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Protein

Platelet-derived growth factor D

Gene

PDGFD

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-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

Complete GO annotation...

Keywords - Molecular functioni

Developmental protein, Growth factor, Mitogen

Enzyme and pathway databases

BioCyciZFISH:ENSG00000170962-MONOMER.
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

HGNCiHGNC:30620. PDGFD.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

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.

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...)Sequence 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

HPAiHPA066271.

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. 19 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
Contains 1 CUB domain.PROSITE-ProRule annotation

Keywords - Domaini

Signal

Phylogenomic databases

eggNOGiENOG410IGUN. Eukaryota.
ENOG41106HA. LUCA.
GeneTreeiENSGT00390000005171.
HOGENOMiHOG000261610.
HOVERGENiHBG057324.
InParanoidiQ9GZP0.
KOiK05450.
OMAiGHFKRRG.
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.
InterProiIPR000859. CUB_dom.
IPR029034. Cystine-knot_cytokine.
IPR000072. PDGF/VEGF_dom.
IPR027123. PDGFD.
[Graphical view]
PANTHERiPTHR11633:SF4. PTHR11633:SF4. 1 hit.
PfamiPF00431. CUB. 1 hit.
PF00341. PDGF. 1 hit.
[Graphical view]
SMARTiSM00042. CUB. 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. 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 rs35045740dbSNPEnsembl.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

Cross-referencesi

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.

3D structure databases

ProteinModelPortaliQ9GZP0.
SMRiQ9GZP0.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi123223. 19 interactors.
STRINGi9606.ENSP00000376865.

PTM databases

iPTMnetiQ9GZP0.
PhosphoSitePlusiQ9GZP0.

Polymorphism and mutation databases

BioMutaiPDGFD.
DMDMi74717921.

Proteomic databases

PaxDbiQ9GZP0.
PeptideAtlasiQ9GZP0.
PRIDEiQ9GZP0.

Protocols and materials databases

DNASUi80310.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Organism-specific databases

CTDi80310.
DisGeNETi80310.
GeneCardsiPDGFD.
HGNCiHGNC:30620. PDGFD.
HPAiHPA066271.
MIMi609673. gene.
neXtProtiNX_Q9GZP0.
OpenTargetsiENSG00000170962.
PharmGKBiPA134892327.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiENOG410IGUN. Eukaryota.
ENOG41106HA. LUCA.
GeneTreeiENSGT00390000005171.
HOGENOMiHOG000261610.
HOVERGENiHBG057324.
InParanoidiQ9GZP0.
KOiK05450.
OMAiGHFKRRG.
OrthoDBiEOG091G08SH.
PhylomeDBiQ9GZP0.
TreeFamiTF332130.

Enzyme and pathway databases

BioCyciZFISH:ENSG00000170962-MONOMER.
ReactomeiR-HSA-186797. Signaling by PDGF.
SignaLinkiQ9GZP0.

Miscellaneous databases

ChiTaRSiPDGFD. human.
GeneWikiiPDGFD.
GenomeRNAii80310.
PMAP-CutDBQ9GZP0.
PROiQ9GZP0.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000170962.
CleanExiHS_PDGFD.
ExpressionAtlasiQ9GZP0. baseline and differential.
GenevisibleiQ9GZP0. HS.

Family and domain databases

CDDicd00041. CUB. 1 hit.
cd00135. PDGF. 1 hit.
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]
PANTHERiPTHR11633:SF4. PTHR11633:SF4. 1 hit.
PfamiPF00431. CUB. 1 hit.
PF00341. PDGF. 1 hit.
[Graphical view]
SMARTiSM00042. CUB. 1 hit.
[Graphical view]
SUPFAMiSSF49854. SSF49854. 1 hit.
SSF57501. SSF57501. 1 hit.
PROSITEiPS01180. CUB. 1 hit.
PS50278. PDGF_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiPDGFD_HUMAN
AccessioniPrimary (citable) accession number: Q9GZP0
Secondary accession number(s): A8K9T6, Q9BWV5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 19, 2006
Last sequence update: March 1, 2001
Last modified: November 30, 2016
This is version 128 of the entry and version 1 of the sequence. [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

Documents

  1. Human chromosome 11
    Human chromosome 11: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.