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Protein

Platelet-derived growth factor D

Gene

Pdgfd

Organism
Rattus norvegicus (Rat)
Status
Reviewed-Annotation score: -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

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionDevelopmental protein, Growth factor, Mitogen

Enzyme and pathway databases

ReactomeiR-RNO-186797 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 lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaMyomorphaMuroideaMuridaeMurinaeRattus
Proteomesi
  • UP000002494 Componenti: Chromosome 8

Organism-specific databases

RGDi621880 Pdgfd

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Secreted

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Signal peptidei1 – 23Sequence analysisAdd BLAST23
ChainiPRO_000025019624 – 370Platelet-derived growth factor D, latent formAdd BLAST347
ChainiPRO_0000250197250 – 370Platelet-derived growth factor D, receptor-binding formSequence analysisAdd BLAST121

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Disulfide bondi109 ↔ 131PROSITE-ProRule annotation
Glycosylationi276N-linked (GlcNAc...) asparagineSequence analysis1
Disulfide bondi296InterchainPROSITE-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

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei247 – 248CleavageSequence analysis2
Sitei249 – 250CleavageSequence analysis2

Keywords - PTMi

Cleavage on pair of basic residues, Disulfide bond, Glycoprotein

Proteomic databases

PaxDbiQ9EQT1
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

BgeeiENSRNOG00000029148
ExpressionAtlasiQ9EQT1 baseline and differential
GenevisibleiQ9EQT1 RN

Interactioni

Subunit structurei

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

GO - Molecular functioni

Protein-protein interaction databases

STRINGi10116.ENSRNOP00000039308

Structurei

3D structure databases

ProteinModelPortaliQ9EQT1
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini52 – 170CUBPROSITE-ProRule annotationAdd BLAST119

Sequence similaritiesi

Belongs to the PDGF/VEGF growth factor family.Curated

Keywords - Domaini

Signal

Phylogenomic databases

eggNOGiENOG410IGUN Eukaryota
ENOG41106HA LUCA
GeneTreeiENSGT00390000005171
HOGENOMiHOG000214105
HOVERGENiHBG057324
InParanoidiQ9EQT1
KOiK05450
OMAiYHSPSVT
OrthoDBiEOG091G08SH
PhylomeDBiQ9EQT1

Family and domain databases

CDDicd00041 CUB, 1 hit
cd00135 PDGF, 1 hit
Gene3Di2.10.90.10, 1 hit
2.60.120.290, 1 hit
InterProiView protein in InterPro
IPR000859 CUB_dom
IPR029034 Cystine-knot_cytokine
IPR000072 PDGF/VEGF_dom
IPR027123 PDGFD
IPR035914 Sperma_CUB_dom_sf
PANTHERiPTHR11633:SF4 PTHR11633:SF4, 1 hit
PfamiView protein in Pfam
PF00431 CUB, 1 hit
PF00341 PDGF, 1 hit
SMARTiView protein in SMART
SM00042 CUB, 1 hit
SM00141 PDGF, 1 hit
SUPFAMiSSF49854 SSF49854, 1 hit
SSF57501 SSF57501, 1 hit
PROSITEiView protein in PROSITE
PS01180 CUB, 1 hit
PS50278 PDGF_2, 1 hit

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. AlignAdd to basket

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)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_02061942 – 47Missing in isoform 2. Curated6

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB052170 mRNA Translation: BAB18920.1
PIRiJC7592
RefSeqiNP_076452.1, NM_023962.2 [Q9EQT1-1]
UniGeneiRn.64493

Genome annotation databases

EnsembliENSRNOT00000049325; ENSRNOP00000039308; ENSRNOG00000029148 [Q9EQT1-2]
ENSRNOT00000076529; ENSRNOP00000068187; ENSRNOG00000029148 [Q9EQT1-1]
GeneIDi66018
KEGGirno:66018
UCSCiRGD:621880 rat [Q9EQT1-1]

Keywords - Coding sequence diversityi

Alternative splicing

Similar proteinsi

Entry informationi

Entry nameiPDGFD_RAT
AccessioniPrimary (citable) accession number: Q9EQT1
Entry historyiIntegrated into UniProtKB/Swiss-Prot: September 19, 2006
Last sequence update: March 1, 2001
Last modified: May 23, 2018
This is version 98 of the entry and version 1 of the sequence. See 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

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