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    PDXK pyridoxal kinase [ Homo sapiens (human) ]

    Gene ID: 8566, updated on 2-May-2024

    Summary

    Official Symbol
    PDXKprovided by HGNC
    Official Full Name
    pyridoxal kinaseprovided by HGNC
    Primary source
    HGNC:HGNC:8819
    See related
    Ensembl:ENSG00000160209 MIM:179020; AllianceGenome:HGNC:8819
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    PKH; PNK; HMSN6C; PRED79; C21orf97; HEL-S-1a; C21orf124
    Summary
    The protein encoded by this gene phosphorylates vitamin B6, a step required for the conversion of vitamin B6 to pyridoxal-5-phosphate, an important cofactor in intermediary metabolism. The encoded protein is cytoplasmic and probably acts as a homodimer. Alternatively spliced transcript variants have been described, but their biological validity has not been determined. [provided by RefSeq, Jul 2008]
    Expression
    Broad expression in testis (RPKM 24.7), fat (RPKM 18.6) and 25 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Location:
    21q22.3
    Exon count:
    19
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 21 NC_000021.9 (43719129..43762299)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 21 NC_060945.1 (42074671..42117910)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 21 NC_000021.8 (45139010..45182180)

    Chromosome 21 - NC_000021.9Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124905031 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:45131022-45131903 Neighboring gene RRP1B-PDXK intergenic CAGE-defined mid-level expression enhancer Neighboring gene uncharacterized LOC124905032 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18546 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13364 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13365 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:45139703-45140612 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18547 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:45146555-45147396 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:45148239-45149080 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:45149081-45149922 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:45151396-45151896 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:45152891-45153850 Neighboring gene uncharacterized LOC105372824 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:45157073-45157572 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:45159504-45160242 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:45160243-45160981 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:45183829-45184574 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:45184575-45185320 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:45186633-45187246 Neighboring gene PDXK-CSTB intergenic CAGE-defined low expression enhancer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:45189831-45190753 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:45190754-45191675 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13368 Neighboring gene cystatin B upstream repeat instability region Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:45198401-45199200 Neighboring gene uncharacterized LOC105372825 Neighboring gene cystatin B

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ31940, FLJ37311, MGC15873, MGC31754, MGC52346, DKFZp566A071

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables ATP binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables lithium ion binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables magnesium ion binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables potassium ion binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables protein homodimerization activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables pyridoxal kinase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables pyridoxal kinase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables pyridoxal kinase activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    enables pyridoxal phosphate binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables sodium ion binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables zinc ion binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in pyridoxal 5'-phosphate salvage IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in pyridoxal 5'-phosphate salvage IC
    Inferred by Curator
    more info
    PubMed 
    involved_in pyridoxal 5'-phosphate salvage IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in pyridoxal 5'-phosphate salvage IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in pyridoxal metabolic process IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in pyridoxamine metabolic process IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    located_in cytosol HDA PubMed 
    is_active_in cytosol IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in cytosol TAS
    Traceable Author Statement
    more info
     
    located_in extracellular exosome HDA PubMed 
    located_in extracellular region TAS
    Traceable Author Statement
    more info
     
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleus HDA PubMed 
    located_in secretory granule lumen TAS
    Traceable Author Statement
    more info
     
    located_in specific granule lumen TAS
    Traceable Author Statement
    more info
     

    General protein information

    Preferred Names
    pyridoxal kinase
    Names
    epididymis secretory sperm binding protein Li 1a
    pyridoxal (pyridoxine, vitamin B6) kinase
    pyridoxamine kinase
    pyridoxine kinase
    vitamin B6 kinase
    NP_001317959.1
    NP_003672.1
    XP_005261252.2
    XP_005261253.1
    XP_005261256.1
    XP_011528063.1
    XP_011528064.1
    XP_047296957.1
    XP_047296958.1
    XP_047296959.1
    XP_047296960.1
    XP_047296961.1
    XP_047296962.1
    XP_054180859.1
    XP_054180860.1
    XP_054180861.1
    XP_054180862.1
    XP_054180863.1
    XP_054180864.1
    XP_054180865.1
    XP_054180866.1
    XP_054180867.1

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001331030.2NP_001317959.1  pyridoxal kinase isoform 2

      Status: REVIEWED

      Source sequence(s)
      AP001052, AP001053
      Consensus CDS
      CCDS82679.1
      UniProtKB/TrEMBL
      F2Z2Y4
      Related
      ENSP00000420708.1, ENST00000467908.1
      Conserved Domains (1) summary
      cl00192
      Location:8264
      ribokinase_pfkB_like; ribokinase/pfkB superfamily: Kinases that accept a wide variety of substrates, including carbohydrates and aromatic small molecules, all are phosphorylated at a hydroxyl group. The superfamily includes ribokinase, fructokinase, ketohexokinase, ...
    2. NM_003681.5NP_003672.1  pyridoxal kinase isoform 1

      See identical proteins and their annotated locations for NP_003672.1

      Status: REVIEWED

      Source sequence(s)
      AP001052, AP001053
      Consensus CDS
      CCDS13699.1
      UniProtKB/Swiss-Prot
      O00764, Q7Z2Y0, Q9BS02
      UniProtKB/TrEMBL
      V9HWC3
      Related
      ENSP00000291565.4, ENST00000291565.9
      Conserved Domains (1) summary
      cl00192
      Location:6304
      ribokinase_pfkB_like; ribokinase/pfkB superfamily: Kinases that accept a wide variety of substrates, including carbohydrates and aromatic small molecules, all are phosphorylated at a hydroxyl group. The superfamily includes ribokinase, fructokinase, ketohexokinase, ...

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000021.9 Reference GRCh38.p14 Primary Assembly

      Range
      43719129..43762299
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047441005.1XP_047296961.1  pyridoxal kinase isoform X5

    2. XM_005261195.3XP_005261252.2  pyridoxal kinase isoform X1

      Conserved Domains (1) summary
      cl00192
      Location:105398
      ribokinase_pfkB_like; ribokinase/pfkB superfamily: Kinases that accept a wide variety of substrates, including carbohydrates and aromatic small molecules, all are phosphorylated at a hydroxyl group. The superfamily includes ribokinase, fructokinase, ketohexokinase, ...
    3. XM_011529762.3XP_011528064.1  pyridoxal kinase isoform X6

      Conserved Domains (1) summary
      cl00192
      Location:105141
      ribokinase_pfkB_like; ribokinase/pfkB superfamily: Kinases that accept a wide variety of substrates, including carbohydrates and aromatic small molecules, all are phosphorylated at a hydroxyl group. The superfamily includes ribokinase, fructokinase, ketohexokinase, ...
    4. XM_047441004.1XP_047296960.1  pyridoxal kinase isoform X5

    5. XM_005261199.3XP_005261256.1  pyridoxal kinase isoform X5

      See identical proteins and their annotated locations for XP_005261256.1

      UniProtKB/Swiss-Prot
      O00764
      Conserved Domains (1) summary
      cl00192
      Location:1231
      ribokinase_pfkB_like; ribokinase/pfkB superfamily: Kinases that accept a wide variety of substrates, including carbohydrates and aromatic small molecules, all are phosphorylated at a hydroxyl group. The superfamily includes ribokinase, fructokinase, ketohexokinase, ...
    6. XM_047441001.1XP_047296957.1  pyridoxal kinase isoform X2

    7. XM_047441006.1XP_047296962.1  pyridoxal kinase isoform X5

    8. XM_005261196.4XP_005261253.1  pyridoxal kinase isoform X3

      Conserved Domains (1) summary
      cl00192
      Location:39313
      ribokinase_pfkB_like; ribokinase/pfkB superfamily: Kinases that accept a wide variety of substrates, including carbohydrates and aromatic small molecules, all are phosphorylated at a hydroxyl group. The superfamily includes ribokinase, fructokinase, ketohexokinase, ...
    9. XM_047441002.1XP_047296958.1  pyridoxal kinase isoform X4

    10. XM_011529761.2XP_011528063.1  pyridoxal kinase isoform X5

      See identical proteins and their annotated locations for XP_011528063.1

      UniProtKB/Swiss-Prot
      O00764
      Conserved Domains (1) summary
      cl00192
      Location:1231
      ribokinase_pfkB_like; ribokinase/pfkB superfamily: Kinases that accept a wide variety of substrates, including carbohydrates and aromatic small molecules, all are phosphorylated at a hydroxyl group. The superfamily includes ribokinase, fructokinase, ketohexokinase, ...
    11. XM_047441003.1XP_047296959.1  pyridoxal kinase isoform X4

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060945.1 Alternate T2T-CHM13v2.0

      Range
      42074671..42117910
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054324889.1XP_054180864.1  pyridoxal kinase isoform X5

    2. XM_054324890.1XP_054180865.1  pyridoxal kinase isoform X6

    3. XM_054324884.1XP_054180859.1  pyridoxal kinase isoform X1

    4. XM_054324891.1XP_054180866.1  pyridoxal kinase isoform X5

    5. XM_054324885.1XP_054180860.1  pyridoxal kinase isoform X2

    6. XM_054324892.1XP_054180867.1  pyridoxal kinase isoform X5

    7. XM_054324886.1XP_054180861.1  pyridoxal kinase isoform X3

    8. XM_054324887.1XP_054180862.1  pyridoxal kinase isoform X4

    9. XM_054324888.1XP_054180863.1  pyridoxal kinase isoform X4

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_021941.1: Suppressed sequence

      Description
      NM_021941.1: This RefSeq was permanently suppressed because it is entirely UTR sequence.