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Protein

Platelet-derived growth factor D

Gene

PDGFD

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -Experimental evidence at protein 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. Can initiate events that lead to a mesangial proliferative glomerulonephritis, including influx of monocytes and macrophages and production of extracellular matrix (By similarity).By similarity2 Publications

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionDevelopmental protein, Growth factor, Mitogen

Enzyme and pathway databases

ReactomeiR-HSA-186797 Signaling by PDGF
SignaLinkiQ9GZP0

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
ORF Names:MSTP036, UNQ1899/PRO4345
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 11

Organism-specific databases

EuPathDBiHostDB:ENSG00000170962.12
HGNCiHGNC:30620 PDGFD
MIMi609673 gene
neXtProtiNX_Q9GZP0

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

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi247R → A: Abolishes cleavage into active form; when associated with A-249. 1 Publication1
Mutagenesisi249R → A: Abolishes cleavage into active form; when associated with A-247. 1 Publication1

Keywords - Diseasei

Proto-oncogene

Organism-specific databases

DisGeNETi80310
OpenTargetsiENSG00000170962
PharmGKBiPA134892327

Chemistry databases

DrugBankiDB05139 CR002
DB05465 MLN-518

Polymorphism and mutation databases

BioMutaiPDGFD
DMDMi74717921

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Signal peptidei1 – 18Sequence analysisAdd BLAST18
ChainiPRO_000025018819 – 370Platelet-derived growth factor D, latent formAdd BLAST352
ChainiPRO_0000250189250 – 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.

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

PaxDbiQ9GZP0
PeptideAtlasiQ9GZP0
PRIDEiQ9GZP0

PTM databases

iPTMnetiQ9GZP0
PhosphoSitePlusiQ9GZP0

Miscellaneous databases

PMAP-CutDBQ9GZP0

Expressioni

Tissue specificityi

Expressed at high levels in the heart, pancreas, adrenal gland and ovary and at low levels in placenta, liver, kidney, prostate, testis, small intestine, spleen and colon. In the kidney, expressed by the visceral epithelial cells of the glomeruli. A widespread expression is also seen in the medial smooth muscle cells of arteries and arterioles, as well as in smooth muscle cells of vasa rectae in the medullary area. Expressed in the adventitial connective tissue surrounding the suprarenal artery. In chronic obstructive nephropathy, a persistent expression is seen in glomerular visceral epithelial cells and vascular smooth muscle cells, as well as de novo expression by periglomerular interstitial cells and by some neointimal cells of atherosclerotic vessels. Expression in normal prostate is seen preferentially in the mesenchyme of the gland while expression is increased and more profuse in prostate carcinoma. Expressed in many ovarian, lung, renal and brain cancer-derived cell lines.7 Publications

Developmental stagei

Not detectable in the earliest stages of glomerulogenesis, and not detected in the metanephric blastema or surrounding cortical interstitial cells. In later stages of glomerulogenesis, localized to epithelial cells transitioning from the early developing nephrons of the comma- and S-shaped stages to the visceral epithelial cells of differentiated glomeruli. In the developing pelvis, expressed at the basement membrane of immature collecting ducts and by presumptive fibroblastic cells in the interstitium.1 Publication

Gene expression databases

BgeeiENSG00000170962
CleanExiHS_PDGFD
ExpressionAtlasiQ9GZP0 baseline and differential
GenevisibleiQ9GZP0 HS

Organism-specific databases

HPAiHPA046183
HPA066271

Interactioni

Subunit structurei

Homodimer; disulfide-linked. Interacts with PDGFRB homodimers, and with heterodimers formed by PDGFRA and PDGFRB.2 Publications

GO - Molecular functioni

Protein-protein interaction databases

BioGridi123223, 21 interactors
STRINGi9606.ENSP00000376865

Structurei

3D structure databases

ProteinModelPortaliQ9GZP0
SMRiQ9GZP0
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
HOGENOMiHOG000261610
HOVERGENiHBG057324
InParanoidiQ9GZP0
KOiK05450
OMAiYHSPSVT
OrthoDBiEOG091G08SH
PhylomeDBiQ9GZP0
TreeFamiTF332130

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
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: Q9GZP0-1) [UniParc]FASTAAdd to basket
Also known as: Long, SCDGF-B-L

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
MHRLIFVYTL ICANFCSCRD TSATPQSASI KALRNANLRR DESNHLTDLY
60 70 80 90 100
RRDETIQVKG NGYVQSPRFP NSYPRNLLLT WRLHSQENTR IQLVFDNQFG
110 120 130 140 150
LEEAENDICR YDFVEVEDIS ETSTIIRGRW CGHKEVPPRI KSRTNQIKIT
160 170 180 190 200
FKSDDYFVAK PGFKIYYSLL EDFQPAAASE TNWESVTSSI SGVSYNSPSV
210 220 230 240 250
TDPTLIADAL DKKIAEFDTV EDLLKYFNPE SWQEDLENMY LDTPRYRGRS
260 270 280 290 300
YHDRKSKVDL DRLNDDAKRY SCTPRNYSVN IREELKLANV VFFPRCLLVQ
310 320 330 340 350
RCGGNCGCGT VNWRSCTCNS GKTVKKYHEV LQFEPGHIKR RGRAKTMALV
360 370
DIQLDHHERC DCICSSRPPR
Length:370
Mass (Da):42,848
Last modified:March 1, 2001 - v1
Checksum:iD387F485E7BB7674
GO
Isoform 2 (identifier: Q9GZP0-2) [UniParc]FASTAAdd to basket
Also known as: Short, SCDGF-B-S

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

Show »
Length:364
Mass (Da):42,167
Checksum:i245C53E8DDEA9EAC
GO

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_051563190I → V. Corresponds to variant dbSNP:rs35045740Ensembl.1
Natural variantiVAR_036418202D → Y in a colorectal cancer sample; somatic mutation. 1 Publication1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_02061542 – 47Missing in isoform 2. 4 Publications6

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB033832 mRNA Translation: BAB18903.1
AF336376 mRNA Translation: AAK56136.1
AF335584 mRNA Translation: AAK38840.1
AY027517 mRNA Translation: AAK20081.1
AY027518 mRNA Translation: AAK20082.1
AF113216 mRNA Translation: AAG39287.1
AY359116 mRNA Translation: AAQ89474.1
AK292801 mRNA Translation: BAF85490.1
CH471065 Genomic DNA Translation: EAW67045.1
BC030645 mRNA Translation: AAH30645.1
CCDSiCCDS41703.1 [Q9GZP0-1]
CCDS8326.1 [Q9GZP0-2]
PIRiJC7591
RefSeqiNP_079484.1, NM_025208.4 [Q9GZP0-1]
NP_149126.1, NM_033135.3 [Q9GZP0-2]
UniGeneiHs.352298

Genome annotation databases

EnsembliENST00000302251; ENSP00000302193; ENSG00000170962 [Q9GZP0-2]
ENST00000393158; ENSP00000376865; ENSG00000170962 [Q9GZP0-1]
GeneIDi80310
KEGGihsa:80310
UCSCiuc001php.4 human [Q9GZP0-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Similar proteinsi

Entry informationi

Entry nameiPDGFD_HUMAN
AccessioniPrimary (citable) accession number: Q9GZP0
Secondary accession number(s): A8K9T6, Q9BWV5
Entry historyiIntegrated into UniProtKB/Swiss-Prot: September 19, 2006
Last sequence update: March 1, 2001
Last modified: May 23, 2018
This is version 138 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

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