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P28328 (PEX2_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 147. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (5) | 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:
Peroxisome biogenesis factor 2
Alternative name(s):
35 kDa peroxisomal membrane protein
Peroxin-2
Peroxisomal membrane protein 3
Peroxisome assembly factor 1
Short name=PAF-1
RING finger protein 72
Gene names
Name:PEX2
Synonyms:PAF1, PMP3, PMP35, PXMP3, RNF72
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length305 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Somewhat implicated in the biogenesis of peroxisomes.

Subcellular location

Peroxisome membrane; Multi-pass membrane protein.

Involvement in disease

Peroxisome biogenesis disorder complementation group 5 (PBD-CG5) [MIM:614866]: 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.

Peroxisome biogenesis disorder 5A (PBD5A) [MIM:614866]: 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.1

Peroxisome biogenesis disorder 5B (PBD5B) [MIM:614867]: A peroxisome biogenesis disorder that includes neonatal adrenoleukodystrophy (NALD) and infantile Refsum disease (IRD), two milder manifestations of the Zellweger disease spectrum. The clinical course of patients with the NALD and IRD presentation is variable and may include developmental delay, hypotonia, liver dysfunction, sensorineural hearing loss, retinal dystrophy and vision impairment. Children with the NALD presentation may reach their teens, while patients with the IRD presentation may reach adulthood. The clinical conditions are often slowly progressive in particular with respect to loss of hearing and vision. The biochemical abnormalities include accumulation of phytanic acid, very long chain fatty acids (VLCFA), di- and trihydroxycholestanoic acid and pipecolic acid.
Note: The disease is caused by mutations affecting the gene represented in this entry. Ref.8

Sequence similarities

Belongs to the pex2/pex10/pex12 family.

Contains 1 RING-type zinc finger.

Ontologies

Keywords
   Biological processPeroxisome biogenesis
   Cellular componentMembrane
Peroxisome
   DiseaseDisease mutation
Peroxisome biogenesis disorder
Zellweger syndrome
   DomainTransmembrane
Transmembrane helix
Zinc-finger
   LigandMetal-binding
Zinc
   PTMAcetylation
   Technical termComplete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processbile acid biosynthetic process

Inferred from electronic annotation. Source: Ensembl

cholesterol homeostasis

Inferred from electronic annotation. Source: Ensembl

fatty acid beta-oxidation

Inferred from mutant phenotype Ref.8PubMed 9765053. Source: UniProtKB

negative regulation of epithelial cell proliferation

Inferred from mutant phenotype PubMed 18987311. Source: UniProtKB

negative regulation of fibroblast proliferation

Inferred from mutant phenotype PubMed 18987311. Source: UniProtKB

negative regulation of transcription from RNA polymerase II promoter

Inferred from mutant phenotype PubMed 18987311. Source: UniProtKB

neuron migration

Inferred from electronic annotation. Source: Ensembl

peroxisome organization

Inferred from mutant phenotype Ref.1PubMed 9765053. Source: UniProtKB

protein destabilization

Inferred from mutant phenotype PubMed 18987311. Source: UniProtKB

protein import into peroxisome matrix

Inferred from mutant phenotype Ref.8. Source: UniProtKB

regulation of cholesterol biosynthetic process

Inferred from electronic annotation. Source: Ensembl

very long-chain fatty acid metabolic process

Inferred from mutant phenotype PubMed 9765053. Source: UniProtKB

   Cellular_componentCdc73/Paf1 complex

Inferred from direct assay PubMed 18987311. Source: UniProtKB

integral component of peroxisomal membrane

Inferred from mutant phenotype PubMed 12751901. Source: UniProtKB

peroxisomal membrane

Inferred from direct assay PubMed 21525035. Source: UniProtKB

   Molecular_functionprotein binding

Inferred from physical interaction PubMed 10837480PubMed 11590176. Source: UniProtKB

zinc ion binding

Inferred from electronic annotation. Source: InterPro

Complete GO annotation...

Binary interactions

With

Entry

#Exp.

IntAct

Notes

PEX19P408553EBI-713978,EBI-594747

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 305305Peroxisome biogenesis factor 2
PRO_0000056369

Regions

Transmembrane140 – 15920Helical; Potential
Transmembrane195 – 21319Helical; Potential
Zinc finger244 – 28441RING-type

Amino acid modifications

Modified residue841N6-acetyllysine Ref.7

Natural variations

Natural variant551E → K in PBD5B; infantile Refsum disease. Ref.8
VAR_011389
Natural variant1841C → R. Ref.1 Ref.2 Ref.3 Ref.5
Corresponds to variant rs10087163 [ dbSNP | Ensembl ].
VAR_060784

Sequences

Sequence LengthMass (Da)Tools
P28328 [UniParc].

Last modified December 15, 2009. Version 2.
Checksum: F624F93C613FF2DB

FASTA30534,843
        10         20         30         40         50         60 
MASRKENAKS ANRVLRISQL DALELNKALE QLVWSQFTQC FHGFKPGLLA RFEPEVKACL 

        70         80         90        100        110        120 
WVFLWRFTIY SKNATVGQSV LNIKYKNDFS PNLRYQPPSK NQKIWYAVCT IGGRWLEERC 

       130        140        150        160        170        180 
YDLFRNHHLA SFGKVKQCVN FVIGLLKLGG LINFLIFLQR GKFATLTERL LGIHSVFCKP 

       190        200        210        220        230        240 
QNICEVGFEY MNRELLWHGF AEFLIFLLPL INVQKLKAKL SSWCIPLTGA PNSDNTLATS 

       250        260        270        280        290        300 
GKECALCGEW PTMPHTIGCE HIFCYFCAKS SFLFDVYFTC PKCGTEVHSL QPLKSGIEMS 


EVNAL 

« Hide

References

« Hide 'large scale' references
[1]"A human gene responsible for Zellweger syndrome that affects peroxisome assembly."
Shimozawa N., Tsukamoto T., Suzuki Y., Orii T., Shirayoshi Y., Mori T., Fujiki Y.
Science 255:1132-1134(1992) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA], VARIANT ARG-184, INVOLVEMENT IN PBD5A.
Tissue: Liver.
[2]"Genomic organization and characterization of human PEX2 encoding a 35-kDa peroxisomal membrane protein."
Biermanns M., Gaertner J.
Biochem. Biophys. Res. Commun. 273:985-990(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], VARIANT ARG-184.
[3]Gartner J.
Submitted (FEB-1992) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [MRNA], VARIANT ARG-184.
Tissue: Liver.
[4]"DNA sequence and analysis of human chromosome 8."
Nusbaum C., Mikkelsen T.S., Zody M.C., Asakawa S., Taudien S., Garber M., Kodira C.D., Schueler M.G., Shimizu A., Whittaker C.A., Chang J.L., Cuomo C.A., Dewar K., FitzGerald M.G., Yang X., Allen N.R., Anderson S., Asakawa T. expand/collapse author list , Blechschmidt K., Bloom T., Borowsky M.L., Butler J., Cook A., Corum B., DeArellano K., DeCaprio D., Dooley K.T., Dorris L. III, Engels R., Gloeckner G., Hafez N., Hagopian D.S., Hall J.L., Ishikawa S.K., Jaffe D.B., Kamat A., Kudoh J., Lehmann R., Lokitsang T., Macdonald P., Major J.E., Matthews C.D., Mauceli E., Menzel U., Mihalev A.H., Minoshima S., Murayama Y., Naylor J.W., Nicol R., Nguyen C., O'Leary S.B., O'Neill K., Parker S.C.J., Polley A., Raymond C.K., Reichwald K., Rodriguez J., Sasaki T., Schilhabel M., Siddiqui R., Smith C.L., Sneddon T.P., Talamas J.A., Tenzin P., Topham K., Venkataraman V., Wen G., Yamazaki S., Young S.K., Zeng Q., Zimmer A.R., Rosenthal A., Birren B.W., Platzer M., Shimizu N., Lander E.S.
Nature 439:331-335(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[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] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA], VARIANT ARG-184.
Tissue: Kidney and Liver.
[6]"Ring finger in the peroxisome assembly factor-1."
Patarca R., Fletcher M.A.
FEBS Lett. 312:1-2(1992) [PubMed] [Europe PMC] [Abstract]
Cited for: DOMAIN RING FINGER.
[7]"Lysine acetylation targets protein complexes and co-regulates major cellular functions."
Choudhary C., Kumar C., Gnad F., Nielsen M.L., Rehman M., Walther T.C., Olsen J.V., Mann M.
Science 325:834-840(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-84, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[8]"Defective PEX gene products correlate with the protein import, biochemical abnormalities, and phenotypic heterogeneity in peroxisome biogenesis disorders."
Shimozawa N., Imamura A., Zhang Z., Suzuki Y., Orii T., Tsukamoto T., Osumi T., Fujiki Y., Wanders R.J.A., Besley G., Kondo N.
J. Med. Genet. 36:779-781(1999) [PubMed] [Europe PMC] [Abstract]
Cited for: VARIANT PBD5B LYS-55.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
M86852 mRNA. Translation: AAC12785.1.
AF133826 Genomic DNA. Translation: AAF97687.1.
M85038 mRNA. Translation: AAA60141.1.
AC090810 Genomic DNA. No translation available.
BC000661 mRNA. No translation available.
BC005375 mRNA. Translation: AAH05375.1.
BC093043 mRNA. Translation: AAH93043.1.
CCDSCCDS6221.1.
PIRA41812.
RefSeqNP_000309.1. NM_000318.2.
NP_001073336.1. NM_001079867.1.
NP_001165557.1. NM_001172086.1.
NP_001165558.1. NM_001172087.1.
UniGeneHs.437966.

3D structure databases

ProteinModelPortalP28328.
SMRP28328. Positions 239-290.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid111786. 6 interactions.
IntActP28328. 8 interactions.
MINTMINT-1377091.

Protein family/group databases

TCDB3.A.20.1.1. the peroxisomal protein importer (ppi) family.

PTM databases

PhosphoSiteP28328.

Polymorphism databases

DMDM281185478.

Proteomic databases

MaxQBP28328.
PaxDbP28328.
PRIDEP28328.

Protocols and materials databases

DNASU5828.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000357039; ENSP00000349543; ENSG00000164751.
ENST00000419564; ENSP00000400984; ENSG00000164751.
ENST00000520103; ENSP00000428590; ENSG00000164751.
ENST00000522527; ENSP00000428638; ENSG00000164751.
GeneID5828.
KEGGhsa:5828.
UCSCuc003yax.3. human.

Organism-specific databases

CTD5828.
GeneCardsGC08M077892.
GeneReviewsPEX2.
HGNCHGNC:9717. PEX2.
HPAHPA011410.
HPA027729.
MIM170993. gene.
614866. phenotype.
614867. phenotype.
neXtProtNX_P28328.
Orphanet772. Infantile Refsum disease.
44. Neonatal adrenoleukodystrophy.
912. Zellweger syndrome.
PharmGKBPA34060.
GenAtlasSearch...

Phylogenomic databases

eggNOGNOG245402.
HOGENOMHOG000294074.
HOVERGENHBG000416.
InParanoidP28328.
KOK06664.
OMATQCFHGF.
OrthoDBEOG7SR4NB.
PhylomeDBP28328.
TreeFamTF105312.

Gene expression databases

ArrayExpressP28328.
BgeeP28328.
CleanExHS_PAF1.
HS_PXMP3.
GenevestigatorP28328.

Family and domain databases

Gene3D3.30.40.10. 1 hit.
InterProIPR006845. Pex_N.
IPR018957. Znf_C3HC4_RING-type.
IPR001841. Znf_RING.
IPR013083. Znf_RING/FYVE/PHD.
IPR017907. Znf_RING_CS.
[Graphical view]
PfamPF04757. Pex2_Pex12. 1 hit.
PF00097. zf-C3HC4. 1 hit.
[Graphical view]
SMARTSM00184. RING. 1 hit.
[Graphical view]
PROSITEPS00518. ZF_RING_1. 1 hit.
PS50089. ZF_RING_2. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

ChiTaRSPEX2. human.
GeneWikiPXMP3.
GenomeRNAi5828.
NextBio22704.
PROP28328.
SOURCESearch...

Entry information

Entry namePEX2_HUMAN
AccessionPrimary (citable) accession number: P28328
Secondary accession number(s): Q567S6, Q9BW41
Entry history
Integrated into UniProtKB/Swiss-Prot: December 1, 1992
Last sequence update: December 15, 2009
Last modified: July 9, 2014
This is version 147 of the entry and version 2 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

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 8

Human chromosome 8: entries, gene names and cross-references to MIM