Pdxp pyridoxal (pyridoxine, vitamin B6) phosphatase [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Pdxpprovided by MGI
Official Full Name: pyridoxal (pyridoxine, vitamin B6) phosphataseprovided by MGI
Primary source: MGI:MGI:1919282
See related: Ensembl:ENSMUSG00000116165 AllianceGenome:MGI:1919282
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: PLPP; 1600027H05Rik
Summary: Enables magnesium ion binding activity; protein homodimerization activity; and pyridoxal phosphatase activity. Involved in dephosphorylation; pyridoxal phosphate catabolic process; and regulation of modification of postsynaptic structure. Located in cell-cell junction. Is active in glutamatergic synapse and postsynapse. Is expressed in alimentary system; eye; limb; nervous system; and tail. Orthologous to human PDXP (pyridoxal phosphatase). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Broad expression in cortex adult (RPKM 56.1), frontal lobe adult (RPKM 56.0) and 17 other tissues See more
Orthologs: human all
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Genomic context

Location:: 15 E1; 15 37.7 cM

Exon count:: 2

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	15	NC_000081.7 (78796342..78803717)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	15	NC_000081.6 (78912160..78919517)

Chromosome 15 - NC_000081.7 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: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

PLPP/CIN-mediated NF2-serine 10 dephosphorylation regulates F-actin stability and Mdm2 degradation in an activity-dependent manner.
Title: PLPP/CIN-mediated NF2-serine 10 dephosphorylation regulates F-actin stability and Mdm2 degradation in an activity-dependent manner.
PLPP/CIN deletion inhibited NEDD4-2 ubiquitination, and diminished the responsiveness of alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor by facilitating NEDD4-2-mediated ubiquitination of GluA1 subunit under physiological condition. PLPP/CIN overexpression reversed these effects. These PLPP/CIN-mediated processes were required for the increased seizure severity and its progression in response to kaini...
Title: PLPP/CIN-mediated NEDD4-2 S448 dephosphorylation regulates neuronal excitability via GluA1 ubiquitination.
Results provided novel evidence that PLPP is involved in controlling dendritic spine as well as synaptic plasticity. It showed also for the first time the role of PLPP in GluN functionality via regulation of GluN2A interaction with postsynaptic proteins. These findings suggest that PLPP/CIN may play an important role in information storage and recall capacity, which manifests as a learning memory.
Title: PLPP/CIN regulates bidirectional synaptic plasticity via GluN2A interaction with postsynaptic proteins.
Dimer formation is essential for an intermolecular arginine-arginine-tryptophan stacking interaction that positions a critical histidine residue in the substrate specificity loop of chronophin for PLP coordination.
Title: Chronophin dimerization is required for proper positioning of its substrate specificity loop.
Evolutionary and structural analyses of mammalian haloacid dehalogenase-type phosphatases AUM and chronophin provide insight into the basis of their different substrate specificities.
Title: Evolutionary and structural analyses of mammalian haloacid dehalogenase-type phosphatases AUM and chronophin provide insight into the basis of their different substrate specificities.
analysis of pyridoxal phosphatase cloning, expression and tissue distribution
Title: Human pyridoxal phosphatase. Molecular cloning, functional expression, and tissue distribution.

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Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Endonuclease-mediated (1)
Targeted (3) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by MGI

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 growth factor binding	ISO Inferred from Sequence Orthology more info
enables heat shock protein binding	ISO Inferred from Sequence Orthology more info	PubMed
enables histone H2AXS140 phosphatase activity	IEA Inferred from Electronic Annotation more info
enables magnesium ion binding	IDA Inferred from Direct Assay more info	PubMed
enables myosin phosphatase activity	IEA Inferred from Electronic Annotation more info
enables phosphoprotein phosphatase activity	ISO Inferred from Sequence Orthology more info	PubMed
enables phosphoprotein phosphatase activity	ISS Inferred from Sequence or Structural Similarity more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein homodimerization activity	IDA Inferred from Direct Assay more info	PubMed
enables protein homodimerization activity	IPI Inferred from Physical Interaction more info	PubMed
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
enables pyridoxal phosphatase activity	ISO Inferred from Sequence Orthology more info

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

Component	Evidence Code	Pubs
colocalizes_with actin cytoskeleton	ISO Inferred from Sequence Orthology more info
colocalizes_with actin cytoskeleton	ISS Inferred from Sequence or Structural Similarity more info
located_in cell-cell junction	IDA Inferred from Direct Assay more info	PubMed
colocalizes_with cleavage furrow	ISO Inferred from Sequence Orthology more info
colocalizes_with cleavage furrow	ISS Inferred from Sequence or Structural Similarity more info
colocalizes_with contractile ring	ISO Inferred from Sequence Orthology more info
colocalizes_with contractile ring	ISS Inferred from Sequence or Structural Similarity more info
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
is_active_in cytosol	ISO Inferred from Sequence Orthology more info	PubMed
located_in cytosol	ISO Inferred from Sequence Orthology more info
located_in cytosol	ISS Inferred from Sequence or Structural Similarity more info
is_active_in glutamatergic synapse	IDA Inferred from Direct Assay more info	PubMed
is_active_in glutamatergic synapse	IMP Inferred from Mutant Phenotype more info	PubMed
is_active_in glutamatergic synapse	NAS Non-traceable Author Statement more info	PubMed
colocalizes_with lamellipodium	ISO Inferred from Sequence Orthology more info
colocalizes_with lamellipodium	ISS Inferred from Sequence or Structural Similarity more info
located_in lamellipodium membrane	IEA Inferred from Electronic Annotation more info
colocalizes_with midbody	ISO Inferred from Sequence Orthology more info
colocalizes_with midbody	ISS Inferred from Sequence or Structural Similarity more info
colocalizes_with plasma membrane	ISO Inferred from Sequence Orthology more info
colocalizes_with plasma membrane	ISS Inferred from Sequence or Structural Similarity more info
is_active_in postsynapse	IDA Inferred from Direct Assay more info	PubMed
is_active_in postsynapse	IMP Inferred from Mutant Phenotype more info	PubMed
is_active_in postsynapse	NAS Non-traceable Author Statement more info	PubMed
colocalizes_with ruffle membrane	ISO Inferred from Sequence Orthology more info
colocalizes_with ruffle membrane	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: chronophin

Names: PLP phosphatase; PLP-phosophatase; chronophilin; pyridoxal 5'-phosphate phosphatase; pyridoxal phosphate phosphatase

NP_064667.2

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.

mRNA and Protein(s)

NM_020271.3 → NP_064667.2 chronophin

See identical proteins and their annotated locations for NP_064667.2

Status: VALIDATED

Source sequence(s)

AI845716, BC069982, CX236940

Consensus CDS

CCDS27627.1

UniProtKB/Swiss-Prot

P60487

Related

ENSMUSP00000086796.5, ENSMUST00000089378.5

Conserved Domains (3) summary

TIGR01452
Location:18 → 286

PGP_euk; phosphoglycolate/pyridoxal phosphate phosphatase family

pfam13242
Location:206 → 286

Hydrolase_like; HAD-hyrolase-like

pfam13344
Location:22 → 128

Hydrolase_6; Haloacid dehalogenase-like hydrolase