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Protein

Platelet-derived growth factor D

Gene

Pdgfd

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-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 (By similarity). Has oncogenic potential and can induce tumor formation. 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 similarity3 Publications

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sitei247 – 2482CleavageSequence Analysis
Sitei249 – 2502CleavageSequence Analysis

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Developmental protein, Growth factor, Mitogen

Enzyme and pathway databases

ReactomeiREACT_280178. Signaling by PDGF.

Names & Taxonomyi

Protein namesi
Recommended name:
Platelet-derived growth factor D
Short name:
PDGF-D
Alternative name(s):
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:Scdgfb
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
ProteomesiUP000000589 Componenti: Chromosome 9

Organism-specific databases

MGIiMGI:1919035. Pdgfd.

Subcellular locationi

  • Secreted By similarity

  • Note: Released by platelets upon wounding.By similarity

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Secreted

Pathology & Biotechi

Keywords - Diseasei

Proto-oncogene

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 2323Sequence AnalysisAdd
BLAST
Chaini24 – 370347Platelet-derived growth factor D, latent formPRO_0000250190Add
BLAST
Chaini250 – 370121Platelet-derived growth factor D, receptor-binding formSequence AnalysisPRO_0000250191Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi109 ↔ 131PROSITE-ProRule annotation
Glycosylationi276 – 2761N-linked (GlcNAc...)Sequence Analysis
Disulfide bondi296 – 296InterchainPROSITE-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

Keywords - PTMi

Cleavage on pair of basic residues, Disulfide bond, Glycoprotein

Proteomic databases

PaxDbiQ925I7.
PRIDEiQ925I7.

PTM databases

PhosphoSiteiQ925I7.

Expressioni

Tissue specificityi

Expressed at high levels in developing heart, lung, kidney and some muscle derivatives. Moderately expressed in liver, brain and testis. In the kidney, localized to glomerular mesangial cells and vascular smooth muscle cells. Up-regulated in areas of renal fibrosis. In mice with unilateral ureteral obstruction, expressed in interstitial cells at day 4, with an increased to maximal expression at day 14.4 Publications

Gene expression databases

BgeeiQ925I7.
CleanExiMM_PDGFD.
GenevestigatoriQ925I7.

Interactioni

Subunit structurei

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

Protein-protein interaction databases

STRINGi10090.ENSMUSP00000056240.

Structurei

3D structure databases

ProteinModelPortaliQ925I7.
SMRiQ925I7. Positions 62-206, 253-363.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini52 – 170119CUBPROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

Belongs to the PDGF/VEGF growth factor family.Curated
Contains 1 CUB domain.PROSITE-ProRule annotation

Keywords - Domaini

Signal

Phylogenomic databases

eggNOGiNOG148355.
GeneTreeiENSGT00390000005171.
HOGENOMiHOG000261610.
HOVERGENiHBG057324.
InParanoidiQ925I7.
KOiK05450.
OMAiHYRGRSY.
OrthoDBiEOG7VB2FN.
PhylomeDBiQ925I7.
TreeFamiTF332130.

Family and domain databases

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]
PANTHERiPTHR10127:SF13. PTHR10127:SF13. 1 hit.
PfamiPF00431. CUB. 1 hit.
PF00341. PDGF. 1 hit.
[Graphical view]
SMARTiSM00042. CUB. 1 hit.
SM00141. PDGF. 1 hit.
[Graphical view]
SUPFAMiSSF49854. SSF49854. 1 hit.
SSF57501. SSF57501. 1 hit.
PROSITEiPS01180. CUB. 1 hit.
PS50278. PDGF_2. 1 hit.
[Graphical view]

Sequences (3)i

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

This entry describes 3 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q925I7-1) [UniParc]FASTAAdd to basket

Also known as: Long

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
MQRLVLVSIL LCANFSCYPD TFATPQRASI KALRNANLRR DESNHLTDLY
60 70 80 90 100
QREENIQVTS NGHVQSPRFP NSYPRNLLLT WWLRSQEKTR IQLSFDHQFG
110 120 130 140 150
LEEAENDICR YDFVEVEEVS ESSTVVRGRW CGHKEIPPRI TSRTNQIKIT
160 170 180 190 200
FKSDDYFVAK PGFKIYYSFV EDFQPEAASE TNWESVTSSF SGVSYHSPSI
210 220 230 240 250
TDPTLTADAL DKTVAEFDTV EDLLKHFNPV SWQDDLENLY LDTPHYRGRS
260 270 280 290 300
YHDRKSKVDL DRLNDDVKRY SCTPRNHSVN LREELKLTNA VFFPRCLLVQ
310 320 330 340 350
RCGGNCGCGT VNWKSCTCSS GKTVKKYHEV LKFEPGHFKR RGKAKNMALV
360 370
DIQLDHHERC DCICSSRPPR
Length:370
Mass (Da):42,809
Last modified:December 1, 2001 - v1
Checksum:i9E80B4CF6813BFBE
GO
Isoform 2 (identifier: Q925I7-2) [UniParc]FASTAAdd to basket

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

Show »
Length:364
Mass (Da):42,127
Checksum:i4273B8715A7DBC97
GO
Isoform 3 (identifier: Q925I7-3) [UniParc]FASTAAdd to basket

Also known as: Short

The sequence of this isoform differs from the canonical sequence as follows:
     258-261: VDLD → GIEV
     262-370: Missing.

Show »
Length:261
Mass (Da):30,289
Checksum:i3AA92B3236B16809
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti173 – 1731F → S in AAH30896 (PubMed:15489334).Curated

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei42 – 476Missing in isoform 2. 1 PublicationVSP_020616
Alternative sequencei258 – 2614VDLD → GIEV in isoform 3. 2 PublicationsVSP_020617
Alternative sequencei262 – 370109Missing in isoform 3. 2 PublicationsVSP_020618Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF335583 mRNA. Translation: AAK38839.1.
AK003359 mRNA. Translation: BAB22735.2.
AK141551 mRNA. Translation: BAE24732.1.
BC030896 mRNA. Translation: AAH30896.1.
CCDSiCCDS22801.1. [Q925I7-1]
RefSeqiNP_082200.1. NM_027924.2. [Q925I7-1]
XP_006509948.1. XM_006509885.2. [Q925I7-2]
XP_006509949.1. XM_006509886.2. [Q925I7-3]
UniGeneiMm.390122.

Genome annotation databases

EnsembliENSMUST00000058692; ENSMUSP00000056240; ENSMUSG00000032006. [Q925I7-2]
ENSMUST00000168039; ENSMUSP00000128388; ENSMUSG00000032006. [Q925I7-1]
GeneIDi71785.
KEGGimmu:71785.
UCSCiuc009oby.1. mouse. [Q925I7-1]
uc009obz.1. mouse. [Q925I7-2]
uc012gnq.1. mouse. [Q925I7-3]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF335583 mRNA. Translation: AAK38839.1.
AK003359 mRNA. Translation: BAB22735.2.
AK141551 mRNA. Translation: BAE24732.1.
BC030896 mRNA. Translation: AAH30896.1.
CCDSiCCDS22801.1. [Q925I7-1]
RefSeqiNP_082200.1. NM_027924.2. [Q925I7-1]
XP_006509948.1. XM_006509885.2. [Q925I7-2]
XP_006509949.1. XM_006509886.2. [Q925I7-3]
UniGeneiMm.390122.

3D structure databases

ProteinModelPortaliQ925I7.
SMRiQ925I7. Positions 62-206, 253-363.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi10090.ENSMUSP00000056240.

PTM databases

PhosphoSiteiQ925I7.

Proteomic databases

PaxDbiQ925I7.
PRIDEiQ925I7.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000058692; ENSMUSP00000056240; ENSMUSG00000032006. [Q925I7-2]
ENSMUST00000168039; ENSMUSP00000128388; ENSMUSG00000032006. [Q925I7-1]
GeneIDi71785.
KEGGimmu:71785.
UCSCiuc009oby.1. mouse. [Q925I7-1]
uc009obz.1. mouse. [Q925I7-2]
uc012gnq.1. mouse. [Q925I7-3]

Organism-specific databases

CTDi80310.
MGIiMGI:1919035. Pdgfd.

Phylogenomic databases

eggNOGiNOG148355.
GeneTreeiENSGT00390000005171.
HOGENOMiHOG000261610.
HOVERGENiHBG057324.
InParanoidiQ925I7.
KOiK05450.
OMAiHYRGRSY.
OrthoDBiEOG7VB2FN.
PhylomeDBiQ925I7.
TreeFamiTF332130.

Enzyme and pathway databases

ReactomeiREACT_280178. Signaling by PDGF.

Miscellaneous databases

NextBioi334516.
PROiQ925I7.
SOURCEiSearch...

Gene expression databases

BgeeiQ925I7.
CleanExiMM_PDGFD.
GenevestigatoriQ925I7.

Family and domain databases

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]
PANTHERiPTHR10127:SF13. PTHR10127:SF13. 1 hit.
PfamiPF00431. CUB. 1 hit.
PF00341. PDGF. 1 hit.
[Graphical view]
SMARTiSM00042. CUB. 1 hit.
SM00141. PDGF. 1 hit.
[Graphical view]
SUPFAMiSSF49854. SSF49854. 1 hit.
SSF57501. SSF57501. 1 hit.
PROSITEiPS01180. CUB. 1 hit.
PS50278. PDGF_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
    Strain: BALB/c.
  2. "A novel murine PDGF-D splicing variant results in significant differences in peptide expression and function."
    Zhuo Y., Hoyle G.W., Zhang J., Morris G., Lasky J.A.
    Biochem. Biophys. Res. Commun. 308:126-132(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 1 AND 3), TISSUE SPECIFICITY.
  3. "The transcriptional landscape of the mammalian genome."
    Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N., Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K., Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J.
    , Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R., Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T., Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A., Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B., Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M., Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S., Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E., Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D., Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M., Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H., Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V., Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S., Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H., Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N., Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F., Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G., Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z., Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C., Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y., Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S., Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K., Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R., van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H., Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M., Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C., Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S., Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K., Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M., Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C., Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A., Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.
    Science 309:1559-1563(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 2).
    Strain: C57BL/6J.
    Tissue: Hippocampus.
  4. "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 3).
    Strain: FVB/N.
    Tissue: Mammary gland.
  5. "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: TISSUE SPECIFICITY.
  6. "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: FUNCTION.
  7. Cited for: REVIEW.
  8. "Exogenous PDGF-D is a potent mesangial cell mitogen and causes a severe mesangial proliferative glomerulopathy."
    Hudkins K.L., Gilbertson D.G., Carling M., Taneda S., Hughes S.D., Holdren M.S., Palmer T.E., Topouzis S., Haran A.C., Feldhaus A.L., Alpers C.E.
    J. Am. Soc. Nephrol. 15:286-298(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, TISSUE SPECIFICITY.
  9. "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.
  10. "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.

Entry informationi

Entry nameiPDGFD_MOUSE
AccessioniPrimary (citable) accession number: Q925I7
Secondary accession number(s): Q3URF6, Q8K2L3, Q9D1L8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 19, 2006
Last sequence update: December 1, 2001
Last modified: May 27, 2015
This is version 99 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.