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Q9EQT1

- PDGFD_RAT

UniProt

Q9EQT1 - PDGFD_RAT

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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

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
Complete GO annotation...

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 vesicular exosome Source: Ensembl
  2. membrane Source: InterPro
Complete GO annotation...

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.
InParanoidiQ9EQT1.
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

        10         20         30         40         50
MHRLILVSIL VCANFCCYRD TFATPQSASI KALRNANLRR DESNHLTDLY
60 70 80 90 100
RRDENIRVTG TGHVQSPRFP NSYPRNLLLT WRLHSQEKTR IQLAFDHQFG
110 120 130 140 150
LEEAENDICR YDFVEVEDVS ESSTVVRGRW CGHKEIPPRI TSRTNQIKIT
160 170 180 190 200
FQSDDYFVAK PGFKIYYSFV EDFQPEAASE INWESVTSSF SGVSYHSPSV
210 220 230 240 250
MDSTLTADAL DKAIAEFDTV EDLLKYFNPA SWQDDLENLY MDTPRYRGRS
260 270 280 290 300
YHERKSKVDL DRLNDDVKRY SCTPRNHSVN LREELKLTNA VFFPRCLLVQ
310 320 330 340 350
RCGGNCGCGT LNWKSCTCSS GKTVKKYHEV LKFEPGHFKR RGKAKNMALV
360 370
DIQLDHHERC DCICSSRPPR
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.
InParanoidi Q9EQT1.
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 29, 2014
This is version 76 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