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P56589 (PEX3_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 127. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (6) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Peroxisomal biogenesis factor 3
Alternative name(s):
Peroxin-3
Peroxisomal assembly protein PEX3
Gene names
Name:PEX3
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length373 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Involved in peroxisome biosynthesis and integrity. Assembles membrane vesicles before the matrix proteins are translocated. As a docking factor for PEX19, is necessary for the import of peroxisomal membrane proteins in the peroxisomes. Ref.4 Ref.12

Subunit structure

Interacts with PEX19. Ref.10 Ref.11 Ref.15 Ref.16

Subcellular location

Peroxisome membrane; Multi-pass membrane protein Ref.11.

Tissue specificity

Found in all examined tissues.

Involvement in disease

Peroxisome biogenesis disorder complementation group 12 (PBD-CG12) [MIM:614882]: A peroxisomal disorder arising from a failure of protein import into the peroxisomal membrane or matrix. The peroxisome biogenesis disorders (PBD group) are genetically heterogeneous with at least 14 distinct genetic groups as concluded from complementation studies. Include disorders are: Zellweger syndrome (ZWS), neonatal adrenoleukodystrophy (NALD), infantile Refsum disease (IRD), and classical rhizomelic chondrodysplasia punctata (RCDP). ZWS, NALD and IRD are distinct from RCDP and constitute a clinical continuum of overlapping phenotypes known as the Zellweger spectrum (PBD-ZSS).
Note: The disease is caused by mutations affecting the gene represented in this entry. Ref.13

Peroxisome biogenesis disorder 10A (PBD10A) [MIM:614882]: A fatal peroxisome biogenesis disorder belonging to the Zellweger disease spectrum and clinically characterized by severe neurologic dysfunction with profound psychomotor retardation, severe hypotonia and neonatal seizures, craniofacial abnormalities, liver dysfunction, and biochemically by the absence of peroxisomes. Additional features include cardiovascular and skeletal defects, renal cysts, ocular abnormalities, and hearing impairment. Most severely affected individuals with the classic form of the disease (classic Zellweger syndrome) die within the first year of life.
Note: The disease is caused by mutations affecting the gene represented in this entry. Ref.4 Ref.13

Sequence similarities

Belongs to the peroxin-3 family.

Ontologies

Keywords
   Biological processPeroxisome biogenesis
   Cellular componentMembrane
Peroxisome
   Coding sequence diversityPolymorphism
   DiseaseDisease mutation
Peroxisome biogenesis disorder
Zellweger syndrome
   DomainTransmembrane
Transmembrane helix
   Technical term3D-structure
Complete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processperoxisome membrane biogenesis

Inferred from electronic annotation. Source: Ensembl

peroxisome organization

Inferred from mutant phenotype Ref.13PubMed 12924628PubMed 18174172PubMed 19479899. Source: UniProtKB

protein import into peroxisome membrane

Inferred from mutant phenotype Ref.12. Source: UniProtKB

transmembrane transport

Traceable author statement. Source: Reactome

   Cellular_componentcytosol

Inferred from electronic annotation. Source: Ensembl

endoplasmic reticulum

Inferred from direct assay PubMed 19479899PubMed 21768384. Source: UniProtKB

integral component of peroxisomal membrane

Inferred from direct assay Ref.2Ref.1. Source: UniProtKB

intracellular membrane-bounded organelle

Inferred from direct assay. Source: HPA

nucleus

Inferred from direct assay. Source: HPA

peroxisomal membrane

Inferred from direct assay PubMed 21525035. Source: UniProtKB

peroxisome

Inferred from mutant phenotype PubMed 12924628. Source: UniProtKB

protein complex

Inferred from direct assay PubMed 18174172. Source: UniProtKB

protein-lipid complex

Inferred from direct assay PubMed 19715730. Source: UniProtKB

   Molecular_functionlipid binding

Inferred from direct assay PubMed 19715730. Source: UniProtKB

protein binding

Inferred from physical interaction Ref.10PubMed 11883941PubMed 18174172PubMed 19715730. Source: UniProtKB

protein dimerization activity

Inferred from direct assay PubMed 19715730. Source: UniProtKB

Complete GO annotation...

Binary interactions

With

Entry

#Exp.

IntAct

Notes

PEX19P4085520EBI-594885,EBI-594747

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 373373Peroxisomal biogenesis factor 3
PRO_0000208737

Regions

Topological domain1 – 1515Cytoplasmic Potential
Transmembrane16 – 3621Helical; Potential
Topological domain37 – 11680Peroxisomal Potential
Transmembrane117 – 14024Helical; Potential
Topological domain141 – 373233Cytoplasmic Potential
Region1 – 4545Targeting to peroxisomes
Region120 – 13617Interaction with PEX19

Natural variations

Natural variant821Q → R.
Corresponds to variant rs35220041 [ dbSNP | Ensembl ].
VAR_053572
Natural variant1381G → E in PBD10A. Ref.4
VAR_009304

Experimental info

Mutagenesis1251L → P: Abolishes binding to PEX19 without affecting targeting to peroxisomes; when associated with D-134. Ref.12
Mutagenesis1341N → D: Abolishes binding to PEX19 without affecting targeting to peroxisomes; when associated with P-125. Ref.12

Secondary structure

..................................... 373
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P56589 [UniParc].

Last modified December 15, 1998. Version 1.
Checksum: 3515A1F29656B7CC

FASTA37342,140
        10         20         30         40         50         60 
MLRSVWNFLK RHKKKCIFLG TVLGGVYILG KYGQKKIREI QEREAAEYIA QARRQYHFES 

        70         80         90        100        110        120 
NQRTCNMTVL SMLPTLREAL MQQLNSESLT ALLKNRPSNK LEIWEDLKII SFTRSTVAVY 

       130        140        150        160        170        180 
STCMLVVLLR VQLNIIGGYI YLDNAAVGKN GTTILAPPDV QQQYLSSIQH LLGDGLTELI 

       190        200        210        220        230        240 
TVIKQAVQKV LGSVSLKHSL SLLDLEQKLK EIRNLVEQHK SSSWINKDGS KPLLCHYMMP 

       250        260        270        280        290        300 
DEETPLAVQA CGLSPRDITT IKLLNETRDM LESPDFSTVL NTCLNRGFSR LLDNMAEFFR 

       310        320        330        340        350        360 
PTEQDLQHGN SMNSLSSVSL PLAKIIPIVN GQIHSVCSET PSHFVQDLLT MEQVKDFAAN 

       370 
VYEAFSTPQQ LEK 

« Hide

References

« Hide 'large scale' references
[1]"Cloning and characterization of the gene encoding the human peroxisomal assembly protein Pex3p."
Kammerer S., Holzinger A., Welsch U., Roscher A.A.
FEBS Lett. 429:53-60(1998) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA].
[2]"Identification and characterization of the human peroxin PEX3."
Soukupova M., Sprenger C., Gorgas K., Kunau W.H., Dodt G.
Eur. J. Cell Biol. 78:357-374(1999) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA].
[3]"The human PEX3 gene encoding a peroxisomal assembly protein: genomic organization, positional mapping, and mutation analysis in candidate phenotypes."
Muntau A.C., Holzinger A., Mayerhofer P.U., Gartner J., Roscher A.A., Kammerer S.
Biochem. Biophys. Res. Commun. 268:704-710(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[4]"The peroxin pex3p initiates membrane assembly in peroxisome biogenesis."
Ghaedi K., Tamura S., Okumoto K., Matsuzono Y., Fujiki Y.
Mol. Biol. Cell 11:2085-2102(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, CHARACTERIZATION, VARIANT PBD10A GLU-138.
Tissue: Liver.
[5]"Identification of a human transforming gene."
Kim J.W.
Submitted (APR-2003) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [MRNA].
[6]"Cloning of human full open reading frames in Gateway(TM) system entry vector (pDONR201)."
Ebert L., Schick M., Neubert P., Schatten R., Henze S., Korn B.
Submitted (JUN-2004) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
[7]"The DNA sequence and analysis of human chromosome 6."
Mungall A.J., Palmer S.A., Sims S.K., Edwards C.A., Ashurst J.L., Wilming L., Jones M.C., Horton R., Hunt S.E., Scott C.E., Gilbert J.G.R., Clamp M.E., Bethel G., Milne S., Ainscough R., Almeida J.P., Ambrose K.D., Andrews T.D. expand/collapse author list , Ashwell R.I.S., Babbage A.K., Bagguley C.L., Bailey J., Banerjee R., Barker D.J., Barlow K.F., Bates K., Beare D.M., Beasley H., Beasley O., Bird C.P., Blakey S.E., Bray-Allen S., Brook J., Brown A.J., Brown J.Y., Burford D.C., Burrill W., Burton J., Carder C., Carter N.P., Chapman J.C., Clark S.Y., Clark G., Clee C.M., Clegg S., Cobley V., Collier R.E., Collins J.E., Colman L.K., Corby N.R., Coville G.J., Culley K.M., Dhami P., Davies J., Dunn M., Earthrowl M.E., Ellington A.E., Evans K.A., Faulkner L., Francis M.D., Frankish A., Frankland J., French L., Garner P., Garnett J., Ghori M.J., Gilby L.M., Gillson C.J., Glithero R.J., Grafham D.V., Grant M., Gribble S., Griffiths C., Griffiths M.N.D., Hall R., Halls K.S., Hammond S., Harley J.L., Hart E.A., Heath P.D., Heathcott R., Holmes S.J., Howden P.J., Howe K.L., Howell G.R., Huckle E., Humphray S.J., Humphries M.D., Hunt A.R., Johnson C.M., Joy A.A., Kay M., Keenan S.J., Kimberley A.M., King A., Laird G.K., Langford C., Lawlor S., Leongamornlert D.A., Leversha M., Lloyd C.R., Lloyd D.M., Loveland J.E., Lovell J., Martin S., Mashreghi-Mohammadi M., Maslen G.L., Matthews L., McCann O.T., McLaren S.J., McLay K., McMurray A., Moore M.J.F., Mullikin J.C., Niblett D., Nickerson T., Novik K.L., Oliver K., Overton-Larty E.K., Parker A., Patel R., Pearce A.V., Peck A.I., Phillimore B.J.C.T., Phillips S., Plumb R.W., Porter K.M., Ramsey Y., Ranby S.A., Rice C.M., Ross M.T., Searle S.M., Sehra H.K., Sheridan E., Skuce C.D., Smith S., Smith M., Spraggon L., Squares S.L., Steward C.A., Sycamore N., Tamlyn-Hall G., Tester J., Theaker A.J., Thomas D.W., Thorpe A., Tracey A., Tromans A., Tubby B., Wall M., Wallis J.M., West A.P., White S.S., Whitehead S.L., Whittaker H., Wild A., Willey D.J., Wilmer T.E., Wood J.M., Wray P.W., Wyatt J.C., Young L., Younger R.M., Bentley D.R., Coulson A., Durbin R.M., Hubbard T., Sulston J.E., Dunham I., Rogers J., Beck S.
Nature 425:805-811(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[8]Mural R.J., Istrail S., Sutton 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. expand/collapse author list , Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C.
Submitted (SEP-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].
Tissue: Skin and Uterus.
[10]"PEX19 binds multiple peroxisomal membrane proteins, is predominantly cytoplasmic, and is required for peroxisome membrane synthesis."
Sacksteder K.A., Jones J.M., South S.T., Li X., Liu Y., Gould S.J.
J. Cell Biol. 148:931-944(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH PEX19.
[11]"Human pex19p binds peroxisomal integral membrane proteins at regions distinct from their sorting sequences."
Fransen M., Wylin T., Brees C., Mannaerts G.P., Van Veldhoven P.P.
Mol. Cell. Biol. 21:4413-4424(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH PEX19, SUBCELLULAR LOCATION.
[12]"PEX3 functions as a PEX19 docking factor in the import of class I peroxisomal membrane proteins."
Fang Y., Morrell J.C., Jones J.M., Gould S.J.
J. Cell Biol. 164:863-875(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, MUTAGENESIS OF LEU-125 AND ASN-134.
[13]"Defective peroxisome membrane synthesis due to mutations in human PEX3 causes Zellweger syndrome, complementation group G."
Muntau A.C., Mayerhofer P.U., Paton B.C., Kammerer S., Roscher A.A.
Am. J. Hum. Genet. 67:967-975(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: INVOLVEMENT IN PBD-CG12 AND PBD10A.
[14]"Initial characterization of the human central proteome."
Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J.
BMC Syst. Biol. 5:17-17(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[15]"Structural basis for docking of peroxisomal membrane protein carrier Pex19p onto its receptor Pex3p."
Sato Y., Shibata H., Nakatsu T., Nakano H., Kashiwayama Y., Imanaka T., Kato H.
EMBO J. 29:4083-4093(2010) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.50 ANGSTROMS) OF 49-373 IN COMPLEX WITH PEX19, SUBUNIT.
[16]"Insights into peroxisome function from the structure of PEX3 in complex with a soluble fragment of PEX19."
Schmidt F., Treiber N., Zocher G., Bjelic S., Steinmetz M.O., Kalbacher H., Stehle T., Dodt G.
J. Biol. Chem. 285:25410-25417(2010) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.42 ANGSTROMS) OF 41-373 IN COMPLEX WITH PEX19, SUBUNIT.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AJ001625 mRNA. Translation: CAA04879.1.
AJ131389 mRNA. Translation: CAA10362.1.
AJ009866 expand/collapse EMBL AC list , AJ009867, AJ009868, AJ009869, AJ009870, AJ009871, AJ009872, AJ009873, AJ009874 Genomic DNA. Translation: CAA08904.1.
AB035307 mRNA. Translation: BAA97993.1.
AY277600 mRNA. Translation: AAQ18039.1.
CR542062 mRNA. Translation: CAG46859.1.
AL031320 Genomic DNA. Translation: CAB53744.1.
CH471051 Genomic DNA. Translation: EAW47866.1.
BC014551 mRNA. Translation: AAH14551.1.
BC015506 mRNA. Translation: AAH15506.1.
CCDSCCDS5199.1.
RefSeqNP_003621.1. NM_003630.2.
UniGeneHs.592832.
Hs.7277.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
3AJBX-ray2.50A49-373[»]
3MK4X-ray2.42A41-373[»]
ProteinModelPortalP56589.
SMRP56589. Positions 52-368.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid114076. 9 interactions.
IntActP56589. 4 interactions.
MINTMINT-241504.
STRING9606.ENSP00000356563.

Protein family/group databases

TCDB9.A.17.1.2. the integral membrane peroxisomal protein importer-2 (ppi2) family.

PTM databases

PhosphoSiteP56589.

Polymorphism databases

DMDM3914303.

Proteomic databases

MaxQBP56589.
PaxDbP56589.
PeptideAtlasP56589.
PRIDEP56589.

Protocols and materials databases

DNASU8504.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000367591; ENSP00000356563; ENSG00000034693.
GeneID8504.
KEGGhsa:8504.
UCSCuc003qjl.3. human.

Organism-specific databases

CTD8504.
GeneCardsGC06P143772.
GeneReviewsPEX3.
HGNCHGNC:8858. PEX3.
HPAHPA042830.
MIM603164. gene.
614882. phenotype.
neXtProtNX_P56589.
Orphanet772. Infantile Refsum disease.
44. Neonatal adrenoleukodystrophy.
912. Zellweger syndrome.
PharmGKBPA33200.
GenAtlasSearch...

Phylogenomic databases

eggNOGNOG259038.
HOGENOMHOG000007212.
HOVERGENHBG000467.
InParanoidP56589.
KOK13336.
OMAARRQFHF.
OrthoDBEOG71ZP1Q.
PhylomeDBP56589.
TreeFamTF352826.

Enzyme and pathway databases

ReactomeREACT_15518. Transmembrane transport of small molecules.

Gene expression databases

ArrayExpressP56589.
BgeeP56589.
CleanExHS_PEX3.
GenevestigatorP56589.

Family and domain databases

InterProIPR006966. Peroxin-3.
[Graphical view]
PfamPF04882. Peroxin-3. 2 hits.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP56589.
GeneWikiPEX3.
GenomeRNAi8504.
NextBio31825.
PROP56589.
SOURCESearch...

Entry information

Entry namePEX3_HUMAN
AccessionPrimary (citable) accession number: P56589
Secondary accession number(s): Q6FGP5
Entry history
Integrated into UniProtKB/Swiss-Prot: December 15, 1998
Last sequence update: December 15, 1998
Last modified: July 9, 2014
This is version 127 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (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.

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

Human polymorphisms and disease mutations

Index of human polymorphisms and disease mutations

Human entries with polymorphisms or disease mutations

List of human entries with polymorphisms or disease mutations

Human chromosome 6

Human chromosome 6: entries, gene names and cross-references to MIM