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Aliases for PDXP Gene

Aliases for PDXP Gene

  • Pyridoxal (Pyridoxine, Vitamin B6) Phosphatase 2 3
  • PLP Phosphatase 3 4
  • EC 3.1.3.74 4 63
  • Chronophin 3 4
  • CIN 3 4
  • PLP 3 4
  • Pyridoxal Phosphate Phosphatase 3
  • EC 3.1.3.3 4
  • DJ37E16.5 3
  • EC 3.1.3 63
  • 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 (Pyridoxine, Vitamin B6) Phosphatase) is a Protein Coding gene. Diseases associated with PDXP include laurence-moon syndrome. Among its related pathways are Cytoskeletal Signaling and Metabolism. GO annotations related to this gene include phosphoprotein phosphatase activity and phosphoserine phosphatase activity. An important paralog of this gene is PGP.

UniProtKB/Swiss-Prot 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. Pyridoxal phosphate phosphatase. Has some activity towards pyridoxal 5-phosphate (PLP), pyridoxine 5-phosphate (PMP) and pyridoxine 5-phosphate (PNP), with a highest activity with PLP followed by PNP.

No data available for Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PDXP Gene

Genomics for PDXP Gene

Regulatory Elements for PDXP Gene

Genomic Location for PDXP Gene

Start:
37,658,727 bp from pter
End:
37,666,934 bp from pter
Size:
8,208 bases
Orientation:
Plus strand

Genomic View for PDXP Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
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; Note=Divalent metal ions. Mg(2+) is the most effective.;
    Quaternary structure:
    • Homodimer.

    Three dimensional structures from OCA and Proteopedia for PDXP Gene

neXtProt entry for PDXP Gene

Proteomics data for PDXP Gene at MOPED

Selected DME Specific Peptides for PDXP Gene

Post-translational modifications for PDXP Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for PDXP Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibody Products

  • Cell Signaling Technology (CST) Antibodies for PDXP (PDXP)

Domains for PDXP Gene

Protein Domains for PDXP Gene

Suggested Antigen Peptide Sequences for PDXP Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q96GD0

UniProtKB/Swiss-Prot:

PLPP_HUMAN :
  • Q96GD0
Family:
  • Belongs to the HAD-like hydrolase superfamily.
genes like me logo Genes that share domains with PDXP: view

No data available for Gene Families for PDXP Gene

Function for PDXP Gene

Molecular function for PDXP Gene

UniProtKB/Swiss-Prot CatalyticActivity: Pyridoxal 5-phosphate + H(2)O = pyridoxal + phosphate
UniProtKB/Swiss-Prot CatalyticActivity: O-phospho-L(or D)-serine + H(2)O = L(or D)-serine + phosphate
UniProtKB/Swiss-Prot EnzymeRegulation: Inhibited by NaF, Zn(2+), Ca(2+), Mn(2+) and EDTA.
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. Pyridoxal phosphate phosphatase. Has some activity towards pyridoxal 5-phosphate (PLP), pyridoxine 5-phosphate (PMP) and pyridoxine 5-phosphate (PNP), with a highest activity with PLP followed by PNP.

Enzyme Numbers (IUBMB) 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:0016791 phosphatase activity --
genes like me logo Genes that share ontologies with PDXP: view

Phenotypes for PDXP Gene

GenomeRNAi human phenotypes for PDXP:
genes like me logo Genes that share phenotypes with PDXP: view

Animal Model Products

miRNA for PDXP Gene

miRTarBase miRNAs that target PDXP

No data available for Animal Models , Transcription Factor Targeting 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.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for PDXP Gene COMPARTMENTS Subcellular localization image for PDXP gene
Compartment Confidence
cytoskeleton 5
cytosol 5
plasma membrane 5
extracellular 1
mitochondrion 1
nucleus 1
peroxisome 1

Gene Ontology (GO) - Cellular Components for PDXP Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005829 cytosol IDA 15580268
GO:0005886 colocalizes_with plasma membrane IDA 15580268
GO:0015629 colocalizes_with actin cytoskeleton IDA 15580268
GO:0030027 colocalizes_with lamellipodium IDA 15580268
GO:0030496 colocalizes_with midbody IDA 15580268
genes like me logo Genes that share ontologies with PDXP: view

Pathways for PDXP Gene

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

Pathways by source for PDXP Gene

2 Cell Signaling Technology pathways for PDXP Gene
2 KEGG pathways for PDXP Gene

Gene Ontology (GO) - Biological Process for PDXP Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006470 protein dephosphorylation IDA 15580268
GO:0007088 regulation of mitotic nuclear division IMP 15580268
GO:0008152 metabolic process --
GO:0030836 positive regulation of actin filament depolymerization IMP 15580268
GO:0031247 actin rod assembly IMP 19000834
genes like me logo Genes that share ontologies with PDXP: view

Compounds for PDXP Gene

(9) HMDB Compounds for PDXP Gene

Compound Synonyms Cas Number PubMed IDs
Magnesium
  • Magnesium
7439-95-4
Phosphate
  • NFB Orthophosphate
14265-44-2
Pyridoxal
  • 3-Hydroxy-5-(hydroxymethyl)-2-methylpyridine-4-carboxaldehyde
66-72-8
Pyridoxal 5'-phosphate
  • Apolon B6
54-47-7
Pyridoxamine
  • 2-methyl-4-aminomethyl-5-hydroxymethyl-3-Pyridinol
85-87-0

(1) Drugbank Compounds for PDXP Gene

Compound Synonyms Cas Number Type Actions PubMed IDs
Pyridoxal Phosphate
  • Codecarboxylase
54-47-7 target cofactor

(15) Novoseek inferred chemical compound relationships for PDXP Gene

Compound -log(P) Hits PubMed IDs
pyridoxine 5-phosphate 93 3
pyridoxal 91 20
pyridoxal 5-phosphate 90.4 47
dehydroalanine 79.1 1
vitamin b6 76.9 4
genes like me logo Genes that share compounds with PDXP: view

Transcripts for PDXP Gene

mRNA/cDNA for PDXP Gene

Unigene Clusters for PDXP Gene

Pyridoxal (pyridoxine, vitamin B6) phosphatase:
Representative Sequences:

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for PDXP

Primer Products

  • QuantiTect SYBR Green Assays in human,mouse,rat
  • Pre-validated RT² qPCR Primer Assay in human,mouse,rat
  • QuantiFast Probe-based Assays in human,mouse,rat

Flow Cytometry Products

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

No ASD Table

Relevant External Links for PDXP Gene

GeneLoc Exon Structure for
PDXP
ECgene alternative splicing isoforms for
PDXP

Expression for PDXP Gene

mRNA expression in normal human tissues 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 (5.2), Brain - Anterior cingulate cortex (BA24) (4.6), and Brain - Frontal Cortex (BA9) (4.3).

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for PDXP Gene

SOURCE GeneReport for Unigene cluster for PDXP Gene Hs.632762

mRNA Expression by UniProt/SwissProt for PDXP Gene

Q96GD0-PLPP_HUMAN
Tissue specificity: Ubiquitous. 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.
genes like me logo Genes that share expressions with PDXP: view

In Situ Assay Products

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 35
  • 99.66 (n)
  • 99.66 (a)
PDXP 36
  • 100 (a)
OneToOne
cow
(Bos Taurus)
Mammalia PDXP 35
  • 91.1 (n)
  • 93.92 (a)
PDXP 36
  • 94 (a)
OneToOne
dog
(Canis familiaris)
Mammalia PDXP 35
  • 92.91 (n)
  • 94.26 (a)
PDXP 36
  • 94 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Pdxp 35
  • 89.84 (n)
  • 92.47 (a)
Pdxp 16
Pdxp 36
  • 91 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 36
  • 73 (a)
OneToMany
-- 36
  • 82 (a)
OneToMany
rat
(Rattus norvegicus)
Mammalia Pdxp 35
  • 89.04 (n)
  • 93.49 (a)
chicken
(Gallus gallus)
Aves LOC771207 35
  • 76 (n)
  • 74.06 (a)
PDXP 36
  • 69 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii PDXP 36
  • 51 (a)
OneToOne
zgc:194409 35
  • 64.58 (n)
  • 56.1 (a)
fruit fly
(Drosophila melanogaster)
Insecta CG10352 36
  • 25 (a)
ManyToMany
CG11291 36
  • 25 (a)
ManyToMany
CG15739 36
  • 25 (a)
ManyToMany
CG2680 36
  • 25 (a)
ManyToMany
CG32487 36
  • 27 (a)
ManyToMany
CG32488 36
  • 26 (a)
ManyToMany
CG5567 36
  • 32 (a)
ManyToMany
CG5577 36
  • 27 (a)
ManyToMany
worm
(Caenorhabditis elegans)
Secernentea C45E5.1 36
  • 23 (a)
ManyToMany
C53A3.2 36
  • 26 (a)
ManyToMany
F44E7.2 36
  • 27 (a)
ManyToMany
K02D10.1 36
  • 17 (a)
ManyToMany
K09H11.7 36
  • 29 (a)
ManyToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes PHO13 36
  • 28 (a)
OneToMany
thale cress
(Arabidopsis thaliana)
eudicotyledons AT5G36790 35
  • 44.28 (n)
  • 37.69 (a)
rice
(Oryza sativa)
Liliopsida Os04g0490800 35
  • 48.13 (n)
  • 37.69 (a)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.9766 36
  • 34 (a)
OneToMany
Species with no ortholog for PDXP:
  • A. gosspyii yeast (Ashbya 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 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)

Paralogs for PDXP Gene

Paralogs for PDXP Gene

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

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

Variants for PDXP Gene

Sequence variations from dbSNP and Humsavar for PDXP Gene

SNP ID Clin Chr 22 pos Sequence Context AA Info Type MAF
rs732856 -- 37,664,684(+) ATGAA(C/G)GCCGA intron-variant
rs732857 -- 37,664,843(+) TTATC(A/G)GTTAC intron-variant
rs1894532 -- 37,663,743(+) GCTCC(C/T)GCCTC intron-variant
rs3177075 -- 37,666,933(+) GTGTT(A/C)ACCTG downstream-variant-500B
rs3827353 -- 37,660,831(+) CATGA(C/T)GCAGG intron-variant

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

Variant ID Type Subtype PubMed ID
nsv829203 CNV Loss 20364138
nsv834191 CNV Loss 17160897
dgv4964n71 CNV Loss 21882294
nsv471197 CNV Loss 18288195
dgv4965n71 CNV Loss 21882294
nsv915035 CNV Loss 21882294
dgv1406e1 CNV Complex 17122850
nsv915038 CNV Loss 21882294
esv26329 CNV Loss 19812545

Relevant External Links for PDXP Gene

HapMap Linkage Disequilibrium report
PDXP

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PDXP Gene

Disorders for PDXP Gene

MalaCards: The human disease database

MalaCards: The human disease database. (1) Diseases for PDXP Gene including...

Search for PDXP Gene in MalaCards »

(2) University of Copenhagen DISEASES for PDXP Gene

(3) Novoseek inferred disease relationships for PDXP Gene

Disease -log(P) Hits PubMed IDs
neurological disorders 42.6 1
inflammation 0 1
cancer 0 3
genes like me logo Genes that share disorders with PDXP: view

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

Publications for PDXP Gene

  1. Human pyridoxal phosphatase. Molecular cloning, functional expression, and tissue distribution. (PMID: 14522954) Jang Y.M. … Kwon O.-S. (J. Biol. Chem. 2003) 2 3 4 23 25
  2. Identification of an essential cysteine residue in pyridoxal phosphatase from human erythrocytes. (PMID: 8132548) Gao G.-J. … Fonda M.L. (J. Biol. Chem. 1994) 3 4 23
  3. Chronophin, a novel HAD-type serine protein phosphatase, regulates cofilin-dependent actin dynamics. (PMID: 15580268) Gohla A. … Bokoch G.M. (Nat. Cell Biol. 2005) 3 4 23
  4. Human brain pyridoxal-5'-phosphate phosphatase: production and characterization of monoclonal antibodies. (PMID: 16336786) Kim D.W. … Choi S.Y. (J. Biochem. Mol. Biol. 2005) 3 23 25
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4

Products for PDXP Gene

Sources for PDXP Gene

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