PDXP pyridoxal phosphatase [Homo sapiens (human)] - Gene

Summary

Official Symbol: PDXPprovided by HGNC
Official Full Name: pyridoxal phosphataseprovided by HGNC
Primary source: HGNC:HGNC:30259
See related: Ensembl:ENSG00000241360 MIM:609246; AllianceGenome:HGNC:30259
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: CIN; PLP; dJ37E16.5
Summary: Pyridoxal 5-prime-phosphate (PLP) is the active form of vitamin B6 that acts as a coenzyme in maintaining biochemical homeostasis. The preferred degradation route from PLP to 4-pyridoxic acid involves the dephosphorylation of PLP by PDXP (Jang et al., 2003 [PubMed 14522954]).[supplied by OMIM, Mar 2008]
Expression: Broad expression in brain (RPKM 43.8), small intestine (RPKM 14.2) and 21 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 22q13.1

Exon count:: 2

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	22	NC_000022.11 (37658723..37666932)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	22	NC_060946.1 (38120012..38128169)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	22	NC_000022.10 (38054730..38062939)

Chromosome 22 - NC_000022.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues 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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

In non-adherent glioblastoma cell lines cultured in serum-free medium, chronophin knockdown induces phenotypic changes, e.g. in colony formation and transcription, but these are highly dependent on the cellular background. CIN knockdown in the glioblastoma cell lines NCH421k and NCH644 increased active vitamin B6 levels.
Title: Chronophin regulates active vitamin B6 levels and transcriptomic features of glioblastoma cell lines cultured under non-adherent, serum-free conditions.
Chronophin has a role in coordinating cell leading edge dynamics by controlling active cofilin levels
Title: Chronophin coordinates cell leading edge dynamics by controlling active cofilin levels.
Splicing of SH3BP1 and CIN gene loci produces the novel brain specific splice variant BGIN.
Title: A novel Rac1 GAP splice variant relays poly-Ub accumulation signals to mediate Rac1 inactivation.
analysis of brain pyridoxal-5'-phosphate phosphatase
Title: Human brain pyridoxal-5'-phosphate phosphatase: production and characterization of monoclonal antibodies.
Study demonstrates the ATP-sensitive interaction of the cofilin phosphatase chronophin (CIN) with the chaperone hsp90 to form a biosensor that mediates cofilin/actin rod formation.
Title: Chronophin mediates an ATP-sensing mechanism for cofilin dephosphorylation and neuronal cofilin-actin rod formation.
Results suggest that the transduction of the PEP-1-PLPP fusion protein can be one mode of PLP level regulation, and to replenish this enzyme in the various neurological disorders related to vitamin B(6).
Title: Human brain pyridoxal-5'-phosphate phosphatase (PLPP):protein transduction of PEP-1-PLPP into PC12 cells.
analysis of pyridoxal phosphatase cloning, expression and tissue distribution
Title: Human pyridoxal phosphatase. Molecular cloning, functional expression, and tissue distribution.
We report the biochemical isolation of chronophin (CIN), a unique cofilin-activating phosphatase of the haloacid dehalogenase (HAD) superfamily and an important novel regulator of cofilin-mediated actin reorganization.
Title: Chronophin, a novel HAD-type serine protein phosphatase, regulates cofilin-dependent actin dynamics.

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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

EBI GWAS Catalog

Description
Genes linked to energy metabolism and immunoregulatory mechanisms are associated with subcutaneous adipose tissue distribution in HIV-infected men. EBI GWAS Catalog EBI GWAS CatalogPubMed

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

RH67 (e-PCR)
- UniSTS:87419

WI-19614 (e-PCR)
- UniSTS:11694

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables MAP kinase serine/threonine phosphatase activity	IEA Inferred from Electronic Annotation more info
enables RNA polymerase II CTD heptapeptide repeat S2 phosphatase activity	IEA Inferred from Electronic Annotation more info
enables RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity	IEA Inferred from Electronic Annotation more info
enables RNA polymerase II CTD heptapeptide repeat S7 phosphatase activity	IEA Inferred from Electronic Annotation more info
enables RNA polymerase II CTD heptapeptide repeat T4 phosphatase activity	IEA Inferred from Electronic Annotation more info
enables RNA polymerase II CTD heptapeptide repeat Y1 phosphatase activity	IEA Inferred from Electronic Annotation more info
enables calmodulin-dependent protein phosphatase activity	IEA Inferred from Electronic Annotation more info
enables heat shock protein binding	IDA Inferred from Direct Assay more info	PubMed
enables histone H2AXS140 phosphatase activity	IEA Inferred from Electronic Annotation more info
enables magnesium ion binding	ISS Inferred from Sequence or Structural Similarity more info
enables myosin phosphatase activity	IEA Inferred from Electronic Annotation more info
enables phosphoprotein phosphatase activity	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein homodimerization activity	IEA Inferred from Electronic Annotation more info
enables pyridoxal phosphatase activity	IBA Inferred from Biological aspect of Ancestor more info
enables pyridoxal phosphatase activity	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
acts_upstream_of_or_within actin rod assembly	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within actin rod assembly	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within cellular response to ATP	IDA Inferred from Direct Assay more info	PubMed
involved_in chromatin remodeling	IEA Inferred from Electronic Annotation more info
involved_in dephosphorylation	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of actin filament depolymerization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein dephosphorylation	IDA Inferred from Direct Assay more info	PubMed
involved_in pyridoxal phosphate catabolic process	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of cytokinesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of mitotic nuclear division	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of modification of postsynaptic structure	IEA Inferred from Electronic Annotation more info
involved_in regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
colocalizes_with actin cytoskeleton	IDA Inferred from Direct Assay more info	PubMed
located_in cell-cell junction	IEA Inferred from Electronic Annotation more info
colocalizes_with cleavage furrow	IDA Inferred from Direct Assay more info	PubMed
colocalizes_with contractile ring	IDA Inferred from Direct Assay more info	PubMed
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
is_active_in cytosol	IBA Inferred from Biological aspect of Ancestor more info
located_in cytosol	IDA Inferred from Direct Assay more info	PubMed
located_in glutamatergic synapse	IEA Inferred from Electronic Annotation more info
colocalizes_with lamellipodium	IDA Inferred from Direct Assay more info	PubMed
located_in lamellipodium membrane	IEA Inferred from Electronic Annotation more info
colocalizes_with midbody	IDA Inferred from Direct Assay more info	PubMed
colocalizes_with plasma membrane	IDA Inferred from Direct Assay more info	PubMed
located_in postsynapse	IEA Inferred from Electronic Annotation more info
colocalizes_with ruffle membrane	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: chronophin

Names: PLP phosphatase; pyridoxal (pyridoxine, vitamin B6) phosphatase; pyridoxal phosphate phosphatase; testicular secretory protein Li 36

NP_064711.1

EC 3.1.3.16

EC 3.1.3.74

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.