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Aliases for PDXK Gene

Aliases for PDXK Gene

  • Pyridoxal (Pyridoxine, Vitamin B6) Kinase 2 3 5
  • Pyridoxine Kinase 3 4
  • EC 2.7.1.35 4 63
  • C21orf124 3 4
  • C21orf97 3 4
  • PKH 3 4
  • PNK 3 4
  • Epididymis Secretory Sperm Binding Protein Li 1a 3
  • Chromosome 21 Open Reading Frame 124 2
  • Chromosome 21 Open Reading Frame 97 2
  • Pyridoxamine Kinase 3
  • Vitamin B6 Kinase 3
  • HEL-S-1a 3
  • PRED79 3

External Ids for PDXK Gene

Previous HGNC Symbols for PDXK Gene

  • C21orf97
  • C21orf124

Previous GeneCards Identifiers for PDXK Gene

  • GC21P041648
  • GC21P043996
  • GC21P043997
  • GC21P043998
  • GC21P043964
  • GC21P043965
  • GC21P045138
  • GC21P030506

Summaries for PDXK Gene

Entrez Gene Summary for PDXK Gene

  • 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]

GeneCards Summary for PDXK Gene

PDXK (Pyridoxal (Pyridoxine, Vitamin B6) Kinase) is a Protein Coding gene. Among its related pathways are Vitamin B6 metabolism and Metabolism of water-soluble vitamins and cofactors. GO annotations related to this gene include protein homodimerization activity and pyridoxal phosphate binding.

UniProtKB/Swiss-Prot for PDXK Gene

  • Required for synthesis of pyridoxal-5-phosphate from vitamin B6.

Gene Wiki entry for PDXK Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PDXK Gene

Genomics for PDXK Gene

Regulatory Elements for PDXK Gene

Enhancers for PDXK Gene
GeneHancer Identifier Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

Enhancers around PDXK on UCSC Golden Path with GeneCards custom track

Promoters for PDXK Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around PDXK on UCSC Golden Path with GeneCards custom track

Genomic Location for PDXK Gene

Chromosome:
21
Start:
43,719,094 bp from pter
End:
43,762,307 bp from pter
Size:
43,214 bases
Orientation:
Plus strand

Genomic View for PDXK Gene

Genes around PDXK on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PDXK Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PDXK Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PDXK Gene

Proteins for PDXK Gene

  • Protein details for PDXK Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O00764-PDXK_HUMAN
    Recommended name:
    Pyridoxal kinase
    Protein Accession:
    O00764
    Secondary Accessions:
    • Q7Z2Y0
    • Q9BS02

    Protein attributes for PDXK Gene

    Size:
    312 amino acids
    Molecular mass:
    35102 Da
    Cofactor:
    Name=Zn(2+); Xref=ChEBI:CHEBI:29105; Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
    Quaternary structure:
    • Homodimer.

    Three dimensional structures from OCA and Proteopedia for PDXK Gene

    Alternative splice isoforms for PDXK Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PDXK Gene

Proteomics data for PDXK Gene at MOPED

Selected DME Specific Peptides for PDXK Gene

Post-translational modifications for PDXK Gene

  • Ubiquitination at Lys 76, Lys 139, and Lys 275
  • Modification sites at PhosphoSitePlus

Other Protein References for PDXK Gene

Domains & Families for PDXK Gene

Protein Domains for PDXK Gene

Suggested Antigen Peptide Sequences for PDXK Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

O00764

UniProtKB/Swiss-Prot:

PDXK_HUMAN :
  • Belongs to the pyridoxine kinase family.
Family:
  • Belongs to the pyridoxine kinase family.
genes like me logo Genes that share domains with PDXK: view

No data available for Gene Families for PDXK Gene

Function for PDXK Gene

Molecular function for PDXK Gene

GENATLAS Biochemistry:
pyridoxal kinase,ubiquitously expressed,repressed by ligands of the benzodiazepine receptor
UniProtKB/Swiss-Prot BiophysicochemicalProperties:
pH dependence: Optimum pH is 5.5-6.0.;
UniProtKB/Swiss-Prot CatalyticActivity:
ATP + pyridoxal = ADP + pyridoxal 5-phosphate.
UniProtKB/Swiss-Prot Function:
Required for synthesis of pyridoxal-5-phosphate from vitamin B6.

Enzyme Numbers (IUBMB) for PDXK Gene

Gene Ontology (GO) - Molecular Function for PDXK Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000287 magnesium ion binding IDA 17766369
GO:0042803 protein homodimerization activity IDA 16600635
genes like me logo Genes that share ontologies with PDXK: view
genes like me logo Genes that share phenotypes with PDXK: view

Animal Models for PDXK Gene

MGI Knock Outs for PDXK:
  • Pdxk tm1a(EUCOMM)Wtsi

Animal Model Products

  • Taconic Biosciences Mouse Models for PDXK

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for PDXK Gene

Localization for PDXK Gene

Subcellular locations from UniProtKB/Swiss-Prot for PDXK Gene

Cytoplasm.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for PDXK Gene COMPARTMENTS Subcellular localization image for PDXK gene
Compartment Confidence
cytosol 5
extracellular 5
nucleus 5
cytoskeleton 2
plasma membrane 2

Gene Ontology (GO) - Cellular Components for PDXK Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IDA --
GO:0070062 extracellular exosome IDA 19056867
genes like me logo Genes that share ontologies with PDXK: view

Pathways & Interactions for PDXK Gene

genes like me logo Genes that share pathways with PDXK: view

Pathways by source for PDXK Gene

Gene Ontology (GO) - Biological Process for PDXK Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006767 water-soluble vitamin metabolic process TAS --
GO:0009443 pyridoxal 5-phosphate salvage IEA,IBA --
GO:0042816 vitamin B6 metabolic process TAS --
GO:0044281 small molecule metabolic process TAS --
genes like me logo Genes that share ontologies with PDXK: view

No data available for SIGNOR curated interactions for PDXK Gene

Drugs & Compounds for PDXK Gene

(16) Drugs for PDXK Gene - From: DrugBank, HMDB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Pyridoxal Approved Nutra Target 175
Pyridoxine Approved Nutra Target, ligand 176,176
Adenosine triphosphate Approved Nutra 0
Adenosine-5'-[Beta, Gamma-Methylene]Triphosphate Experimental Pharma Target 0
N6-METHYL-(R)-ROSCOVITINE, R-2-[6-(BENZYL-METHYL-AMINO)-9-ISOPROPYL-9H-PURIN-2-YLAMINO]-BUTAN-1-OL Experimental Pharma Target 0

(6) Additional Compounds for PDXK Gene - From: HMDB and Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
ADP
  • Adenosindiphosphorsaeure
  • Adenosine 5'-pyrophosphate
  • Adenosine diphosphate
  • Adenosine pyrophosphate
  • Adenosine-5'-diphosphate
Full agonist, Agonist 58-64-0
genes like me logo Genes that share compounds with PDXK: view

Transcripts for PDXK Gene

Unigene Clusters for PDXK Gene

Pyridoxal (pyridoxine, vitamin B6) kinase:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for PDXK Gene

ExUns: 1 ^ 2 ^ 3 ^ 4a · 4b · 4c · 4d ^ 5a · 5b · 5c ^ 6 ^ 7a · 7b ^ 8 ^ 9a · 9b ^ 10 ^ 11 ^ 12a · 12b ^ 13 ^ 14 ^ 15 ^ 16a · 16b ^ 17 ^
SP1: - - - - - - - - - - - - - - -
SP2: - - - - - - - - - - - - - - - -
SP3: - -
SP4:
SP5: - - - - - - - - -
SP6: - - - - - - - - - - - - -
SP7: - - -
SP8: - -
SP9: - - -
SP10: - - - - - - - - -
SP11:
SP12: -
SP13: - - - - -

ExUns: 18a · 18b · 18c · 18d
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8: -
SP9:
SP10:
SP11:
SP12:
SP13:

Relevant External Links for PDXK Gene

GeneLoc Exon Structure for
PDXK
ECgene alternative splicing isoforms for
PDXK

Expression for PDXK Gene

mRNA expression in normal human tissues for PDXK Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for PDXK Gene

This gene is overexpressed in Nasopharynx (8.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MOPED, and MaxQB for PDXK Gene



SOURCE GeneReport for Unigene cluster for PDXK Gene Hs.284491

mRNA Expression by UniProt/SwissProt for PDXK Gene

O00764-PDXK_HUMAN
Tissue specificity: Ubiquitous. Isoform 3 is detected in adult testis and spermatozoa.
genes like me logo Genes that share expression patterns with PDXK: view

Protein tissue co-expression partners for PDXK Gene

- Elite partner

Primer Products

No data available for mRNA differential expression in normal tissues for PDXK Gene

Orthologs for PDXK Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for PDXK Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia PDXK 35
  • 86 (n)
  • 86.86 (a)
PDXK 36
  • 87 (a)
OneToOne
dog
(Canis familiaris)
Mammalia PDXK 35
  • 84.14 (n)
  • 85.52 (a)
PDXK 36
  • 87 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Pdxk 35
  • 84.72 (n)
  • 86.22 (a)
Pdxk 16
Pdxk 36
  • 86 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia PDXK 35
  • 98.82 (n)
  • 98.4 (a)
PDXK 36
  • 98 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Pdxk 35
  • 83.55 (n)
  • 85.26 (a)
oppossum
(Monodelphis domestica)
Mammalia PDXK 36
  • 78 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia PDXK 36
  • 75 (a)
OneToOne
chicken
(Gallus gallus)
Aves PDXK 35
  • 75.46 (n)
  • 79.74 (a)
PDXK 36
  • 77 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia PDXK 36
  • 80 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia pdxk 35
  • 70.44 (n)
  • 72.17 (a)
zebrafish
(Danio rerio)
Actinopterygii LOC100535341 35
  • 69.3 (n)
  • 74.67 (a)
PDXK (1 of 3) 36
  • 74 (a)
OneToMany
pdxka 36
  • 65 (a)
OneToMany
pdxkb 36
  • 67 (a)
OneToMany
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.60 35
fruit fly
(Drosophila melanogaster)
Insecta CG4446 37
  • 47 (a)
CG34455 35
  • 55.94 (n)
  • 49.48 (a)
CG34455 36
  • 47 (a)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP005929 35
  • 55.37 (n)
  • 47.26 (a)
worm
(Caenorhabditis elegans)
Secernentea F57C9.1a 37
  • 39 (a)
F57C9.1b 37
  • 40 (a)
F57C9.1 35
  • 51.13 (n)
  • 43.88 (a)
F57C9.1 36
  • 38 (a)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes BUD16 36
  • 34 (a)
OneToMany
BUD17 36
  • 32 (a)
OneToMany
BUD16 38
thale cress
(Arabidopsis thaliana)
eudicotyledons SOS4 35
  • 51.9 (n)
  • 50.17 (a)
rice
(Oryza sativa)
Liliopsida Os12g0600400 35
  • 52.36 (n)
  • 51.21 (a)
wheat
(Triticum aestivum)
Liliopsida Ta.27523 35
corn
(Zea mays)
Liliopsida Zm.3752 35
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.4083 35
sea squirt
(Ciona savignyi)
Ascidiacea CSA.8531 36
  • 59 (a)
OneToOne
Species with no ortholog for PDXK:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)

Evolution for PDXK Gene

ENSEMBL:
Gene Tree for PDXK (if available)
TreeFam:
Gene Tree for PDXK (if available)

Paralogs for PDXK Gene

(2) SIMAP similar genes for PDXK Gene using alignment to 5 proteins:

Pseudogenes.org Pseudogenes for PDXK Gene

genes like me logo Genes that share paralogs with PDXK: view

No data available for Paralogs for PDXK Gene

Variants for PDXK Gene

Sequence variations from dbSNP and Humsavar for PDXK Gene

SNP ID Clin Chr 21 pos Sequence Context AA Info Type
rs1076843 -- 43,750,017(+) GGTCT(C/T)GAGCC intron-variant
rs1076844 -- 43,750,811(-) TGCGC(A/G)CACAC intron-variant
rs1079268 -- 43,750,699(-) ACACA(C/T)ATATC intron-variant
rs1106797 -- 43,750,404(+) TGGGG(A/G)TTTCC intron-variant
rs1107204 -- 43,718,237(-) TGCAG(A/C)CATGG upstream-variant-2KB

Structural Variations from Database of Genomic Variants (DGV) for PDXK Gene

Variant ID Type Subtype PubMed ID
nsv913873 CNV Loss 21882294
nsv913874 CNV Loss 21882294
nsv913875 CNV Loss 21882294
dgv4761n71 CNV Loss 21882294
dgv4762n71 CNV Loss 21882294
nsv509799 CNV Insertion 20534489
nsv913879 CNV Gain 21882294
nsv470904 CNV Loss 18288195
nsv913882 CNV Loss 21882294
esv33771 CNV Gain 17666407
nsv834107 CNV Loss 17160897
esv25264 CNV Loss 19812545
esv2664281 CNV Deletion 23128226
esv1717308 CNV Insertion 17803354
esv33817 CNV Loss 17666407
nsv459291 CNV Loss 19166990
nsv520305 CNV Loss 19592680
nsv834108 CNV Loss 17160897

Variation tolerance for PDXK Gene

Residual Variation Intolerance Score: 45.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.50; 29.27% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for PDXK Gene

Human Gene Mutation Database (HGMD)
PDXK

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PDXK Gene

Disorders for PDXK Gene

Relevant External Links for PDXK

Genetic Association Database (GAD)
PDXK
Human Genome Epidemiology (HuGE) Navigator
PDXK
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
PDXK

No disorders were found for PDXK Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for PDXK Gene

Publications for PDXK Gene

  1. Human pyridoxal kinase. cDNA cloning, expression, and modulation by ligands of the benzodiazepine receptor. (PMID: 9099727) Hanna M.C. … Kirkness E.F. (J. Biol. Chem. 1997) 2 3 4 23 67
  2. Abnormally high plasma levels of vitamin B6 in children with autism not taking supplements compared to controls not taking supplements. (PMID: 16494569) Adams J.B. … Audhya T. (J Altern Complement Med 2006) 23 25 26
  3. Crystal structure of pyridoxal kinase in complex with roscovitine and derivatives. (PMID: 15985434) Tang L. … Liang D.C. (J. Biol. Chem. 2005) 23 25 26
  4. Kinetic and structural studies of the role of the active site residue Asp235 of human pyridoxal kinase. (PMID: 19351586) Gandhi A.K. … Safo M.K. (Biochem. Biophys. Res. Commun. 2009) 3 23
  5. Single-cell expression profiling of dopaminergic neurons combined with association analysis identifies pyridoxal kinase as Parkinson's disease gene. (PMID: 20035503) Elstner M. … Turnbull D.M. (Ann. Neurol. 2009) 3 23

Products for PDXK Gene

Sources for PDXK Gene

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