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Protein

Pyridoxine kinase

Gene

pdxK

Organism
Bacillus subtilis (strain 168)
Status
Reviewed-Annotation score:

Annotation score:5 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the ‘correct annotation’ for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
-Experimental evidence at protein leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the ‘protein existence’ evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>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

Caution

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

<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section describes the catalytic activity of an enzyme, i.e. a chemical reaction that the enzyme catalyzes.<p><a href='/help/catalytic_activity' target='_top'>More...</a></p>Catalytic activityi

<p>This subsection of the ‘Function’ section describes biophysical and chemical properties, such as maximal absorption, kinetic parameters, pH dependence, redox potentials and temperature dependence.<p><a href='/help/biophysicochemical_properties' target='_top'>More...</a></p>Kineticsi

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

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the ‘Function’ section describes the interaction between a single amino acid and another chemical entity. Priority is given to the annotation of physiological ligands.<p><a href='/help/binding' target='_top'>More...</a></p>Binding sitei141ATP1
    <p>This subsection of the ‘Function’ section indicates at which position the protein binds a given metal ion. The nature of the metal is indicated in the ‘Description’ field.<p><a href='/help/metal' target='_top'>More...</a></p>Metal bindingi144MagnesiumBy similarity1
    Binding sitei190ATP1
    Binding sitei206ATP; via amide nitrogen and carbonyl oxygen1
    Binding sitei215ATP; via amide nitrogen1
    Binding sitei240ATP1

    Regions

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the ‘Function’ section describes a region in the protein which binds nucleotide phosphates. It always involves more than one amino acid and includes all residues involved in nucleotide-binding.<p><a href='/help/np_bind' target='_top'>More...</a></p>Nucleotide bindingi178 – 182ATP5

    <p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

    GO - Biological processi

    <p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

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

    Enzyme and pathway databases

    BioCyc Collection of Pathway/Genome Databases

    More...
    BioCyci
    BSUB:BSU38020-MONOMER

    <p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

    <p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>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
    <p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: ‘Name’, ‘Synonyms’, ‘Ordered locus names’ and ‘ORF names’.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
    Name:pdxK
    Synonyms:ywdB
    Ordered Locus Names:BSU38020
    ORF Names:ipa-52r
    <p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiBacillus subtilis (strain 168)
    <p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the ‘taxonomic identifier’ or ‘taxid’.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri224308 [NCBI]
    <p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
    <p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
    • UP000001570 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes_manual">proteome</a> can consist of several components. <br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Chromosome

    <p>This section provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>Subcellular locationi

    GO - Cellular componenti

    • cytosol Source: GO_Central

    <p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the ‘PTM / Processing’ section describes the extent of a polypeptide chain in the mature protein following processing.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00001920171 – 271Pyridoxine kinaseAdd BLAST271

    Proteomic databases

    PaxDb, a database of protein abundance averages across all three domains of life

    More...
    PaxDbi
    P39610

    PRoteomics IDEntifications database

    More...
    PRIDEi
    P39610

    <p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

    <p>This subsection of the <a href="http://www.uniprot.org/help/interaction_section">'Interaction'</a> section provides information about the protein quaternary structure and interaction(s) with other proteins or protein complexes (with the exception of physiological receptor-ligand interactions which are annotated in the <a href="http://www.uniprot.org/help/function_section">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

    Homodimer.1 Publication

    Protein-protein interaction databases

    STRING: functional protein association networks

    More...
    STRINGi
    224308.Bsubs1_010100020531

    <p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

    Secondary structure

    1271
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details

    3D structure databases

    Protein Model Portal of the PSI-Nature Structural Biology Knowledgebase

    More...
    ProteinModelPortali
    P39610

    SWISS-MODEL Repository - a database of annotated 3D protein structure models

    More...
    SMRi
    P39610

    Database of comparative protein structure models

    More...
    ModBasei
    Search...

    MobiDB: a database of protein disorder and mobility annotations

    More...
    MobiDBi
    Search...

    Miscellaneous databases

    Relative evolutionary importance of amino acids within a protein sequence

    More...
    EvolutionaryTracei
    P39610

    <p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

    <p>This subsection of the ‘Family and domains’ section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

    Belongs to the ThiD family.Curated

    Phylogenomic databases

    evolutionary genealogy of genes: Non-supervised Orthologous Groups

    More...
    eggNOGi
    ENOG4105DWF Bacteria
    COG0351 LUCA

    The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

    More...
    HOGENOMi
    HOG000225273

    InParanoid: Eukaryotic Ortholog Groups

    More...
    InParanoidi
    P39610

    KEGG Orthology (KO)

    More...
    KOi
    K00868

    Identification of Orthologs from Complete Genome Data

    More...
    OMAi
    ADECAEK

    Database for complete collections of gene phylogenies

    More...
    PhylomeDBi
    P39610

    Family and domain databases

    Conserved Domains Database

    More...
    CDDi
    cd01169 HMPP_kinase, 1 hit

    Gene3D Structural and Functional Annotation of Protein Families

    More...
    Gene3Di
    3.40.1190.20, 1 hit

    Integrated resource of protein families, domains and functional sites

    More...
    InterProi
    View protein in InterPro
    IPR004399 HMP/HMP-P_kinase
    IPR013749 PM/HMP-P_kinase-1
    IPR029056 Ribokinase-like

    Pfam protein domain database

    More...
    Pfami
    View protein in Pfam
    PF08543 Phos_pyr_kin, 1 hit

    Superfamily database of structural and functional annotation

    More...
    SUPFAMi
    SSF53613 SSF53613, 1 hit

    TIGRFAMs; a protein family database

    More...
    TIGRFAMsi
    TIGR00097 HMP-P_kinase, 1 hit

    <p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence_length">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>.<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequencei

    <p>This subsection of the <a href="http://www.uniprot.org/help/sequences_section">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>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
    <p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:iCCC0DA345DA3724F
    GO

    Sequence databases

    Select the link destinations:

    EMBL nucleotide sequence database

    More...
    EMBLi

    GenBank nucleotide sequence database

    More...
    GenBanki

    DNA Data Bank of Japan; a nucleotide sequence database

    More...
    DDBJi
    Links Updated
    X73124 Genomic DNA Translation: CAA51608.1
    AL009126 Genomic DNA Translation: CAB15828.1

    Protein sequence database of the Protein Information Resource

    More...
    PIRi
    S39707

    NCBI Reference Sequences

    More...
    RefSeqi
    NP_391681.1, NC_000964.3
    WP_003242645.1, NZ_JNCM01000034.1

    Genome annotation databases

    Ensembl bacterial and archaeal genome annotation project

    More...
    EnsemblBacteriai
    CAB15828; CAB15828; BSU38020

    Database of genes from NCBI RefSeq genomes

    More...
    GeneIDi
    937262

    KEGG: Kyoto Encyclopedia of Genes and Genomes

    More...
    KEGGi
    bsu:BSU38020

    Pathosystems Resource Integration Center (PATRIC)

    More...
    PATRICi
    fig|224308.179.peg.4116

    <p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

    <p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>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:

    Protein Data Bank Europe

    More...
    PDBei

    Protein Data Bank RCSB

    More...
    RCSB PDBi

    Protein Data Bank Japan

    More...
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    2I5BX-ray2.80A/B/C/D/E1-271[»]
    ProteinModelPortaliP39610
    SMRiP39610
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi224308.Bsubs1_010100020531

    Proteomic databases

    PaxDbiP39610
    PRIDEiP39610

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiCAB15828; CAB15828; BSU38020
    GeneIDi937262
    KEGGibsu:BSU38020
    PATRICifig|224308.179.peg.4116

    Phylogenomic databases

    eggNOGiENOG4105DWF Bacteria
    COG0351 LUCA
    HOGENOMiHOG000225273
    InParanoidiP39610
    KOiK00868
    OMAiADECAEK
    PhylomeDBiP39610

    Enzyme and pathway databases

    BioCyciBSUB:BSU38020-MONOMER

    Miscellaneous databases

    EvolutionaryTraceiP39610

    Family and domain databases

    CDDicd01169 HMPP_kinase, 1 hit
    Gene3Di3.40.1190.20, 1 hit
    InterProiView protein in InterPro
    IPR004399 HMP/HMP-P_kinase
    IPR013749 PM/HMP-P_kinase-1
    IPR029056 Ribokinase-like
    PfamiView protein in Pfam
    PF08543 Phos_pyr_kin, 1 hit
    SUPFAMiSSF53613 SSF53613, 1 hit
    TIGRFAMsiTIGR00097 HMP-P_kinase, 1 hit

    ProtoNet; Automatic hierarchical classification of proteins

    More...
    ProtoNeti
    Search...

    <p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

    <p>This subsection of the ‘Entry information’ section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiPDXK_BACSU
    <p>This subsection of the ‘Entry information’ section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called ‘Primary (citable) accession number’.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: P39610
    <p>This subsection of the ‘Entry information’ section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification (‘Last modified’). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: February 1, 1995
    Last sequence update: February 1, 1995
    Last modified: December 5, 2018
    This is version 121 of the entry and version 1 of the sequence. See complete history.
    <p>This subsection of the ‘Entry information’ section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    <p>This section contains any relevant information that doesn’t fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    2. SIMILARITY comments
      Index of protein domains and families
    3. Bacillus subtilis
      Bacillus subtilis (strain 168): entries, gene names and cross-references to SubtiList
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