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] See more...

Aliases for PDXP Gene

Aliases for PDXP Gene

  • Pyridoxal Phosphatase 2 3 5
  • Chronophin 2 3 4
  • CIN 2 3 4
  • Pyridoxal (Pyridoxine, Vitamin B6) Phosphatase 2 3
  • Pyridoxal Phosphate Phosphatase 3 4
  • PLP Phosphatase 3 4
  • EC 3.1.3.74 4 51
  • DJ37E16.5 2 3
  • PLP 3 4
  • Testicular Secretory Protein Li 36 3
  • EC 3.1.3.3 4
  • FLJ32703 2
  • EC 3.1.3 51
  • PDXP 5
  • PLPP 4

External Ids for PDXP Gene

Previous GeneCards Identifiers for PDXP Gene

  • GC00U914367
  • GC22P036299
  • GC22P036379
  • GC22P038054
  • GC22P021021

Summaries for PDXP Gene

Entrez Gene Summary for PDXP Gene

  • 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]

GeneCards Summary for PDXP Gene

PDXP (Pyridoxal Phosphatase) is a Protein Coding gene. Diseases associated with PDXP include Dysbaric Osteonecrosis and Epilepsy, Familial Temporal Lobe, 6. Among its related pathways are Vitamin B6 metabolism and Metabolism. Gene Ontology (GO) annotations related to this gene include magnesium ion binding and phosphoprotein phosphatase activity. An important paralog of this gene is PGP.

UniProtKB/Swiss-Prot Summary for PDXP Gene

  • Protein serine phosphatase that dephosphorylates 'Ser-3' in cofilin and probably also dephosphorylates phospho-serine residues in DSTN. Regulates cofilin-dependent actin cytoskeleton reorganization. Required for normal progress through mitosis and normal cytokinesis. Does not dephosphorylate phospho-threonines in LIMK1. Does not dephosphorylate peptides containing phospho-tyrosine (PubMed:15580268). Pyridoxal phosphate (PLP) phosphatase, which also catalyzes the dephosphorylation of pyridoxine 5'-phosphate (PNP) and pyridoxamine 5'-phosphate (PMP), with order of substrate preference PLP > PNP > PMP (PubMed:14522954).

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for PDXP Gene

Genomics for PDXP Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for PDXP Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PDXP on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for PDXP

Top Transcription factor binding sites by QIAGEN in the PDXP gene promoter:
  • AP-1
  • ATF-2
  • c-Jun
  • GATA-2
  • NF-1
  • NF-1/L
  • p53
  • YY1

Genomic Locations for PDXP Gene

Genomic Locations for PDXP Gene
chr22:37,658,723-37,666,932
(GRCh38/hg38)
Size:
8,210 bases
Orientation:
Plus strand
chr22:38,054,734-38,062,941
(GRCh37/hg19)
Size:
8,208 bases
Orientation:
Plus strand

Genomic View for PDXP Gene

Genes around PDXP on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for PDXP Gene

Proteins for PDXP Gene

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

    Protein Symbol:
    Q96GD0-PLPP_HUMAN
    Recommended name:
    Pyridoxal phosphate phosphatase
    Protein Accession:
    Q96GD0
    Secondary Accessions:
    • Q9UGY2

    Protein attributes for PDXP Gene

    Size:
    296 amino acids
    Molecular mass:
    31698 Da
    Cofactor:
    Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
    Quaternary structure:
    • Homodimer.

    Three dimensional structures from OCA and Proteopedia for PDXP Gene

    Alternative splice isoforms for PDXP Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PDXP Gene

Selected DME Specific Peptides for PDXP Gene

Q96GD0:
  • LFDCDGVLW
  • EACAHLRDP
  • LTLTGVS

Post-translational modifications for PDXP Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for PDXP Gene

ENSEMBL proteins:
REFSEQ proteins:

Domains & Families for PDXP Gene

Gene Families for PDXP Gene

HGNC:
Human Protein Atlas (HPA):
  • Enzymes
  • Predicted intracellular proteins

Protein Domains for PDXP Gene

Suggested Antigen Peptide Sequences for PDXP Gene

GenScript: Design optimal peptide antigens:
  • Pyridoxal phosphate phosphatase (PLPP_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q96GD0

UniProtKB/Swiss-Prot:

PLPP_HUMAN :
  • Belongs to the HAD-like hydrolase superfamily.
Family:
  • Belongs to the HAD-like hydrolase superfamily.
genes like me logo Genes that share domains with PDXP: view

Function for PDXP Gene

Molecular function for PDXP Gene

UniProtKB/Swiss-Prot Function:
Protein serine phosphatase that dephosphorylates 'Ser-3' in cofilin and probably also dephosphorylates phospho-serine residues in DSTN. Regulates cofilin-dependent actin cytoskeleton reorganization. Required for normal progress through mitosis and normal cytokinesis. Does not dephosphorylate phospho-threonines in LIMK1. Does not dephosphorylate peptides containing phospho-tyrosine (PubMed:15580268). Pyridoxal phosphate (PLP) phosphatase, which also catalyzes the dephosphorylation of pyridoxine 5'-phosphate (PNP) and pyridoxamine 5'-phosphate (PMP), with order of substrate preference PLP > PNP > PMP (PubMed:14522954).
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=H2O + pyridoxal 5'-phosphate = phosphate + pyridoxal; Xref=Rhea:RHEA:20533, ChEBI:CHEBI:15377, ChEBI:CHEBI:17310, ChEBI:CHEBI:43474, ChEBI:CHEBI:597326; EC=3.1.3.74; Evidence={ECO:0000250|UniProtKB:P60487};.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=H2O + O-phospho-L-serine = L-serine + phosphate; Xref=Rhea:RHEA:21208, ChEBI:CHEBI:15377, ChEBI:CHEBI:33384, ChEBI:CHEBI:43474, ChEBI:CHEBI:57524; EC=3.1.3.3; Evidence={ECO:0000269|PubMed:15580268};.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=H2O + O-phospho-D-serine = D-serine + phosphate; Xref=Rhea:RHEA:24873, ChEBI:CHEBI:15377, ChEBI:CHEBI:35247, ChEBI:CHEBI:43474, ChEBI:CHEBI:58680; EC=3.1.3.3; Evidence={ECO:0000269|PubMed:15580268};.
UniProtKB/Swiss-Prot EnzymeRegulation:
Inhibited by NaF, Zn(2+), Ca(2+), Mn(2+) and EDTA.

Enzyme Numbers (IUBMB) for PDXP Gene

Phenotypes From GWAS Catalog for PDXP Gene

Gene Ontology (GO) - Molecular Function for PDXP Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000287 magnesium ion binding ISS --
GO:0004647 phosphoserine phosphatase activity IEA --
GO:0004721 phosphoprotein phosphatase activity IDA 15580268
GO:0005515 protein binding IPI 17500066
GO:0016787 hydrolase activity IEA --
genes like me logo Genes that share ontologies with PDXP: view
genes like me logo Genes that share phenotypes with PDXP: view

Animal Models for PDXP Gene

MGI Knock Outs for PDXP:
  • Pdxp Pdxp<tm1.2Ango>

Animal Model Products

  • Taconic Biosciences Mouse Models for PDXP

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PDXP

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

Localization for PDXP Gene

Subcellular locations from UniProtKB/Swiss-Prot for PDXP Gene

Cytoplasm, cytosol. Cytoplasm, cytoskeleton. Cell projection, ruffle membrane. Peripheral membrane protein. Cytoplasmic side. Cell projection, lamellipodium membrane. Peripheral membrane protein. Cytoplasmic side. Cell membrane. Peripheral membrane protein. Cytoplasmic side. Note=Colocalizes with the actin cytoskeleton in membrane ruffles and lamellipodia. Diffusely distributed throughout the cytosol during pro-metaphase and metaphase. Detected at the dynamic cell poles during telophase. Detected at the cleavage furrow and contractile ring during cytokinesis. Transiently detected at the plasma membrane in late stages of cytokinesis. Detected at the midbody. {ECO:0000269 PubMed:15580268}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for PDXP gene
Compartment Confidence
cytosol 5
plasma membrane 4
cytoskeleton 4
nucleus 3
extracellular 2
mitochondrion 2
endoplasmic reticulum 1
endosome 1
lysosome 1
golgi apparatus 1
peroxisome 0

Gene Ontology (GO) - Cellular Components for PDXP Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IBA 21873635
GO:0005829 cytosol IEA,IDA 15580268
GO:0005856 cytoskeleton IEA --
GO:0005886 colocalizes_with plasma membrane IEA,IDA 15580268
GO:0005911 cell-cell junction IEA --
genes like me logo Genes that share ontologies with PDXP: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for PDXP Gene

Pathways & Interactions for PDXP Gene

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

Pathways by source for PDXP Gene

1 Sino Biological pathway for PDXP Gene
1 BioSystems pathway for PDXP Gene
2 KEGG pathways for PDXP Gene
1 Cell Signaling Technology pathway for PDXP Gene

SIGNOR curated interactions for PDXP Gene

Inactivates:

Gene Ontology (GO) - Biological Process for PDXP Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006114 glycerol biosynthetic process IBA 21873635
GO:0006470 protein dephosphorylation IDA 15580268
GO:0006650 glycerophospholipid metabolic process IBA 21873635
GO:0007088 regulation of mitotic nuclear division IMP 15580268
GO:0016311 dephosphorylation IBA 21873635
genes like me logo Genes that share ontologies with PDXP: view

Drugs & Compounds for PDXP Gene

(14) Drugs for PDXP Gene - From: DrugBank, HMDB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Pyridoxine Approved, Investigational, Vet_approved Nutra Enzyme, substrate 229,229
Pyridoxal Phosphate Approved, Investigational Nutra Target, cofactor 16
Magnesium Approved, Experimental, Investigational Pharma 0
Phosphoric acid Approved Pharma 0
Water Approved Pharma 0

(9) Additional Compounds for PDXP Gene - From: Novoseek and HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
Phosphate
  • [po(OH)3]
  • Acide phosphorique
  • Acidum phosphoricum
  • H3PO4
  • Orthophosphoric acid
14066-19-4, 14265-44-2
genes like me logo Genes that share compounds with PDXP: view

Transcripts for PDXP Gene

mRNA/cDNA for PDXP Gene

1 REFSEQ mRNAs :
8 NCBI additional mRNA sequence :
2 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PDXP

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

No ASD Table

Relevant External Links for PDXP Gene

GeneLoc Exon Structure for
PDXP

Expression for PDXP Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for PDXP Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for PDXP Gene

This gene is overexpressed in Brain - Cortex (x5.2), Brain - Anterior cingulate cortex (BA24) (x4.6), and Brain - Frontal Cortex (BA9) (x4.3).

Protein differential expression in normal tissues from HIPED for PDXP Gene

This gene is overexpressed in Brain (19.1) and Frontal cortex (11.6).

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



Protein tissue co-expression partners for PDXP Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for PDXP

SOURCE GeneReport for Unigene cluster for PDXP Gene:

Hs.632762

mRNA Expression by UniProt/SwissProt for PDXP Gene:

Q96GD0-PLPP_HUMAN
Tissue specificity: Ubiquitously expressed (at protein level) (PubMed:23223568). Highly expressed in all the regions of central nerve system except the spinal cord. Also expressed at high level in liver and testis. In fetus, it is weakly expressed in all organs except brain (PubMed:14522954, PubMed:15580268).

Evidence on tissue expression from TISSUES for PDXP Gene

  • Nervous system(4.9)
  • Lung(4.5)
  • Eye(4.4)
  • Kidney(2.7)
  • Skin(2.6)
  • Blood(2.6)
  • Liver(2.4)
  • Heart(2.4)
  • Muscle(2.4)
  • Intestine(2.4)
  • Lymph node(2.2)
  • Stomach(2.1)
  • Bone marrow(2)
  • Pancreas(2)
genes like me logo Genes that share expression patterns with PDXP: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for PDXP Gene

Orthologs for PDXP Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for PDXP Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia PDXP 30 31
  • 99.66 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia PDXP 30 31
  • 92.91 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia PDXP 30 31
  • 91.1 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Pdxp 30 17 31
  • 89.84 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Pdxp 30
  • 89.04 (n)
Platypus
(Ornithorhynchus anatinus)
Mammalia -- 31
  • 82 (a)
OneToMany
-- 31
  • 73 (a)
OneToMany
Chicken
(Gallus gallus)
Aves LOC771207 30
  • 76 (n)
PDXP 31
  • 69 (a)
OneToOne
Zebrafish
(Danio rerio)
Actinopterygii zgc:194409 30
  • 64.58 (n)
PDXP 31
  • 51 (a)
OneToOne
Fruit Fly
(Drosophila melanogaster)
Insecta CG5567 31
  • 32 (a)
ManyToMany
CG32487 31
  • 27 (a)
ManyToMany
CG5577 31
  • 27 (a)
ManyToMany
CG32488 31
  • 26 (a)
ManyToMany
CG10352 31
  • 25 (a)
ManyToMany
CG11291 31
  • 25 (a)
ManyToMany
CG2680 31
  • 25 (a)
ManyToMany
CG15739 31
  • 25 (a)
ManyToMany
Worm
(Caenorhabditis elegans)
Secernentea K09H11.7 31
  • 29 (a)
ManyToMany
F44E7.2 31
  • 27 (a)
ManyToMany
C53A3.2 31
  • 26 (a)
ManyToMany
C45E5.1 31
  • 23 (a)
ManyToMany
K02D10.1 31
  • 17 (a)
ManyToMany
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes PHO13 31
  • 28 (a)
OneToMany
Thale Cress
(Arabidopsis thaliana)
eudicotyledons PGLP1 30
  • 44.28 (n)
Rice
(Oryza sativa)
Liliopsida Os04g0490800 30
  • 48.13 (n)
Sea Squirt
(Ciona savignyi)
Ascidiacea CSA.9766 31
  • 34 (a)
OneToMany
Species where no ortholog for PDXP was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • 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)
  • Corn (Zea mays)
  • 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)
  • Lizard (Anolis carolinensis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Oppossum (Monodelphis domestica)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • 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)
  • Tropical Clawed Frog (Silurana tropicalis)
  • Wheat (Triticum aestivum)

Evolution for PDXP Gene

ENSEMBL:
Gene Tree for PDXP (if available)
TreeFam:
Gene Tree for PDXP (if available)
Aminode:
Evolutionary constrained regions (ECRs) for PDXP: view image

Paralogs for PDXP Gene

Paralogs for PDXP Gene

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

  • PLPP_HUMAN
  • B1AHD3_HUMAN
genes like me logo Genes that share paralogs with PDXP: view

Variants for PDXP Gene

Additional dbSNP identifiers (rs#s) for PDXP Gene

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

Variant ID Type Subtype PubMed ID
esv26329 CNV loss 19812545
esv2758838 CNV loss 17122850
nsv1057617 CNV gain 25217958
nsv471197 CNV loss 18288195
nsv589007 CNV gain 21841781
nsv829203 CNV loss 20364138
nsv834191 CNV loss 17160897

Variation tolerance for PDXP Gene

Residual Variation Intolerance Score: 62.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.77; 33.44% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PDXP Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
PDXP

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for PDXP Gene

Disorders for PDXP Gene

MalaCards: The human disease database

(3) MalaCards diseases for PDXP Gene - From: DISEASES

Disorder Aliases PubMed IDs
dysbaric osteonecrosis
  • caisson disease of bone
epilepsy, familial temporal lobe, 6
  • etl6
sialolithiasis
  • salivary gland stone
- elite association - COSMIC cancer census association via MalaCards
Search PDXP in MalaCards View complete list of genes associated with diseases
genes like me logo Genes that share disorders with PDXP: view

No data available for UniProtKB/Swiss-Prot and Genatlas for PDXP Gene

Publications for PDXP Gene

  1. Chronophin, a novel HAD-type serine protein phosphatase, regulates cofilin-dependent actin dynamics. (PMID: 15580268) Gohla A … Bokoch GM (Nature cell biology 2005) 2 3 4 23
  2. Human pyridoxal phosphatase. Molecular cloning, functional expression, and tissue distribution. (PMID: 14522954) Jang YM … Kwon OS (The Journal of biological chemistry 2003) 2 3 4 23
  3. Identification of an essential cysteine residue in pyridoxal phosphatase from human erythrocytes. (PMID: 8132548) Gao G … Fonda ML (The Journal of biological chemistry 1994) 3 4 23
  4. A novel Rac1 GAP splice variant relays poly-Ub accumulation signals to mediate Rac1 inactivation. (PMID: 23223568) Huang TY … DerMardirossian C (Molecular biology of the cell 2013) 3 4
  5. Human brain pyridoxal-5'-phosphate phosphatase (PLPP):protein transduction of PEP-1-PLPP into PC12 cells. (PMID: 18510874) Lee YP … Choi SY (BMB reports 2008) 3 23

Products for PDXP Gene

Sources for PDXP Gene