS39707.
    RefSeqiNP_391681.1. NC_000964.3.
    WP_003242645.1. NZ_JNCM01000034.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2I5BX-ray2.80A/B/C/D/E1-271[»]
    ProteinModelPortaliP39610.
    SMRiP39610. Positions 3-271.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi224308.Bsubs1_010100020531.

    Proteomic databases

    PaxDbiP39610.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiCAB15828; CAB15828; BSU38020.
    GeneIDi937262.
    KEGGibsu:BSU38020.
    PATRICi18979648. VBIBacSub10457_3986.

    Phylogenomic databases

    eggNOGiENOG4105DWF. Bacteria.
    COG0351. LUCA.
    HOGENOMiHOG000225273.
    InParanoidiP39610.
    KOiK00868.
    OMAiCLTAMTD.
    OrthoDBiEOG6XWV53.
    PhylomeDBiP39610.

    Enzyme and pathway databases

    BioCyciBSUB:BSU38020-MONOMER.

    Miscellaneous databases

    EvolutionaryTraceiP39610.

    Family and domain databases

    Gene3Di3.40.1190.20. 1 hit.
    InterProiIPR004399. HMP/HMP-P_kinase.
    IPR013749. PM/HMP-P_kinase-1.
    IPR029056. Ribokinase-like.
    [Graphical view]
    PfamiPF08543. Phos_pyr_kin. 1 hit.
    [Graphical view]
    SUPFAMiSSF53613. SSF53613. 1 hit.
    TIGRFAMsiTIGR00097. HMP-P_kinase. 1 hit.
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: 168.
    2. "The complete genome sequence of the Gram-positive bacterium Bacillus subtilis."
      Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V., Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R., Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S., Bruschi C.V.
      , Caldwell B., Capuano V., Carter N.M., Choi S.-K., Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F., Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D., Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M., Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P., Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K., Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S., Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y., Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G., Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J., Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C., Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S., Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B., Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S., Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M., Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y., Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J., Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A., Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M., Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S., Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E., Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K., Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E., Yoshikawa H., Danchin A.
      Nature 390:249-256(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: 168.
    3. "Characterization of two kinases involved in thiamine pyrophosphate and pyridoxal phosphate biosynthesis in Bacillus subtilis: 4-amino-5-hydroxymethyl-2-methylpyrimidine kinase and pyridoxal kinase."
      Park J.-H., Burns K., Kinsland C., Begley T.P.
      J. Bacteriol. 186:1571-1573(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION AS PYRIDOXAL KINASE, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES.
      Strain: 168 / CU1065.
    4. "The crystal structure of an ADP complex of Bacillus subtilis pyridoxal kinase provides evidence for the parallel emergence of enzyme activity during evolution."
      Newman J.A., Das S.K., Sedelnikova S.E., Rice D.W.
      J. Mol. Biol. 363:520-530(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) IN COMPLEX WITH ADP, SUBUNIT.

    Entry informationi

    Entry nameiPDXK_BACSU
    AccessioniPrimary (citable) accession number: P39610
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: February 1, 1995
    Last sequence update: February 1, 1995
    Last modified: February 17, 2016
    This is version 114 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Caution

    Was originally annotated in the complete genome as thiD.1 Publication

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. Bacillus subtilis
      Bacillus subtilis (strain 168): entries, gene names and cross-references to SubtiList
    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.