PDXK pyridoxal kinase [Homo sapiens (human)] - Gene

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: mouse all
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Genomic context

Location:: 21q22.3

Exon count:: 19

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	21	NC_000021.9 (43719129..43762299)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	21	NC_060945.1 (42074671..42117910)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	21	NC_000021.8 (45139010..45182180)

Chromosome 21 - NC_000021.9 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

The expression of four pyridoxal kinase (PDXK) human variants in Drosophila impacts on genome integrity.
Title: The expression of four pyridoxal kinase (PDXK) human variants in Drosophila impacts on genome integrity.
[Pyridoxal kinase (PDXK) promotes the proliferation of serous ovarian cancer cells and is associated with poor prognosis].
Title: [Pyridoxal kinase (PDXK) promotes the proliferation of serous ovarian cancer cells and is associated with poor prognosis].
The affected pyridoxine metabolism is discussed as an inborn genetic trait in epilepsy in general, rather than a specific sign of pyridoxine-dependent epilepsy solely.
Title: Epilepsy as a pyridoxine-dependent condition: quantified urinary biomarkers for status evaluation and monitoring antiepileptic treatment.
The pyridoxal kinase showed decreased levels and was highly carbonylated in the gene-on mice
Title: Protein oxidation in Huntington disease affects energy production and vitamin B6 metabolism.
This study identified a DNA variant (rs2010795) in PDXK associated with an increased risk of PD in the German cohort This association was confirmed in the British and Italian cohorts individually and reached a combined value.
Title: Single-cell expression profiling of dopaminergic neurons combined with association analysis identifies pyridoxal kinase as Parkinson's disease gene.
These results document the role of Asp235 in PL kinase activity.
Title: Kinetic and structural studies of the role of the active site residue Asp235 of human pyridoxal kinase.
Observational study of gene-disease association. (HuGE Navigator)
Title: The PDXK rs2010795 variant is not associated with Parkinson disease in Italy.
The crystal structure of the MgATP complex also reveals Mg(2+) and Na(+) acting in tandem to anchor the ATP at the active site of pyridoxal kinase.
Title: Crystal Structure of human pyridoxal kinase: structural basis of M(+) and M(2+) activation.
Pyridoxal kinase expression was compared in fetal Down syndrome (DS) brain and controls; PDXK levels were found to be similar.
Title: Expression of cystathionine beta-synthase, pyridoxal kinase, and ES1 protein homolog (mitochondrial precursor) in fetal Down syndrome brain.
A promoter mutation with potential erythroid-specific properties that could be the basis of a novel mechanism of controlling cell-specific decreased activity of an essential enzyme in erythrocytes.
Title: The genetic basis of human erythrocyte pyridoxal kinase activity variation.

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Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Neuropathy, hereditary motor and sensory, type VIc, with optic atrophy MedGen: C5193137 OMIM: 618511 GeneReviews: Not available	Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH66292 (e-PCR)
- UniSTS:53767

SHGC-87677 (e-PCR)
- UniSTS:81165

STS_CEB242 (e-PCR)
- UniSTS:255247

D21S1868 (e-PCR)
- UniSTS:16656

T03311 (e-PCR)
- UniSTS:17173

D21S1859 (e-PCR)
- UniSTS:50467

SHGC-87681 (e-PCR)
- UniSTS:26918

D5S2354 (e-PCR)
- UniSTS:473392

SHGC-149770 (e-PCR)
- UniSTS:177210

G34624 (e-PCR)
- UniSTS:47424

RH36279 (e-PCR)
- UniSTS:5978

G60049 (e-PCR)
- UniSTS:137312

PDXK_8833 (e-PCR)
- UniSTS:468588

bnlg1246b (e-PCR), detects polymorphism
- UniSTS:472187

RH35999 (e-PCR)
- UniSTS:1662

RH120396 (e-PCR)
- UniSTS:132539

SHGC-52026 (e-PCR)
- UniSTS:63675

WIAF-2214 (e-PCR)
- UniSTS:24764

RH120729 (e-PCR)
- UniSTS:132810

SHGC-51899 (e-PCR)
- UniSTS:6347

SHGC-112512 (e-PCR)
- UniSTS:168667

D21S1981 (e-PCR)
- UniSTS:46054

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 more info	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 more info	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 more info	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

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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

EC 2.7.1.35

NP_003672.1

EC 2.7.1.35

XP_005261252.2

EC 2.7.1.35

XP_005261253.1

EC 2.7.1.35

XP_005261256.1

EC 2.7.1.35

XP_011528063.1

EC 2.7.1.35

XP_011528064.1

EC 2.7.1.35

XP_047296957.1

EC 2.7.1.35

XP_047296958.1

EC 2.7.1.35

XP_047296959.1

EC 2.7.1.35

XP_047296960.1

EC 2.7.1.35

XP_047296961.1

EC 2.7.1.35

XP_047296962.1

EC 2.7.1.35

XP_054180859.1

EC 2.7.1.35

XP_054180860.1

EC 2.7.1.35

XP_054180861.1

EC 2.7.1.35

XP_054180862.1

EC 2.7.1.35

XP_054180863.1

EC 2.7.1.35

XP_054180864.1

EC 2.7.1.35

XP_054180865.1

EC 2.7.1.35

XP_054180866.1

EC 2.7.1.35

XP_054180867.1

EC 2.7.1.35

NCBI Reference Sequences (RefSeq)

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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)

NM_001331030.2 → NP_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:8 → 264

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, ...
NM_003681.5 → NP_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:6 → 304

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_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000021.9 Reference GRCh38.p14 Primary Assembly

Range

43719129..43762299

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047441005.1 → XP_047296961.1 pyridoxal kinase isoform X5
XM_005261195.3 → XP_005261252.2 pyridoxal kinase isoform X1

Conserved Domains (1) summary

cl00192
Location:105 → 398

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, ...
XM_011529762.3 → XP_011528064.1 pyridoxal kinase isoform X6

Conserved Domains (1) summary

cl00192
Location:105 → 141

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, ...
XM_047441004.1 → XP_047296960.1 pyridoxal kinase isoform X5
XM_005261199.3 → XP_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:1 → 231

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, ...
XM_047441001.1 → XP_047296957.1 pyridoxal kinase isoform X2
XM_047441006.1 → XP_047296962.1 pyridoxal kinase isoform X5
XM_005261196.4 → XP_005261253.1 pyridoxal kinase isoform X3

Conserved Domains (1) summary

cl00192
Location:39 → 313

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, ...
XM_047441002.1 → XP_047296958.1 pyridoxal kinase isoform X4
XM_011529761.2 → XP_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:1 → 231

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, ...
XM_047441003.1 → XP_047296959.1 pyridoxal kinase isoform X4