Q9GZP0 (PDGFD_HUMAN) Reviewed, UniProtKB/Swiss-Prot
Last modified
May 1, 2013.
Version 90.
History...
Names·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order
Names·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize orderNames and origin
| Protein names | 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:
| ||||||
| Gene names |
| ||||||
| Organism | Homo sapiens (Human) [Reference proteome] | ||||||
| Taxonomic identifier | 9606 [NCBI] | ||||||
| Taxonomic lineage | Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo![]() |
Protein attributes
| Sequence length | 370 AA. |
| Sequence status | Complete. |
| Sequence processing | The displayed sequence is further processed into a mature form. |
| Protein existence | Evidence at protein 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. Can initiate events that lead to a mesangial proliferative glomerulonephritis, including influx of monocytes and macrophages and production of extracellular matrix By similarity. Ref.2 Ref.14 |
| Subunit structure | Homodimer; disulfide-linked. Interacts with PDGFRB homodimers, and with heterodimers formed by PDGFRA and PDGFRB. Ref.2 Ref.3 |
| Subcellular location | |
| Tissue specificity | 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. Ref.2 Ref.3 Ref.10 Ref.11 Ref.12 Ref.13 Ref.16 |
| Developmental stage | 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. Ref.10 |
| 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. |
| Sequence similarities | Belongs to the PDGF/VEGF growth factor family. Contains 1 CUB domain. |
Ontologies
| Keywords | |
|---|---|
| Cellular component | Secreted |
| Coding sequence diversity | Alternative splicing Polymorphism |
| Disease | Proto-oncogene |
| Domain | Signal |
| Molecular function | Developmental protein Growth factor Mitogen |
| PTM | Cleavage on pair of basic residues Disulfide bond Glycoprotein |
| Technical term | Complete proteome Reference proteome |
| Gene Ontology (GO) | |
| Biological_process | cellular response to amino acid stimulus Inferred from electronic annotation. Source: Compara multicellular organismal developmentInferred from electronic annotation. Source: UniProtKB-KW positive regulation of cell divisionInferred from electronic annotation. Source: UniProtKB-KW regulation of peptidyl-tyrosine phosphorylationInferred from electronic annotation. Source: Compara |
| Cellular_component | Golgi membrane Traceable author statement. Source: Reactome endoplasmic reticulum lumenTraceable author statement. Source: Reactome extracellular regionTraceable author statement. Source: Reactome |
| Complete GO annotation... | |
Alternative products
| This entry describes 2 isoforms produced by alternative splicing. [Align] [Select] | ||||||
| Isoform 1 (identifier: Q9GZP0-1) 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. | ||||||
| Isoform 2 (identifier: Q9GZP0-2) Also known as: Short; SCDGF-B-S; The sequence of this isoform differs from the canonical sequence as follows: 42-47: Missing. |
Sequence annotation (Features)
| Feature key | Position(s) | Length | Description | Graphical view | Feature identifier | ||||||
Molecule processing | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Signal peptide | 1 – 18 | 18 | Potential | ||||||||
| Chain | 19 – 370 | 352 | Platelet-derived growth factor D, latent form | PRO_0000250188 | |||||||
| Chain | 250 – 370 | 121 | Platelet-derived growth factor D, receptor-binding form Potential | PRO_0000250189 | |||||||
Regions | |||||||||||
| Domain | 52 – 170 | 119 | CUB | ||||||||
Sites | |||||||||||
| Site | 247 – 248 | 2 | Cleavage Potential | ||||||||
| Site | 249 – 250 | 2 | Cleavage Potential | ||||||||
Amino acid modifications | |||||||||||
| Glycosylation | 276 | 1 | N-linked (GlcNAc...) Potential | ||||||||
| Disulfide bond | 109 ↔ 131 | By similarity | |||||||||
| Disulfide bond | 296 | Interchain By similarity | |||||||||
| Disulfide bond | 302 ↔ 360 | By similarity | |||||||||
| Disulfide bond | 306 ↔ 362 | By similarity | |||||||||
Natural variations | |||||||||||
| Alternative sequence | 42 – 47 | 6 | Missing in isoform 2. | VSP_020615 | |||||||
| Natural variant | 190 | 1 | I → V. Corresponds to variant rs35045740 [ dbSNP | Ensembl ]. | VAR_051563 | |||||||
| Natural variant | 202 | 1 | D → Y in a colorectal cancer sample; somatic mutation. Ref.18 | VAR_036418 | |||||||
Experimental info | |||||||||||
| Mutagenesis | 247 | 1 | R → A: Abolishes cleavage into active form; when associated with A-249. Ref.16 | ||||||||
| Mutagenesis | 249 | 1 | R → A: Abolishes cleavage into active form; when associated with A-247. Ref.16 | ||||||||
Sequences
| ||||||||||||||||||||||||
References
| « Hide 'large scale' 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] (ISOFORMS 1 AND 2). |
| [2] | "PDGF-D is a specific, protease-activated ligand for the PDGF beta-receptor." Bergsten E., Uutela M., Li X., Pietras K., Oestman A., Heldin C.-H., Alitalo K., Eriksson U. Nat. Cell Biol. 3:512-516(2001) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), FUNCTION, SUBUNIT, TISSUE SPECIFICITY. |
| [3] | "PDGF D, a novel protease-activated growth factor." LaRochelle W.J., Jeffers M., McDonald W.F., Chillakuru R.A., Giese N.A., Lokker N.A., Sullivan C., Boldog F.L., Yang M., Vernet C., Burgess C.E., Fernandez E., Deegler L.L., Rittman B., Shimkets J., Shimkets R.A., Rothberg J.M., Lichenstein H.S. Nat. Cell Biol. 3:517-521(2001) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), SUBUNIT, SUBCELLULAR LOCATION, TISSUE SPECIFICITY. |
| [4] | "Expressed sequence tag analysis of adult human iris for the NEIBank project: steroid-response factors and similarities with retinal pigment epithelium." Wistow G., Bernstein S.L., Ray S., Wyatt M.K., Behal A., Touchman J.W., Bouffard G., Smith D., Peterson K. Mol. Vis. 8:185-195(2002) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 1 AND 2). Tissue: Iris. |
| [5] | Liu B., Liu Y.Q., Wang X.Y., Zhao B., Sheng H., Zhao X.W., Liu S., Xu Y.Y., Ye J., Song L., Gao Y., Zhang C.L., Zhang J., Wei Y.J., Cao H.Q., Zhao Y., Liu L.S., Ding J.F. Hui R.T.Submitted (DEC-1998) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1). Tissue: Aorta. |
| [6] | "The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment." Clark H.F., Gurney A.L., Abaya E., Baker K., Baldwin D.T., Brush J., Chen J., Chow B., Chui C., Crowley C., Currell B., Deuel B., Dowd P., Eaton D., Foster J.S., Grimaldi C., Gu Q., Hass P.E. Gray A.M.Genome Res. 13:2265-2270(2003) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2). |
| [7] | "Complete sequencing and characterization of 21,243 full-length human cDNAs." Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S. Sugano S.Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1). Tissue: Trachea. |
| [8] | Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. Venter J.C.Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. |
| [9] | "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)." The MGC Project Team Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2). Tissue: Testis. |
| [10] | "Platelet-derived growth factor-D expression in developing and mature human kidneys." Changsirikulchai S., Hudkins K.L., Goodpaster T.A., Volpone J., Topouzis S., Gilbertson D.G., Alpers C.E. Kidney Int. 62:2043-2054(2002) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 64-369, TISSUE SPECIFICITY, DEVELOPMENTAL STAGE. |
| [11] | "Chromosomal location, exon structure, and vascular expression patterns of the human PDGFC and PDGFC genes." Uutela M., Lauren J., Bergsten E., Li X., Horelli-Kuitunen N., Eriksson U., Alitalo K. Circulation 103:2242-2247(2001) [PubMed] [Europe PMC] [Abstract] Cited for: TISSUE SPECIFICITY. |
| [12] | "Platelet-derived growth factor D: tumorigenicity in mice and dysregulated expression in human cancer." LaRochelle W.J., Jeffers M., Corvalan J.R.F., Jia X.-C., Feng X., Vanegas S., Vickroy J.D., Yang X.-D., Chen F., Gazit G., Mayotte J., Macaluso J., Rittman B., Wu F., Dhanabal M., Herrmann J., Lichenstein H.S. Cancer Res. 62:2468-2473(2002) [PubMed] [Europe PMC] [Abstract] Cited for: TISSUE SPECIFICITY. |
| [13] | "Obstructive uropathy in mice and humans: potential role for PDGF-D in the progression of tubulointerstitial injury." Taneda S., Hudkins K.L., Topouzis S., Gilbertson D.G., Ophascharoensuk V., Truong L., Johnson R.J., Alpers C.E. J. Am. Soc. Nephrol. 14:2544-2555(2003) [PubMed] [Europe PMC] [Abstract] Cited for: TISSUE SPECIFICITY. |
| [14] | "PDGF-D induces macrophage recruitment, increased interstitial pressure, and blood vessel maturation during angiogenesis." Uutela M., Wirzenius M., Paavonen K., Rajantie I., He Y., Karpanen T., Lohela M., Wiig H., Salven P., Pajusola K., Eriksson U., Alitalo K. Blood 104:3198-3204(2004) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION. |
| [15] | "Structural and functional specificities of PDGF-C and PDGF-D, the novel members of the platelet-derived growth factors family." Reigstad L.J., Varhaug J.E., Lillehaug J.R. FEBS J. 272:5723-5741(2005) [PubMed] [Europe PMC] [Abstract] Cited for: REVIEW. |
| [16] | "Platelet-derived growth factor D is activated by urokinase plasminogen activator in prostate carcinoma cells." Ustach C.V., Kim H.-R.C. Mol. Cell. Biol. 25:6279-6288(2005) [PubMed] [Europe PMC] [Abstract] Cited for: TISSUE SPECIFICITY, PTM, MUTAGENESIS OF ARG-247 AND ARG-249. |
| [17] | "Emerging roles of PDGF-D signaling pathway in tumor development and progression." Wang Z., Ahmad A., Li Y., Kong D., Azmi A.S., Banerjee S., Sarkar F.H. Biochim. Biophys. Acta 1806:122-130(2010) [PubMed] [Europe PMC] [Abstract] Cited for: REVIEW. |
| [18] | "The consensus coding sequences of human breast and colorectal cancers." Sjoeblom T., Jones S., Wood L.D., Parsons D.W., Lin J., Barber T.D., Mandelker D., Leary R.J., Ptak J., Silliman N., Szabo S., Buckhaults P., Farrell C., Meeh P., Markowitz S.D., Willis J., Dawson D., Willson J.K.V. Velculescu V.E.Science 314:268-274(2006) [PubMed] [Europe PMC] [Abstract] Cited for: VARIANT [LARGE SCALE ANALYSIS] TYR-202. |
| + | Additional computationally mapped references. |
Cross-references
Sequence databases | |
|---|---|
| EMBL GenBank DDBJ | 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. |
| IPI | IPI00011865. IPI00018822. |
| PIR | JC7591. |
| RefSeq | NP_079484.1. NM_025208.4. NP_149126.1. NM_033135.3. |
| UniGene | Hs.352298. |
3D structure databases | |
| HSSP | HSSP built from PDB template 1NT0 based on UniProtKB Q9QX89. |
| ProteinModelPortal | Q9GZP0. |
| ModBase | Search... |
Protein-protein interaction databases | |
| STRING | 9606.ENSP00000376865. |
PTM databases | |
| PhosphoSite | Q9GZP0. |
Polymorphism databases | |
| DMDM | 74717921. |
Proteomic databases | |
| PaxDb | Q9GZP0. |
| PRIDE | Q9GZP0. |
Protocols and materials databases | |
| DNASU | 80310. |
| StructuralBiologyKnowledgebase | Search... |
Genome annotation databases | |
| Ensembl | ENST00000302251; ENSP00000302193; ENSG00000170962. ENST00000393158; ENSP00000376865; ENSG00000170962. |
| GeneID | 80310. |
| KEGG | hsa:80310. |
| UCSC | uc001php.3. human. uc001phq.3. human. |
Organism-specific databases | |
| CTD | 80310. |
| GeneCards | GC11M103777. |
| HGNC | HGNC:30620. PDGFD. |
| MIM | 609673. gene. |
| neXtProt | NX_Q9GZP0. |
| PharmGKB | PA134892327. |
| GenAtlas | Search... |
Phylogenomic databases | |
| eggNOG | NOG148355. |
| HOGENOM | HOG000261610. |
| HOVERGEN | HBG057324. |
| InParanoid | Q9GZP0. |
| KO | K05450. |
| OMA | LYLDTPH. |
| OrthoDB | EOG4NKBVN. |
Enzyme and pathway databases | |
| Pathway_Interaction_DB | pdgfrbpathway. PDGFR-beta signaling pathway. |
| Reactome | REACT_111102. Signal Transduction. |
Gene expression databases | |
| ArrayExpress | Q9GZP0. |
| Bgee | Q9GZP0. |
| CleanEx | HS_PDGFD. |
| Genevestigator | Q9GZP0. |
| GermOnline | ENSG00000170962. Homo sapiens. |
Family and domain databases | |
| Gene3D | 2.60.120.290. 1 hit. |
| InterPro | IPR000859. CUB_dom. IPR000072. PD_growth_factor. IPR027123. PDGFD. [Graphical view] |
| PANTHER | PTHR10127:SF13. PTHR10127:SF13. 1 hit. |
| Pfam | PF00431. CUB. 1 hit. PF00341. PDGF. 1 hit. [Graphical view] |
| SMART | SM00042. CUB. 1 hit. SM00141. PDGF. 1 hit. [Graphical view] |
| SUPFAM | SSF49854. CUB. 1 hit. |
| PROSITE | PS01180. CUB. 1 hit. PS00249. PDGF_1. False negative. PS50278. PDGF_2. 1 hit. [Graphical view] |
| ProtoNet | Search... |
Other | |
| ChiTaRS | PDGFD. human. |
| GenomeRNAi | 80310. |
| NextBio | 70792. |
| PMAP-CutDB | Q9GZP0. |
| SOURCE | Search... |
Entry information
| Entry name | PDGFD_HUMAN | ||||||||
| Accession | Primary (citable) accession number: Q9GZP0 Secondary accession number(s): A8K9T6, Q9BWV5 | ||||||||
| Entry history |
| ||||||||
| Entry status | Reviewed (UniProtKB/Swiss-Prot) | ||||||||
| Annotation program | Chordata Protein Annotation Program | ||||||||
| Disclaimer | Any 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. | ||||||||
Relevant documents
| Human chromosome 11 Human chromosome 11: entries, gene names and cross-references to MIM |
| Human entries with polymorphisms or disease mutations List of human entries with polymorphisms or disease mutations |
| Human polymorphisms and disease mutations Index of human polymorphisms and disease mutations |
| MIM cross-references Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot |
| SIMILARITY comments Index of protein domains and families |

Clusters with
