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Reviewed, UniProtKB/Swiss-Prot P36955 (PEDF_HUMAN)

Last modified May 5, 2009. Version 103. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (6) | Third-party data | Customize display text xml rdf/xml gff fasta
Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents

Names and origin

Protein namesRecommended name:
    Pigment epithelium-derived factor
      Short name=PEDF
Alternative name(s):
    Serpin-F1
    EPC-1
Gene names
Name: SERPINF1
Synonyms: PEDF
OrganismHomo sapiens (Human)
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length418 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level.

General annotation (Comments)

Function

Neurotrophic protein; induces extensive neuronal differentiation in retinoblastoma cells. Potent inhibitor of angiogenesis. As it does not undergo the S (stressed) to R (relaxed) conformational transition characteristic of active serpins, it exhibits no serine protease inhibitory activity. Ref.9 Ref.10

Subcellular location

Secreted. Melanosome. Note: Enriched in stage I melanosomes. Ref.13

Tissue specificity

Retinal pigment epithelial cells and blood plasma. Ref.8

Developmental stage

Expressed in quiescent cells.

Domain

The N-terminal (AA 44-121) exhibits neurite outgrowth-inducing activity. The C-terminal exposed loop (AA 382-418) is essential for serpin activity.

Post-translational modification

The N-terminus is blocked. Extracellular phosphorylation enhances antiangiogenic activity.

Sequence similarities

Belongs to the serpin family.

Sequence caution

The sequence AAA84914.1 differs from that shown. Reason: Frameshift at position 356.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Signal peptide1 – 1919
Chain20 – 418399Pigment epithelium-derived factor
PRO_0000032508

Amino acid modifications

Modified residue201Pyrrolidone carboxylic acid
Modified residue241Phosphoserine; by CK2 Ref.11
Modified residue1141Phosphoserine; by CK2 Ref.11
Modified residue2271Phosphoserine; by PKA Ref.11
Glycosylation2851N-linked (GlcNAc...) Ref.12 Ref.15

Natural variations

Natural variant721M → T: dbSNP rs1136287. Ref.4 Ref.16
VAR_009126
Natural variant1321P → R: dbSNP rs1804145. Ref.5
VAR_025500

Experimental info

Sequence conflict97 – 982EQ → DE in AAA60058. Ref.1
Sequence conflict97 – 982EQ → DE in AAB38685. Ref.6

Secondary structure

.............................................................. 418
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P36955-1 [UniParc].

Last modified April 16, 2002. Version 3.
Checksum: 29B573A62EA51BE5

FASTA41846,342
        10         20         30         40         50         60 
MQALVLLLCI GALLGHSSCQ NPASPPEEGS PDPDSTGALV EEEDPFFKVP VNKLAAAVSN 

        70         80         90        100        110        120 
FGYDLYRVRS SMSPTTNVLL SPLSVATALS ALSLGAEQRT ESIIHRALYY DLISSPDIHG 

       130        140        150        160        170        180 
TYKELLDTVT APQKNLKSAS RIVFEKKLRI KSSFVAPLEK SYGTRPRVLT GNPRLDLQEI 

       190        200        210        220        230        240 
NNWVQAQMKG KLARSTKEIP DEISILLLGV AHFKGQWVTK FDSRKTSLED FYLDEERTVR 

       250        260        270        280        290        300 
VPMMSDPKAV LRYGLDSDLS CKIAQLPLTG SMSIIFFLPL KVTQNLTLIE ESLTSEFIHD 

       310        320        330        340        350        360 
IDRELKTVQA VLTVPKLKLS YEGEVTKSLQ EMKLQSLFDS PDFSKITGKP IKLTQVEHRA 

       370        380        390        400        410 
GFEWNEDGAG TTPSPGLQPA HLTFPLDYHL NQPFIFVLRD TDTGALLFIG KILDPRGP 

« Hide

References

« Hide 'large scale' references
[1]"Pigment epithelium-derived factor: neurotrophic activity and identification as a member of the serine protease inhibitor gene family."
Steele F.R., Chader G.J., Johnson L.V., Tombran-Tink J.
Proc. Natl. Acad. Sci. U.S.A. 90:1526-1530(1993) [PubMed: 8434014] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA], PARTIAL PROTEIN SEQUENCE.
Tissue: Fetal eye.
[2]"Organization, evolutionary conservation, expression and unusual Alu density of the human gene for pigment epithelium-derived factor, a unique neurotrophic serpin."
Tombran-Tink J., Mazuruk K., Rodriguez I.R., Chung D., Linker T., Englander E., Chader G.J.
Mol. Vis. 2:11-11(1996) [PubMed: 9238088] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[3]Yin B., Peng X., Yuan J., Qiang B.
Submitted (JUL-2001) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [MRNA].
[4]"Cloning of human full-length CDSs in BD Creator(TM) system donor vector."
Kalnine N., Chen X., Rolfs A., Halleck A., Hines L., Eisenstein S., Koundinya M., Raphael J., Moreira D., Kelley T., LaBaer J., Lin Y., Phelan M., Farmer A.
Submitted (MAY-2003) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA], VARIANT THR-72.
[5]"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: 15489334] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA], VARIANT ARG-132.
Tissue: Muscle.
[6]Coljee V.W.
Thesis (1996), Medical College of Pennsylvania, United States
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-332.
Tissue: Fetal lung fibroblast.
[7]"Senescent WI-38 cells fail to express EPC-1, a gene induced in young cells upon entry into the G0 state."
Pignolo R.J., Cristofalo V.J., Rotenberg M.O.
J. Biol. Chem. 268:8949-8957(1993) [PubMed: 8473338] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 60-418.
Tissue: Fetal lung fibroblast.
[8]"Pigment-epithelium-derived factor (PEDF) occurs at a physiologically relevant concentration in human blood: purification and characterization."
Petersen S.V., Valnickova Z., Enghild J.J.
Biochem. J. 374:199-206(2003) [PubMed: 12737624] [Abstract]
Cited for: PROTEIN SEQUENCE OF 21-29; 253-262 AND 282-303, TISSUE SPECIFICITY, PYROGLUTAMATE FORMATION AT GLN-20.
Tissue: Plasma.
[9]"Overexpression of fetal human pigment epithelium-derived factor in Escherichia coli. A functionally active neurotrophic factor."
Becerra S.P., Palmer I., Kumar A., Steele F.R., Shiloach J., Notario V., Chader G.J.
J. Biol. Chem. 268:23148-23156(1993) [PubMed: 8226833] [Abstract]
Cited for: FUNCTION.
[10]"Pigment epithelium-derived factor behaves like a noninhibitory serpin. Neurotrophic activity does not require the serpin reactive loop."
Becerra S.P., Sagasti A., Spinella P., Notario V.
J. Biol. Chem. 270:25992-25999(1995) [PubMed: 7592790] [Abstract]
Cited for: FUNCTION.
[11]"Extracellular phosphorylation converts pigment epithelium-derived factor from a neurotrophic to an antiangiogenic factor."
Maik-Rachline G., Shaltiel S., Seger R.
Blood 105:670-678(2005) [PubMed: 15374885] [Abstract]
Cited for: PHOSPHORYLATION AT SER-24; SER-114 AND SER-227.
[12]"Human plasma N-glycoproteome analysis by immunoaffinity subtraction, hydrazide chemistry, and mass spectrometry."
Liu T., Qian W.-J., Gritsenko M.A., Camp D.G. II, Monroe M.E., Moore R.J., Smith R.D.
J. Proteome Res. 4:2070-2080(2005) [PubMed: 16335952] [Abstract]
Cited for: GLYCOSYLATION [LARGE SCALE ANALYSIS] AT ASN-285, MASS SPECTROMETRY.
Tissue: Plasma.
[13]"Proteomic and bioinformatic characterization of the biogenesis and function of melanosomes."
Chi A., Valencia J.C., Hu Z.-Z., Watabe H., Yamaguchi H., Mangini N.J., Huang H., Canfield V.A., Cheng K.C., Yang F., Abe R., Yamagishi S., Shabanowitz J., Hearing V.J., Wu C., Appella E., Hunt D.F.
J. Proteome Res. 5:3135-3144(2006) [PubMed: 17081065] [Abstract]
Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS], MASS SPECTROMETRY.
[14]"Glycoproteomics analysis of human liver tissue by combination of multiple enzyme digestion and hydrazide chemistry."
Chen R., Jiang X., Sun D., Han G., Wang F., Ye M., Wang L., Zou H.
J. Proteome Res. 8:651-661(2009) [PubMed: 19159218] [Abstract]
Cited for: GLYCOSYLATION [LARGE SCALE ANALYSIS] AT ASN-285, MASS SPECTROMETRY.
Tissue: Liver.
[15]"Crystal structure of human PEDF, a potent anti-angiogenic and neurite growth-promoting factor."
Simonovic M., Gettins P.G.W., Volz K.
Proc. Natl. Acad. Sci. U.S.A. 98:11131-11135(2001) [PubMed: 11562499] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.85 ANGSTROMS) OF 21-418, GLYCOSYLATION AT ASN-285.
[16]"Four polymorphic variations in the PEDF gene identified during the mutation screening of patients with Leber congenital amaurosis."
Koenekoop R., Pina A.L., Loyer M., Davidson J., Robitaille J., Maumenee I., Tombran-Tink J.
Mol. Vis. 5:10-10(1999) [PubMed: 10398730] [Abstract]
Cited for: VARIANT THR-72.
+Additional computationally mapped references.

Cross-references

Sequence databases

M76979 mRNA. Translation: AAA60058.1.
U29953 Genomic DNA. Translation: AAA84914.1. Frameshift.
AF400442 mRNA. Translation: AAK92491.1.
BT007222 mRNA. Translation: AAP35886.1.
BC000522 mRNA. Translation: AAH00522.1.
BC013984 mRNA. Translation: AAH13984.1.
U57450 expand/collapse EMBL AC list , U57445, U57446, U57447, U57448, U57449 Genomic DNA. Translation: AAB38685.1.
M90439 mRNA. Translation: AAA93524.1. Different initiation.
IPIIPI00006114.
PIRA46046.
A47281.
UniGeneHs.532768
Hs.694727

3D structure databases

EntryMethodResolution (Å)ChainPositionsPDBsum
1IMVX-ray2.85A21-418[»]
ModBaseSearch...

Protein family/group databases

MEROPSI04.979.

PTM databases

PhosphoSiteP36955.

2-D gel databases

Cornea-2DPAGEP36955.
REPRODUCTION-2DPAGEIPI00006114.

Proteomic databases

PeptideAtlasP36955.
PRIDEP36955.

Genome annotation databases

EnsemblENSG00000132386. Homo sapiens. [Contig view]

Organism-specific databases

GeneCardsGC17P001612.
H-InvDBHIX0013408.
HGNCHGNC:8824. SERPINF1.
HPACAB004785.
HPA005825.
MIM172860. gene.
PharmGKBPA35508.
GenAtlasSearch...

Phylogenomic databases

HOGENOMP36955.
HOVERGENP36955.

Gene expression databases

ArrayExpressP36955.
BgeeP36955.
CleanExHS_SERPINF1.
GermOnlineENSG00000132386. Homo sapiens.

Family and domain databases

InterProIPR000215. Protease_inhib_I4_serpin.
[Graphical view]
PANTHERPTHR11461. Prot_inh_serpin. 1 hit.
PfamPF00079. Serpin. 1 hit.
[Graphical view]
SMARTSM00093. SERPIN. 1 hit.
[Graphical view]
PROSITEPS00284. SERPIN. 1 hit.
[Graphical view]
ProtoNetSearch...

Other Resources

SOURCESearch...

Entry information

Entry namePEDF_HUMAN
AccessionPrimary (citable) accession number: P36955
Secondary accession number(s): Q13236 expand/collapse secondary AC list , Q96CT1, Q96R01, Q9BWA4
Entry history
Integrated into UniProtKB/Swiss-Prot: June 1, 1994
Last sequence update: April 16, 2002
Last modified: May 5, 2009
This is version 103 of the entry and version 3 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation projectHPI (Human Proteome Initiative)

Relevant documents

Human chromosome 17

Human chromosome 17: 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

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents