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Q9EQT1 (PDGFD_RAT) Reviewed, UniProtKB/Swiss-Prot

Last modified June 11, 2014. Version 73. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (1) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended 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:

  1. Platelet-derived growth factor D, latent form
    Short name=PDGFD latent form
  2. Platelet-derived growth factor D, receptor-binding form
    Short name=PDGFD receptor-binding form
Gene names
Name:Pdgfd
Synonyms:Iegf, Scdgfb
OrganismRattus norvegicus (Rat) [Reference proteome]
Taxonomic identifier10116 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus

Protein attributes

Sequence length370 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at transcript level

General annotation (Comments)

Function

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. Ref.3 Ref.4

Subunit structure

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

Subcellular location

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

Tissue specificity

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. Ref.2 Ref.3 Ref.4

Developmental stage

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. Ref.2

Post-translational modification

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.

Sequence similarities

Belongs to the PDGF/VEGF growth factor family.

Contains 1 CUB domain.

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: Q9EQT1-1)

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.
Isoform 2 (identifier: Q9EQT1-2)

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

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Signal peptide1 – 2323 Potential
Chain24 – 370347Platelet-derived growth factor D, latent form
PRO_0000250196
Chain250 – 370121Platelet-derived growth factor D, receptor-binding form Potential
PRO_0000250197

Regions

Domain52 – 170119CUB

Sites

Site247 – 2482Cleavage Potential
Site249 – 2502Cleavage Potential

Amino acid modifications

Glycosylation2761N-linked (GlcNAc...) Potential
Disulfide bond109 ↔ 131 By similarity
Disulfide bond296Interchain By similarity
Disulfide bond302 ↔ 360 By similarity
Disulfide bond306 ↔ 362 By similarity

Natural variations

Alternative sequence42 – 476Missing in isoform 2.
VSP_020619

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 [UniParc].

Last modified March 1, 2001. Version 1.
Checksum: 7BE8A251F679BF73

FASTA37042,809
        10         20         30         40         50         60 
MHRLILVSIL VCANFCCYRD TFATPQSASI KALRNANLRR DESNHLTDLY RRDENIRVTG 

        70         80         90        100        110        120 
TGHVQSPRFP NSYPRNLLLT WRLHSQEKTR IQLAFDHQFG LEEAENDICR YDFVEVEDVS 

       130        140        150        160        170        180 
ESSTVVRGRW CGHKEIPPRI TSRTNQIKIT FQSDDYFVAK PGFKIYYSFV EDFQPEAASE 

       190        200        210        220        230        240 
INWESVTSSF SGVSYHSPSV MDSTLTADAL DKAIAEFDTV EDLLKYFNPA SWQDDLENLY 

       250        260        270        280        290        300 
MDTPRYRGRS YHERKSKVDL DRLNDDVKRY SCTPRNHSVN LREELKLTNA VFFPRCLLVQ 

       310        320        330        340        350        360 
RCGGNCGCGT LNWKSCTCSS GKTVKKYHEV LKFEPGHFKR RGKAKNMALV DIQLDHHERC 

       370 
DCICSSRPPR 

« Hide

Isoform 2 [UniParc].

Checksum: F5E3F7E8860361E8
Show »

FASTA36442,128

References

[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.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AB052170 mRNA. Translation: BAB18920.1.
PIRJC7592.
RefSeqNP_076452.1. NM_023962.2. [Q9EQT1-1]
UniGeneRn.64493.

3D structure databases

ProteinModelPortalQ9EQT1.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING10116.ENSRNOP00000039308.

Proteomic databases

PRIDEQ9EQT1.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENSRNOT00000049325; ENSRNOP00000039308; ENSRNOG00000029148. [Q9EQT1-1]
GeneID66018.
KEGGrno:66018.
UCSCRGD:621880. rat. [Q9EQT1-1]

Organism-specific databases

CTD80310.
RGD621880. Pdgfd.

Phylogenomic databases

eggNOGNOG148355.
GeneTreeENSGT00390000005171.
HOGENOMHOG000214105.
HOVERGENHBG057324.
KOK05450.
OMAHYRGRSY.
OrthoDBEOG7VB2FN.
PhylomeDBQ9EQT1.

Gene expression databases

GenevestigatorQ9EQT1.

Family and domain databases

Gene3D2.10.90.10. 1 hit.
2.60.120.290. 1 hit.
InterProIPR000859. CUB_dom.
IPR029034. Cystine-knot_cytokine.
IPR000072. PDGF/VEGF_dom.
IPR027123. PDGFD.
[Graphical view]
PANTHERPTHR10127:SF13. PTHR10127:SF13. 1 hit.
PfamPF00431. CUB. 1 hit.
PF00341. PDGF. 1 hit.
[Graphical view]
SMARTSM00042. CUB. 1 hit.
SM00141. PDGF. 1 hit.
[Graphical view]
SUPFAMSSF49854. SSF49854. 1 hit.
SSF57501. SSF57501. 1 hit.
PROSITEPS01180. CUB. 1 hit.
PS50278. PDGF_2. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

NextBio614300.
PROQ9EQT1.

Entry information

Entry namePDGFD_RAT
AccessionPrimary (citable) accession number: Q9EQT1
Entry history
Integrated into UniProtKB/Swiss-Prot: September 19, 2006
Last sequence update: March 1, 2001
Last modified: June 11, 2014
This is version 73 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families