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PTPRD (protein tyrosine phosphatase, receptor type, D)

Identity

Other namesEC 3.1.3.48
HPTP
HPTP-DELTA
HPTPD
MGC119750
MGC119751
MGC119752
MGC119753
OTTHUMP00000022727
PTPD
R-PTP-DELTA
R-PTP-delta
HGNC (Hugo) PTPRD
LocusID (NCBI) 5789
Location 9p24.1
Location_base_pair Starts at 8314246 and ends at 8733946 bp from pter ( according to hg19-Feb_2009)  [Mapping]

DNA/RNA

Description The PTPRD gene is composed of 36 coding sequence exons and a 5' UTR spliced together from 11 non-coding exons.
Transcription There are five known transcript variants for PTPRD.
Transcript Variant 1: This variant encodes the longest isoform 1 and is 10078 bp in length (Figure A).
Transcript Variant 2: This variant lacks two separate internal segments within the coding region. It thus encodes a protein that lacks a 9 aa, and a 4 aa internal fragments, as compared to isoform 1 and is 10039 bp in length (Figure C).
Transcript Variant 3: This variant lacks an internal segment within the coding region. It thus encodes a protein that lacks a 9 aa internal fragment, as compared to isoform 1 and is 10051 bp in length (Figure D).
Transcript Variant 4: This variant lacks an internal segment within the coding region. It thus encodes a protein that lacks a 411 aa internal fragment, and has one amino acid change, as compared to isoform 1 and is 8845 bp in length (Figure B).
Transcript Variant 5: This variant omits several exons, and utilizes an alternate exon, in the coding region. The resulting protein (isoform 5) retains the same reading frame and has the same N- and C-terminus as isoform 1. This variant is 8848 bp in length (Figure E).
Pseudogene No pseudogenes have been reported.

Protein

 
  Figure A - E: Illustrates the differences between the known PTPRD isoforms, as described in the text.
Description Amino acids: 1912.
Molecular Weight: 214760 Da.
The PTPRD gene belongs to the receptor class 2A subfamily of the protein-tyrosine phosphatases. It contains an extracellular region composed of 8 fibronectin type-III domains and 3 Ig-like C2-type (immunoglobulin-like) domains, a single transmembrane segment and two tandem intracytoplasmic tyrosine-protein phosphatase domains.
Molecular Class: Receptor Tyrosine Phosphatase.
Molecular Function: Receptor Signalling Protein Tyrosine Phosphatase Activity.
Biological Process: Cell Communication ; Signal Transduction.
Expression Brain, Kidney.
Multiple isoforms are generated by either alternate splicing or by alternate transcriptional start sites in a tissue specific manner. The predominant isoform in brain has an extended 711 base pair 5' UTR (L isoform), while the isoform (S) expressed in kidney lacks the extended 5' UTR. In addition, the brain isoform is characterized by the absence of exons 14 to 18 corresponding to amino acid residues 568 to 978 of the 4th through 7th fibronectin III-like domain and by the insertion of a 12 base pair mini-exon sequence between exons 23 and 24 (Nair et al., 2008).
The full length PTPRD isoform has an extracellular region containing three Ig-like and eight FN-III like domains connected via a transmembrane peptide to an intracellular region with two PTPase domains (A), whereas another isoform lacks four of the eight FN-III like domains (B). Furthermore, other PTPRD isoforms exist that lack 9 AA within the second Ig-like domain and 4 AA at the junction of the 2nd and 3rd Ig-like domains (C) or 9 AAs within the 5th FN-III like domain (D). The fifth isoform lacks four of the eight FN-III like domains and has mutation in the second Ig-like domain (E). RT-PCR analysis demonstrated that PTPRD isoforms lacking these short peptides are expressed in kidney, whereas isoforms containing these peptides are expressed in the brain (Pulido et al., 1995).
Localisation Membrane; Single-pass type I membrane protein.
Function A cleavage occurs, separating the extracellular domain from the transmembrane segment. This process called 'ectodomain shedding' is thought to be involved in receptor desensitization, signal transduction and/or membrane localization. Plays key role in promoting neurite growth and regulating axon guidance.
Homology PTPRD shares a PTP domain, involved in dephosphorylating phosphorylated tyrosine residues, with the other receptor-like protein tyrosine phosphatases. The human and mouse PTPRD sequences are 93% identical and 95% homologous.

Implicated in

Entity Lung Adenocarcinoma
Disease Early evidence for the involvement of PTPRD in lung adenocarcinoma came from the detection of homozygous deletions in both primary tumours and cell lines representing both small cell lung carcinoma and non-small cell lung carcinoma (Cox et al., 2005; Zhao et al., 2005; Sato et al., 2005; Nagayama et al., 2007). In addition, somatically acquired PTPRD mutations were found in 11 out of 188 lung adenocarcinoma samples (Weir et al., 2007). Notably, three of the mutations encode predicated inactivating changes in the tyrosine phosphatase domain. Screening for somatic mutations in 623 candidate genes using 188 primary lung adenocarcinoma tissues also revealed sequence changes in PTPRD (Ding et al., 2008).
  
Entity Neuroblastoma
Disease High resolution a CGH analysis of neuroblastoma (NBL) tumours and cell lines identified homozygous and hemizygous intragenic deletions of the PTPRD gene, implicating the gene as a candidate tumor suppressor gene in this type of cancer (Stallings et al., 2006). In addition, the 5' UTR of PTPRD, consisting of 11 noncoding exons, was found to be aberrantly spliced in > 50% of NBL primary tumors and cell lines (Nair et al., 2008). mRNA levels were determined to be significantly reduced in unfavorable tumour subtypes relative to more favorable tumor subtypes.
  
Entity Squamous Cell Carcinoma
Disease Both homozygous and hemizygous deletions affecting the PTPRD gene have been reported in squamous cell carcinoma (Purdie et al., 2007).
  
Entity Colorectal Carcinoma
Disease PTPRD was found to be somatically mutated in colorectal carcinoma with the sequence changes, R28Q, L276P, V901A (Sjoblom et al., 2006).
  
Entity Glioblastoma Multiforme and Malignant Melanoma
Disease A high frequency of deletions in the PTPRD gene were detected in glioblastoma multiforme (GBM) tumours using Affymetrix 250K single nucleotide polymorphism arrays (Solomon et al., 2008). Missense and nonsense mutations of PTPRD were also identified in a subset of the samples lacking deletions, including an inherited mutation with somatic loss of the wild-type allele. The same group also identified 10 somatically acquired mutations in PTPRD among 7 of 57 melanoma tumors (12%). Ectopic reconstitution of wild-type PTPRD expression in GBM and melanoma cell lines harboring deletions or mutations of the endogenous PTPRD gene led to growth suppression and apoptosis, indicating that this gene functions as a tumour suppressor in multiple forms of cancer (Solomon et al., 2008).
  
Entity Restless Leg Syndrome (RLS)
Disease Genome-wide association study of RLS identified three SNPs within the PTPRD gene in the chromosome 9 linkage region (RLS3) as nominally significant (Winkelmann et al., 2007). PTPRD is identified as the fourth genome-wide significant locus for RLS from the genome wide association study in 2458 affected individuals and 4749 controls from Germany, Austria, Czech Republic and Canada (Schormair et al., 2008).
  
Entity Pediatric Asthma
Disease A whole-genome linkage disequilibrium mapping study for asthma on 190 allergic and nonallergic asthma children in Taiwan revealed that polymorphisms of PTPRD are strongly associated with pediatric bronchial asthma in the Taiwanese population (Shyur et al., 2008).
  

External links

Nomenclature
HGNC (Hugo)PTPRD   9668
Entrez_Gene (NCBI)PTPRD  5789  protein tyrosine phosphatase, receptor type, D
Cards
AtlasPTPRDID41927ch9p23
GeneCards (Weizmann)PTPRD
Ensembl (Hinxton)ENSG00000153707 [Gene_View]  chr9:8314246-8733946 [Contig_View]  PTPRD [Vega]
AceView (NCBI)PTPRD
Genatlas (Paris)PTPRD
SOURCE (Stanford)NM_001040712 NM_001171025 NM_002839 NM_130391 NM_130392 NM_130393
Genomic and cartography
GoldenPath (UCSC)PTPRD  -  9p24.1   chr9:8314246-8733946 -  9p24.1-p23   [Description]    (hg19-Feb_2009)
EnsemblPTPRD - 9p24.1-p23 [CytoView]
Mapping of homologs : NCBIPTPRD [Mapview]
OMIM601598   
Gene and transcription
Genbank (Entrez)AB208869 AB211400 AK296392 BC028038 BC037801
RefSeq transcript (SRS)NM_001040712 NM_001171025 NM_002839 NM_130391 NM_130392 NM_130393
RefSeq transcript (Entrez)NM_001040712 NM_001171025 NM_002839 NM_130391 NM_130392 NM_130393
RefSeq genomic (SRS)AC_000141 NC_000009 NC_018920 NT_008413 NW_001839149 NW_004078038
RefSeq genomic (Entrez)AC_000141 NC_000009 NC_018920 NT_008413 NW_001839149 NW_004078038
Consensus coding sequences : CCDS (NCBI)PTPRD
Cluster EST : UnigeneHs.446083 [ SRS ] Hs.446083 [ NCBI ]
CGAP (NCI)Hs.446083
Alternative Splicing : Fast-db (Paris)GSHG0030664
Alternative Splicing GalleryENSG00000153707
Gene ExpressionPTPRD [ NCBI-GEO ]   PTPRD [ EBI - ARRAY_EXPRESS ]
Protein : pattern, domain, 3D structure
UniProt/SwissProtP23468 (SRS) P23468 (Uniprot)
NextProtP23468
With graphics : InterProP23468
Splice isoforms : SwissVarP23468(Swissvar)
Domaine pattern : Prosite (SRS)FN3 (PS50853)    IG_LIKE (PS50835)    TYR_PHOSPHATASE_1 (PS00383)    TYR_PHOSPHATASE_2 (PS50056)    TYR_PHOSPHATASE_PTP (PS50055)   
Domaine pattern : Prosite (Expaxy)FN3 (PS50853)    IG_LIKE (PS50835)    TYR_PHOSPHATASE_1 (PS00383)    TYR_PHOSPHATASE_2 (PS50056)    TYR_PHOSPHATASE_PTP (PS50055)   
Domains : Interpro (SRS)Fibronectin_type3    Ig-like    Ig-like_fold    Ig_I-set    Ig_sub2    Tyr/Dual-specificity_Pase    Tyr_Pase_AS    Tyr_Pase_rcpt/non-rcpt   
Domains : Interpro (EBI)Fibronectin_type3    Ig-like    Ig-like_fold    Ig_I-set    Ig_sub2    Tyr/Dual-specificity_Pase    Tyr_Pase_AS    Tyr_Pase_rcpt/non-rcpt   
Related proteins : CluSTrP23468
Domain families : Pfam (SRS)fn3 (PF00041)    I-set (PF07679)    Y_phosphatase (PF00102)   
Domain families : Pfam (Sanger)fn3 (PF00041)    I-set (PF07679)    Y_phosphatase (PF00102)   
Domain families : Pfam (NCBI)pfam00041    pfam07679    pfam00102   
Domain families : Smart (EMBL)FN3 (SM00060)  IGc2 (SM00408)  PTPc (SM00194)  
DMDM5789
Blocks (Seattle)P23468
PDB (SRS)1X5Z    2DLH    2YD6    2YD7   
PDB (PDBSum)1X5Z    2DLH    2YD6    2YD7   
PDB (IMB)1X5Z    2DLH    2YD6    2YD7   
PDB (RSDB)1X5Z    2DLH    2YD6    2YD7   
Human Protein AtlasENSG00000153707
HPRD03358
IPIIPI00852829   IPI00954886   IPI00219860   IPI00375548   IPI00375547   IPI00955467   IPI00796452   IPI01018655   IPI00946346   IPI00947407   IPI00872363   
Protein Interaction databases
DIP (DOE-UCLA)P23468
IntAct (EBI)P23468
FunCoupENSG00000153707
REACTOMEPTPRD
Protein Interaction Database5789
BioGRIDPTPRD
InParanoidP23468
Interologous Interaction database P23468
IntegromeDBPTPRD
Polymorphism : SNP, mutations, diseases
SNP Single Nucleotide Polymorphism (NCBI)PTPRD
SNP (GeneSNP Utah)PTPRD
SNP : HGBasePTPRD
Genetic variants : HAPMAPPTPRD
Somatic Mutations in Cancer : COSMICPTPRD 
CONAN: Copy Number AnalysisPTPRD 
Mutations and Diseases : HGMDPTPRD
OMIM601598   
GENETests601598   
Disease Genetic AssociationPTPRD
Huge Navigator PTPRD [HugePedia]  PTPRD [HugeCancerGEM]
Genomic VariantsPTPRD  PTPRD [DGVbeta]
snp3D : Map Gene to Disease5789
General knowledge
Homologs : HomoloGenePTPRD
Homology/Alignments : Family Browser (UCSC)PTPRD
Phylogenetic Trees/Animal Genes : TreeFamPTPRD
Catalytic activity : Enzyme3.1.3.48 [ Enzyme-Expasy ]   3.1.3.48 [ Enzyme-SRS ]   3.1.3.48 [ IntEnz-EBI ]   3.1.3.48 [ BRENDA ]   3.1.3.48 [ KEGG ]   
Chemical/Protein Interactions : CTD5789
Chemical/Pharm GKB GenePA34013
Clinical trialPTPRD
Cancer Resource (Charite)ENSG00000153707
Ontology : AmiGOtransmembrane receptor protein tyrosine phosphatase activity  receptor binding  protein binding  integral to plasma membrane  protein dephosphorylation  phosphate-containing compound metabolic process  heterophilic cell-cell adhesion  transmembrane receptor protein tyrosine phosphatase signaling pathway  neuron differentiation  positive regulation of dendrite morphogenesis  cell adhesion molecule binding  presynaptic membrane assembly  
Ontology : EGO-EBItransmembrane receptor protein tyrosine phosphatase activity  receptor binding  protein binding  integral to plasma membrane  protein dephosphorylation  phosphate-containing compound metabolic process  heterophilic cell-cell adhesion  transmembrane receptor protein tyrosine phosphatase signaling pathway  neuron differentiation  positive regulation of dendrite morphogenesis  cell adhesion molecule binding  presynaptic membrane assembly  
Other databases
Probes
Litterature
PubMed49 Pubmed reference(s) in Entrez
PubGenePTPRD
iHOPPTPRD

Bibliography

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Screening of AMP-activated protein kinase alpha2 subunit interacting proteins by bacterial two-hybrid system.
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Contributor(s)

Written01-2009Laavanya Parthasarathi, Raymond L Stallings
Royal College of Surgeons in Ireland and Children's Research Centre, Our Lady's Children's Hospital, Crumlin, Dublin, Ireland

Citation

This paper should be referenced as such :
Parthasarathi L, Stallings RL . PTPRD (protein tyrosine phosphatase, receptor type, D). Atlas Genet Cytogenet Oncol Haematol. January 2009 .
URL : http://AtlasGeneticsOncology.org/Genes/PTPRDID41927ch9p23.html

This paper is referenced by INIST as such :
http://documents.irevues.inist.fr/bitstream/2042/44644/1/01-2009-PTPRDID41927ch9p23.pdf   [ Bibliographic record ]

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