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PDXK pyridoxal kinase [ Homo sapiens (human) ]

Gene ID: 8566, updated on 6-Jan-2019

Summary

Official Symbol
PDXKprovided by HGNC
Official Full Name
pyridoxal kinaseprovided by HGNC
Primary source
HGNC:HGNC:8819
See related
Ensembl:ENSG00000160209 MIM:179020
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; 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

Genomic context

See PDXK in Genome Data Viewer
Location:
21q22.3
Exon count:
19
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 21 NC_000021.9 (43719097..43762307)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 21 NC_000021.8 (45138978..45182188)

Chromosome 21 - NC_000021.9Genomic Context describing neighboring genes Neighboring gene ribosomal RNA processing 1B Neighboring gene RRP1B-PDXK intergenic CAGE-defined mid-level expression enhancer Neighboring gene uncharacterized LOC105372824 Neighboring gene PDXK-CSTB intergenic CAGE-defined low expression enhancer 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 FunctionsWhat's a GeneRIF?

Pathways from BioSystems

  • Immune System, organism-specific biosystem (from REACTOME)
    Immune System, organism-specific biosystemHumans are exposed to millions of potential pathogens daily, through contact, ingestion, and inhalation. Our ability to avoid infection depends on the adaptive immune system and during the first crit...
  • Innate Immune System, organism-specific biosystem (from REACTOME)
    Innate Immune System, organism-specific biosystemInnate immunity encompases the nonspecific part of immunity tha are part of an individual's natural biologic makeup
  • Metabolic pathways, organism-specific biosystem (from KEGG)
    Metabolic pathways, organism-specific biosystem
    Metabolic pathways
  • Metabolism, organism-specific biosystem (from REACTOME)
    Metabolism, organism-specific biosystemMetabolic processes in human cells generate energy through the oxidation of molecules consumed in the diet and mediate the synthesis of diverse essential molecules not taken in the diet as well as th...
  • Metabolism of vitamins and cofactors, organism-specific biosystem (from REACTOME)
    Metabolism of vitamins and cofactors, organism-specific biosystemVitamins are a diverse group of organic compounds, classified according to their solubility, either fat-soluble or water-soluble, that are either not synthesized or synthesized only in limited amount...
  • Metabolism of water-soluble vitamins and cofactors, organism-specific biosystem (from REACTOME)
    Metabolism of water-soluble vitamins and cofactors, organism-specific biosystemVitamins are a diverse group of organic compounds, required in small amounts in the diet. They have distinct biochemical roles, often as coenzymes, and are either not synthesized or synthesized only ...
  • Neutrophil degranulation, organism-specific biosystem (from REACTOME)
    Neutrophil degranulation, organism-specific biosystemNeutrophils are the most abundant leukocytes (white blood cells), indispensable in defending the body against invading microorganisms. In response to infection, neutrophils leave the circulation and ...
  • Vitamin B6 metabolism, organism-specific biosystem (from KEGG)
    Vitamin B6 metabolism, organism-specific biosystem
    Vitamin B6 metabolism
  • Vitamin B6 metabolism, conserved biosystem (from KEGG)
    Vitamin B6 metabolism, conserved biosystem
    Vitamin B6 metabolism
  • Vitamins B6 activation to pyridoxal phosphate, organism-specific biosystem (from REACTOME)
    Vitamins B6 activation to pyridoxal phosphate, organism-specific biosystemAnimals cannot synthesize pyridoxal 5'-phosphate (PLP) which is a ligand in aminotransferases and other enzymes. PLP's accessible derivatives pyridoxine, pyridoxal, and pyridoxamine are traditionally...
  • pyridoxal 5'-phosphate salvage, organism-specific biosystem (from BIOCYC)
    pyridoxal 5'-phosphate salvage, organism-specific biosystemGeneral Background : PYRIDOXAL_PHOSPHATE "Pyridoxal-5'-phosphate" (PLP) is a pyridine compound that belongs to the ensemble of vitamin B6 compounds that include : PYRIDOXAL, : PYRIDOXAMINE and : PYR...
  • pyridoxal 5'-phosphate salvage I, conserved biosystem (from BIOCYC)
    pyridoxal 5'-phosphate salvage I, conserved biosystemPyridoxal 5'-phosphate (PLP) , a coenzyme for many enzymes that participate in amino acid and glycogen metabolism, can be synthesized de novo and by salvage pathways from pyridoxal, pyroxidine an...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

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

Gene Ontology Provided by GOA

Function Evidence Code Pubs
ATP binding IDA
Inferred from Direct Assay
more info
PubMed 
lithium ion binding IDA
Inferred from Direct Assay
more info
PubMed 
magnesium ion binding IDA
Inferred from Direct Assay
more info
PubMed 
potassium ion binding IDA
Inferred from Direct Assay
more info
PubMed 
protein homodimerization activity IDA
Inferred from Direct Assay
more info
PubMed 
pyridoxal kinase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
pyridoxal kinase activity IDA
Inferred from Direct Assay
more info
PubMed 
pyridoxal kinase activity TAS
Traceable Author Statement
more info
 
pyridoxal phosphate binding IDA
Inferred from Direct Assay
more info
PubMed 
sodium ion binding IDA
Inferred from Direct Assay
more info
PubMed 
zinc ion binding IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
cell proliferation IDA
Inferred from Direct Assay
more info
PubMed 
neutrophil degranulation TAS
Traceable Author Statement
more info
 
phosphorylation IEA
Inferred from Electronic Annotation
more info
 
pyridoxal 5'-phosphate salvage IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
pyridoxal phosphate biosynthetic process IDA
Inferred from Direct Assay
more info
PubMed 
vitamin B6 metabolic process IC
Inferred by Curator
more info
PubMed 
vitamin B6 metabolic process TAS
Traceable Author Statement
more info
 
Component Evidence Code Pubs
cytosol HDA PubMed 
cytosol IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytosol TAS
Traceable Author Statement
more info
 
extracellular exosome HDA PubMed 
extracellular region TAS
Traceable Author Statement
more info
 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleus HDA PubMed 
secretory granule lumen TAS
Traceable Author Statement
more info
 
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_011528060.1
XP_011528062.1
XP_011528063.1
XP_011528064.1
XP_016883972.1
XP_016883973.1

NCBI Reference Sequences (RefSeq)

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_001331030.1NP_001317959.1  pyridoxal kinase isoform 2

    Status: REVIEWED

    Source sequence(s)
    AP001052, BX382033, BX382034, EU794642
    Consensus CDS
    CCDS82679.1
    UniProtKB/TrEMBL
    F2Z2Y4, V9HWC3
    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
    UniProtKB/TrEMBL
    V9HWC3
    Related
    ENSP00000291565.4, ENST00000291565.8
    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: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000021.9 Reference GRCh38.p12 Primary Assembly

    Range
    43719097..43762307
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011529762.2XP_011528064.1  pyridoxal kinase isoform X5

    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, ...
  2. XM_005261195.2XP_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_005261199.2XP_005261256.1  pyridoxal kinase isoform X4

    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, ...
  4. XM_011529758.3XP_011528060.1  pyridoxal kinase isoform X2

    See identical proteins and their annotated locations for XP_011528060.1

    Conserved Domains (1) summary
    cl00192
    Location:91365
    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, ...
  5. XM_017028483.2XP_016883972.1  pyridoxal kinase isoform X4

    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_017028484.1XP_016883973.1  pyridoxal kinase isoform X4

    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, ...
  7. XM_005261196.3XP_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, ...
  8. XM_011529760.2XP_011528062.1  pyridoxal kinase isoform X4

    See identical proteins and their annotated locations for XP_011528062.1

    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, ...
  9. XM_011529761.1XP_011528063.1  pyridoxal kinase isoform X4

    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, ...

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.
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