PDXK pyridoxal (pyridoxine, vitamin B6) kinase [Homo sapiens] - Gene

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Summary

Official Symbol: PDXKprovided by HGNC
Official Full Name: pyridoxal (pyridoxine, vitamin B6) kinaseprovided by HGNC
Primary source: HGNC:8819
Locus tag: PRED79
See related: Ensembl:ENSG00000160209; HPRD:01526; MIM:179020; Vega:OTTHUMG00000086870
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; C21orf124; FLJ31940; FLJ37311; MGC15873; MGC31754; MGC52346; DKFZp566A071
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]

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Genomic context

Location :: 21q22.3

Sequence :: Chromosome: 21; NC_000021.8 (45138978..45182188)

See PDXK in Epigenomics, MapViewer

Chromosome 21 - NC_000021.8 Genomic Context describing neighboring genes

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Genomic regions, transcripts, and products

Genomic Sequence

Go to nucleotideGraphics FASTA GenBank

Go to reference sequence details

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Bibliography

GeneRIFs: Gene References Into Functions What's a GeneRIF?

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.

Submit: New GeneRIF Correction

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Phenotypes

Review eQTL and phenotype association data in this region using PheGenI

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description
BioGRID:114135	BioGRID:113164	UBC		BioGRID	PubMed	Affinity Capture-MS; Co-purification
BioGRID:114135	BioGRID:116168	YWHAQ		BioGRID	PubMed	Affinity Capture-MS

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
nucleotide binding	IEA Inferred from Electronic Annotation more info
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	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
transferase activity	IEA Inferred from Electronic Annotation more info
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
pyridoxal 5'-phosphate salvage	IEA Inferred from Electronic Annotation more info
pyridoxal phosphate biosynthetic process	IDA Inferred from Direct Assay more info	PubMed
small molecule metabolic process	TAS Traceable Author Statement more info
vitamin B6 metabolic process	IC Inferred by Curator more info	PubMed
vitamin B6 metabolic process	TAS Traceable Author Statement more info
vitamin metabolic process	TAS Traceable Author Statement more info
water-soluble vitamin metabolic process	TAS Traceable Author Statement more info

Component	Evidence Code	Pubs
cytoplasm	IDA Inferred from Direct Assay more info	PubMed
cytosol	IDA Inferred from Direct Assay more info	PubMed
cytosol	TAS Traceable Author Statement more info
NOT nucleolus	IDA Inferred from Direct Assay more info	PubMed
nucleus	IDA Inferred from Direct Assay more info	PubMed

General protein information

Preferred Names: pyridoxal kinase

Names: pyridoxal kinase; pyridoxine kinase; vitamin B6 kinase; pyridoxamine kinase

NP_003672.1

EC 2.7.1.35

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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)

NM_003681.4 → NP_003672.1 pyridoxal kinase

Status: REVIEWED

Source sequence(s)

AP001052, AP001053, AW245602, BC000123, BC005825, CX867421, DA116202, DA398180, DA736443, DA772127, DB010203

Consensus CDS

CCDS13699.1

UniProtKB/Swiss-Prot

O00764

Related

ENSP00000291565, OTTHUMP00000109454, ENST00000291565, OTTHUMT00000195636

Conserved Domains (2) summary

cd01173
Location:6 – 272
Blast Score: 766

pyridoxal_pyridoxamine_kinase; Pyridoxal kinase plays a key role in the synthesis of the active coenzyme pyridoxal-5'-phosphate (PLP), by catalyzing the phosphorylation of the precursor vitamin B6 in the presence of Zn2+ and ATP. Mammals are unable to synthesize PLP de novo and ...

PRK05756
Location:7 – 312
Blast Score: 592

PRK05756; pyridoxamine kinase; Validated

RefSeqs of Annotated Genomes: Build 37.3

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

Reference GRCh37.p5 Primary Assembly

Genomic

NC_000021.8 Reference GRCh37.p5 Primary Assembly

Range

45138978..45182188

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Alternate HuRef

Genomic

AC_000153.1 Alternate HuRef

Range

30506765..30550585

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_021941.1: Suppressed sequence

Description

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

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Related Sequences

Nucleotide		Protein
Heading	Accession and Version	Protein
genomic	AL122067.1	None
genomic	AP001052.1 (90893..129951)	None
genomic	AP001053.1	None
genomic	AP001752.1	BAA95540.1
genomic	CH471079.2	EAX09475.1
genomic	HH961854.1	CBX51400.1
mRNA	AB621819.1	BAK64155.1
mRNA	AI131245.1	None
mRNA	AI652877.1	None
mRNA	AK024977.1	BAB15048.1
mRNA	AK027018.1	None
mRNA	AK056502.1	None
mRNA	AK094630.1	None
mRNA	AK225206.1	None
mRNA	AL109793.1	None
mRNA	AL110184.1	None
mRNA	AL137632.1	None
mRNA	AL161960.1	None
mRNA	AL355712.1	None
mRNA	AL355713.1	None
mRNA	AW245602.1	None
mRNA	AW245860.1	None
mRNA	AY303972.1	AAP73047.1
mRNA	BC000123.1	AAH00123.1
mRNA	BC003651.2	None
mRNA	BC005825.2	AAH05825.1
mRNA	BC008008.1	AAH08008.1
mRNA	BC021550.1	AAH21550.1
mRNA	BC041020.1	AAH41020.1
mRNA	BC063541.1	None
mRNA	BE671761.1	None
mRNA	BI871733.1	None
mRNA	BQ653540.1	None
mRNA	BU192292.1	None
mRNA	CB989301.1	None
mRNA	CX867421.1	None
mRNA	DA116202.1	None
mRNA	DA398180.1	None
mRNA	DA736443.1	None
mRNA	DA772127.1	None
mRNA	DB010203.1	None
mRNA	U89606.1	AAC51233.1