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Aliases for PDXP Gene

Aliases for PDXP Gene

  • Pyridoxal Phosphatase 2 3
  • Pyridoxal (Pyridoxine, Vitamin B6) Phosphatase 2 3 5
  • Chronophin 2 3 4
  • PLP Phosphatase 3 4
  • EC 3.1.3.74 4 63
  • CIN 3 4
  • PLP 3 4
  • Testicular Secretory Protein Li 36 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 Phosphatase) is a Protein Coding gene. Diseases associated with PDXP include laurence-moon syndrome. Among its related pathways are Metabolism and Vitamin B6 metabolism. 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 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

Enhancers for PDXP Gene
GeneHancer Identifier Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

Enhancers around PDXP on UCSC Golden Path with GeneCards custom track

Promoters for PDXP Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around PDXP on UCSC Golden Path with GeneCards custom track

Genomic Location for PDXP Gene

Chromosome:
22
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

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

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:

Domains & Families for PDXP Gene

Gene Families 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 :
  • 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 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:0005515 protein binding IPI 17500066
genes like me logo Genes that share ontologies with PDXP: view
genes like me logo Genes that share phenotypes with PDXP: view

Animal Model Products

  • Taconic Biosciences Mouse Models for PDXP

No data available for Human Phenotype Ontology , Animal Models , 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
Jensen Localization Image for PDXP Gene COMPARTMENTS Subcellular localization image for PDXP gene
Compartment Confidence
cytosol 5
extracellular 5
cytoskeleton 4
plasma membrane 4
mitochondrion 1
nucleus 1
peroxisome 1

Gene Ontology (GO) - Cellular Components for PDXP Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 colocalizes_with plasma membrane IDA 15580268
GO:0032154 colocalizes_with cleavage furrow IDA 15580268
genes like me logo Genes that share ontologies with PDXP: view

Pathways & Interactions for PDXP Gene

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

Pathways by source for PDXP Gene

1 Cell Signaling Technology pathway for PDXP Gene
1 BioSystems pathway 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:0030836 positive regulation of actin filament depolymerization IMP 15580268
genes like me logo Genes that share ontologies with PDXP: view

No data available for SIGNOR curated interactions for PDXP Gene

Drugs & Compounds for PDXP Gene

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

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Pyridoxal Approved Nutra 175
Pyridoxine Approved Nutra 176,176
Pyridoxamine-5'-Phosphate Experimental Pharma 0
Pyridoxine-5'-Phosphate Experimental Pharma 0
Pyridoxal Phosphate Nutra Target, cofactor 14

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

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
Phosphate
  • NFB Orthophosphate
  • O-Phosphoric acid
  • Ortho-phosphate
  • Orthophosphate (PO43-)
  • Orthophosphate(3-)
14265-44-2
phosphoric acid
  • Acide phosphorique (FRENCH)
  • Acido fosforico [Italian]
  • Acidum phosphoricum
  • Diphosphate tetrasodium
  • Fosforzuuroplossingen [Dutch]
7664-38-2
Water
  • Dihydrogen oxide
  • Steam
7732-18-5
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:

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 (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, 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 expression patterns with PDXP: view

Protein tissue co-expression partners for PDXP Gene

- Elite partner

Primer 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
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
chimpanzee
(Pan troglodytes)
Mammalia PDXP 35
  • 99.66 (n)
  • 99.66 (a)
PDXP 36
  • 100 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Pdxp 35
  • 89.04 (n)
  • 93.49 (a)
platypus
(Ornithorhynchus anatinus)
Mammalia -- 36
  • 73 (a)
OneToMany
-- 36
  • 82 (a)
OneToMany
chicken
(Gallus gallus)
Aves LOC771207 35
  • 76 (n)
  • 74.06 (a)
PDXP 36
  • 69 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii zgc:194409 35
  • 64.58 (n)
  • 56.1 (a)
PDXP 36
  • 51 (a)
OneToOne
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

(2) 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
rs7291867 -- 37,666,105(+) CTGAC(C/G)CAGCC utr-variant-3-prime
rs8138057 -- 37,665,537(+) ACTGC(A/G)TCTCC intron-variant
rs34419650 -- 37,665,215(+) GCAGG(-/C)ACTGA intron-variant
rs34499129 -- 37,662,878(+) GCTAC(-/T)TTGGG intron-variant
rs3177075 -- 37,666,933(+) GTGTT(A/C)ACCTG downstream-variant-500B

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

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)

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

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

Disorder Aliases PubMed IDs
laurence-moon syndrome
  • laurence-moon-biedl syndrome
- elite association - COSMIC cancer census association via MalaCards
Search PDXP in MalaCards View complete list of genes associated with diseases

Relevant External Links for PDXP

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
PDXP
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 G.M. (Nat. Cell Biol. 2005) 2 3 4 23 67
  2. Human pyridoxal phosphatase. Molecular cloning, functional expression, and tissue distribution. (PMID: 14522954) Jang Y.M. … Kwon O.-S. (J. Biol. Chem. 2003) 2 3 23 25
  3. 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
  4. Human brain pyridoxal-5'-phosphate phosphatase (PLPP):protein transduction of PEP-1-PLPP into PC12 cells. (PMID: 18510874) Lee Y.P. … Choi S.Y. (BMB Rep 2008) 3 23
  5. Chronophin mediates an ATP-sensing mechanism for cofilin dephosphorylation and neuronal cofilin-actin rod formation. (PMID: 19000834) Huang T.Y. … Bokoch G.M. (Dev. Cell 2008) 3 23

Products for PDXP Gene

Sources for PDXP Gene

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