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Q9EQT1

- PDGFD_RAT

UniProt

Q9EQT1 - PDGFD_RAT

Protein

Platelet-derived growth factor D

Gene

Pdgfd

Organism
Rattus norvegicus (Rat)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at transcript leveli
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    • History
      Entry version 75 (01 Oct 2014)
      Sequence version 1 (01 Mar 2001)
      Previous versions | rss
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    Functioni

    Growth factor that plays an essential role in the regulation of embryonic development, cell proliferation, cell migration, survival and chemotaxis. Potent mitogen for cells of mesenchymal origin. Plays an important role in wound healing. Induces macrophage recruitment, increased interstitial pressure, and blood vessel maturation during angiogenesis By similarity. May play an important role in control of lens epithelial cell proliferation. Can initiate events that lead to a mesangial proliferative glomerulonephritis, including influx of monocytes and macrophages and production of extracellular matrix.By similarity2 Publications

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sitei247 – 2482CleavageSequence Analysis
    Sitei249 – 2502CleavageSequence Analysis

    GO - Biological processi

    1. cellular response to amino acid stimulus Source: Ensembl
    2. multicellular organismal development Source: UniProtKB-KW
    3. platelet-derived growth factor receptor signaling pathway Source: InterPro
    4. positive regulation of cell division Source: UniProtKB-KW
    5. regulation of peptidyl-tyrosine phosphorylation Source: Ensembl

    Keywords - Molecular functioni

    Developmental protein, Growth factor, Mitogen

    Enzyme and pathway databases

    ReactomeiREACT_212371. Signaling by PDGF.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Platelet-derived growth factor D
    Short name:
    PDGF-D
    Alternative name(s):
    Iris-expressed growth factor
    Spinal cord-derived growth factor B
    Short name:
    SCDGF-B
    Cleaved into the following 2 chains:
    Platelet-derived growth factor D, receptor-binding form
    Short name:
    PDGFD receptor-binding form
    Gene namesi
    Name:Pdgfd
    Synonyms:Iegf, Scdgfb
    OrganismiRattus norvegicus (Rat)
    Taxonomic identifieri10116 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus
    ProteomesiUP000002494: Chromosome 8

    Organism-specific databases

    RGDi621880. Pdgfd.

    Subcellular locationi

    Secreted By similarity
    Note: Released by platelets upon wounding.By similarity

    GO - Cellular componenti

    1. extracellular region Source: UniProtKB-SubCell
    2. membrane Source: InterPro

    Keywords - Cellular componenti

    Secreted

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Signal peptidei1 – 2323Sequence AnalysisAdd
    BLAST
    Chaini24 – 370347Platelet-derived growth factor D, latent formPRO_0000250196Add
    BLAST
    Chaini250 – 370121Platelet-derived growth factor D, receptor-binding formSequence AnalysisPRO_0000250197Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Disulfide bondi109 ↔ 131PROSITE-ProRule annotation
    Glycosylationi276 – 2761N-linked (GlcNAc...)Sequence Analysis
    Disulfide bondi296 – 296InterchainPROSITE-ProRule annotation
    Disulfide bondi302 ↔ 360PROSITE-ProRule annotation
    Disulfide bondi306 ↔ 362PROSITE-ProRule annotation

    Post-translational modificationi

    Activated by proteolytic cleavage. Proteolytic removal of the N-terminal CUB domain releasing the core domain is necessary for unmasking the receptor-binding epitopes of the core domain. Cleavage after Arg-247 or Arg-249 by urokinase plasminogen activator gives rise to the active form By similarity.By similarity

    Keywords - PTMi

    Cleavage on pair of basic residues, Disulfide bond, Glycoprotein

    Proteomic databases

    PRIDEiQ9EQT1.

    Expressioni

    Tissue specificityi

    Widely expressed. Expressed at high levels in the kidney, adrenal glands, eye and CNS. In the kidney the localization is confined to arterial and arteriolar vascular smooth muscle cells and is also detected at low levels in the glomeruli In the eye in the anterior segment it is localized to the iris and ciliary body. In the retina localizes intensely to the outer plexiform layer, which contains photoreceptor axons and the synaptic layer between photoreceptors and second order neurons. In the spinal cord, prominently expressed in the motorneurons.3 Publications

    Developmental stagei

    Not detected in the spinal cord at E21. Expressed weakly at postnatal day 1 (P1) and a strong expression seen at P21 and this continues into adulthood.1 Publication

    Gene expression databases

    GenevestigatoriQ9EQT1.

    Interactioni

    Subunit structurei

    Homodimer; disulfide-linked. Interacts with PDGFRB homodimers, and with heterodimers formed by PDGFRA and PDGFRB By similarity.By similarity

    Protein-protein interaction databases

    STRINGi10116.ENSRNOP00000039308.

    Structurei

    3D structure databases

    ProteinModelPortaliQ9EQT1.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini52 – 170119CUBPROSITE-ProRule annotationAdd
    BLAST

    Sequence similaritiesi

    Belongs to the PDGF/VEGF growth factor family.Curated
    Contains 1 CUB domain.PROSITE-ProRule annotation

    Keywords - Domaini

    Signal

    Phylogenomic databases

    eggNOGiNOG148355.
    GeneTreeiENSGT00390000005171.
    HOGENOMiHOG000214105.
    HOVERGENiHBG057324.
    KOiK05450.
    OMAiHYRGRSY.
    OrthoDBiEOG7VB2FN.
    PhylomeDBiQ9EQT1.

    Family and domain databases

    Gene3Di2.10.90.10. 1 hit.
    2.60.120.290. 1 hit.
    InterProiIPR000859. CUB_dom.
    IPR029034. Cystine-knot_cytokine.
    IPR000072. PDGF/VEGF_dom.
    IPR027123. PDGFD.
    [Graphical view]
    PANTHERiPTHR10127:SF13. PTHR10127:SF13. 1 hit.
    PfamiPF00431. CUB. 1 hit.
    PF00341. PDGF. 1 hit.
    [Graphical view]
    SMARTiSM00042. CUB. 1 hit.
    SM00141. PDGF. 1 hit.
    [Graphical view]
    SUPFAMiSSF49854. SSF49854. 1 hit.
    SSF57501. SSF57501. 1 hit.
    PROSITEiPS01180. CUB. 1 hit.
    PS50278. PDGF_2. 1 hit.
    [Graphical view]

    Sequences (2)i

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    This entry describes 2 isoformsi produced by alternative splicing. Align

    Isoform 1 (identifier: Q9EQT1-1) [UniParc]FASTAAdd to Basket

    This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

    « Hide

    MHRLILVSIL VCANFCCYRD TFATPQSASI KALRNANLRR DESNHLTDLY    50
    RRDENIRVTG TGHVQSPRFP NSYPRNLLLT WRLHSQEKTR IQLAFDHQFG 100
    LEEAENDICR YDFVEVEDVS ESSTVVRGRW CGHKEIPPRI TSRTNQIKIT 150
    FQSDDYFVAK PGFKIYYSFV EDFQPEAASE INWESVTSSF SGVSYHSPSV 200
    MDSTLTADAL DKAIAEFDTV EDLLKYFNPA SWQDDLENLY MDTPRYRGRS 250
    YHERKSKVDL DRLNDDVKRY SCTPRNHSVN LREELKLTNA VFFPRCLLVQ 300
    RCGGNCGCGT LNWKSCTCSS GKTVKKYHEV LKFEPGHFKR RGKAKNMALV 350
    DIQLDHHERC DCICSSRPPR 370
    Length:370
    Mass (Da):42,809
    Last modified:March 1, 2001 - v1
    Checksum:i7BE8A251F679BF73
    GO
    Isoform 2 (identifier: Q9EQT1-2) [UniParc]FASTAAdd to Basket

    The sequence of this isoform differs from the canonical sequence as follows:
         42-47: Missing.

    Show »
    Length:364
    Mass (Da):42,128
    Checksum:iF5E3F7E8860361E8
    GO

    Alternative sequence

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Alternative sequencei42 – 476Missing in isoform 2. CuratedVSP_020619

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AB052170 mRNA. Translation: BAB18920.1.
    PIRiJC7592.
    RefSeqiNP_076452.1. NM_023962.2. [Q9EQT1-1]
    UniGeneiRn.64493.

    Genome annotation databases

    EnsembliENSRNOT00000049325; ENSRNOP00000039308; ENSRNOG00000029148. [Q9EQT1-1]
    GeneIDi66018.
    KEGGirno:66018.
    UCSCiRGD:621880. rat. [Q9EQT1-1]

    Keywords - Coding sequence diversityi

    Alternative splicing

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AB052170 mRNA. Translation: BAB18920.1 .
    PIRi JC7592.
    RefSeqi NP_076452.1. NM_023962.2. [Q9EQT1-1 ]
    UniGenei Rn.64493.

    3D structure databases

    ProteinModelPortali Q9EQT1.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 10116.ENSRNOP00000039308.

    Proteomic databases

    PRIDEi Q9EQT1.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENSRNOT00000049325 ; ENSRNOP00000039308 ; ENSRNOG00000029148 . [Q9EQT1-1 ]
    GeneIDi 66018.
    KEGGi rno:66018.
    UCSCi RGD:621880. rat. [Q9EQT1-1 ]

    Organism-specific databases

    CTDi 80310.
    RGDi 621880. Pdgfd.

    Phylogenomic databases

    eggNOGi NOG148355.
    GeneTreei ENSGT00390000005171.
    HOGENOMi HOG000214105.
    HOVERGENi HBG057324.
    KOi K05450.
    OMAi HYRGRSY.
    OrthoDBi EOG7VB2FN.
    PhylomeDBi Q9EQT1.

    Enzyme and pathway databases

    Reactomei REACT_212371. Signaling by PDGF.

    Miscellaneous databases

    NextBioi 614300.
    PROi Q9EQT1.

    Gene expression databases

    Genevestigatori Q9EQT1.

    Family and domain databases

    Gene3Di 2.10.90.10. 1 hit.
    2.60.120.290. 1 hit.
    InterProi IPR000859. CUB_dom.
    IPR029034. Cystine-knot_cytokine.
    IPR000072. PDGF/VEGF_dom.
    IPR027123. PDGFD.
    [Graphical view ]
    PANTHERi PTHR10127:SF13. PTHR10127:SF13. 1 hit.
    Pfami PF00431. CUB. 1 hit.
    PF00341. PDGF. 1 hit.
    [Graphical view ]
    SMARTi SM00042. CUB. 1 hit.
    SM00141. PDGF. 1 hit.
    [Graphical view ]
    SUPFAMi SSF49854. SSF49854. 1 hit.
    SSF57501. SSF57501. 1 hit.
    PROSITEi PS01180. CUB. 1 hit.
    PS50278. PDGF_2. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Molecular cloning of SCDGF-B, a novel growth factor homologous to SCDGF/PDGF-C/fallotein."
      Hamada T., Ui-Tei K., Imaki J., Miyata Y.
      Biochem. Biophys. Res. Commun. 280:733-737(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
      Tissue: Fetal brain.
    2. "The expression of SCDGF/PDGF-C/fallotein and SCDGF-B/PDGF-D in the rat central nervous system."
      Hamada T., Ui-Tei K., Imaki J., Takahashi F., Onodera H., Mishima T., Miyata Y.
      Mech. Dev. 112:161-164(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION OF ISOFORM 2, TISSUE SPECIFICITY, DEVELOPMENTAL STAGE.
    3. "A fully human monoclonal antibody (CR002) identifies PDGF-D as a novel mediator of mesangioproliferative glomerulonephritis."
      Ostendorf T., van Roeyen C.R.C., Peterson J.D., Kunter U., Eitner F., Hamad A.J., Chan G., Jia X.-C., Macaluso J., Gazit-Bornstein G., Keyt B.A., Lichenstein H.S., LaRochelle W.J., Floege J.
      J. Am. Soc. Nephrol. 14:2237-2247(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, TISSUE SPECIFICITY.
    4. "Platelet-derived growth factor D, tissue-specific expression in the eye, and a key role in control of lens epithelial cell proliferation."
      Ray S., Gao C., Wyatt K., Fariss R.N., Bundek A., Zelenka P., Wistow G.
      J. Biol. Chem. 280:8494-8502(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, TISSUE SPECIFICITY.

    Entry informationi

    Entry nameiPDGFD_RAT
    AccessioniPrimary (citable) accession number: Q9EQT1
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: September 19, 2006
    Last sequence update: March 1, 2001
    Last modified: October 1, 2014
    This is version 75 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programChordata Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    Complete proteome, Reference proteome

    Documents

    1. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3