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Protein

Peroxisome biogenesis factor 2

Gene

PEX2

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Somewhat implicated in the biogenesis of peroxisomes.

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri244 – 28441RING-typePROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

  1. zinc ion binding Source: InterPro

GO - Biological processi

  1. bile acid biosynthetic process Source: Ensembl
  2. cholesterol homeostasis Source: Ensembl
  3. fatty acid beta-oxidation Source: UniProtKB
  4. negative regulation of epithelial cell proliferation Source: UniProtKB
  5. negative regulation of fibroblast proliferation Source: UniProtKB
  6. negative regulation of transcription from RNA polymerase II promoter Source: UniProtKB
  7. neuron migration Source: Ensembl
  8. peroxisome organization Source: UniProtKB
  9. protein destabilization Source: UniProtKB
  10. protein import into peroxisome matrix Source: UniProtKB
  11. regulation of cholesterol biosynthetic process Source: Ensembl
  12. very long-chain fatty acid metabolic process Source: UniProtKB
Complete GO annotation...

Keywords - Biological processi

Peroxisome biogenesis

Keywords - Ligandi

Metal-binding, Zinc

Protein family/group databases

TCDBi3.A.20.1.1. the peroxisomal protein importer (ppi) family.

Names & Taxonomyi

Protein namesi
Recommended 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 namesi
Name:PEX2
Synonyms:PAF1, PMP3, PMP35, PXMP3, RNF72
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
ProteomesiUP000005640: Chromosome 8

Organism-specific databases

HGNCiHGNC:9717. PEX2.

Subcellular locationi

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Transmembranei140 – 15920HelicalSequence AnalysisAdd
BLAST
Transmembranei195 – 21319HelicalSequence AnalysisAdd
BLAST

GO - Cellular componenti

  1. Cdc73/Paf1 complex Source: UniProtKB
  2. integral component of peroxisomal membrane Source: UniProtKB
  3. membrane Source: UniProtKB
  4. peroxisomal membrane Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Membrane, Peroxisome

Pathology & Biotechi

Involvement in diseasei

Peroxisome biogenesis disorder complementation group 5

The disease is caused by mutations affecting the gene represented in this entry.

Disease descriptionA 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).

See also OMIM:614866
Peroxisome biogenesis disorder 5A1 Publication

The disease is caused by mutations affecting the gene represented in this entry.

Disease descriptionA 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.

See also OMIM:614866
Peroxisome biogenesis disorder 5B1 Publication

The disease is caused by mutations affecting the gene represented in this entry.

Disease descriptionA 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.

See also OMIM:614867
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti55 – 551E → K in PBD5B; infantile Refsum disease. 1 Publication
VAR_011389

Keywords - Diseasei

Disease mutation, Peroxisome biogenesis disorder, Zellweger syndrome

Organism-specific databases

MIMi614866. phenotype.
614867. phenotype.
Orphaneti772. Infantile Refsum disease.
44. Neonatal adrenoleukodystrophy.
912. Zellweger syndrome.
PharmGKBiPA34060.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 305305Peroxisome biogenesis factor 2PRO_0000056369Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei84 – 841N6-acetyllysine1 Publication

Keywords - PTMi

Acetylation

Proteomic databases

MaxQBiP28328.
PaxDbiP28328.
PRIDEiP28328.

PTM databases

PhosphoSiteiP28328.

Expressioni

Gene expression databases

BgeeiP28328.
CleanExiHS_PAF1.
HS_PXMP3.
ExpressionAtlasiP28328. baseline and differential.
GenevestigatoriP28328.

Organism-specific databases

HPAiHPA011410.
HPA027729.

Interactioni

Binary interactionsi

WithEntry#Exp.IntActNotes
PEX19P408553EBI-713978,EBI-594747

Protein-protein interaction databases

BioGridi111786. 6 interactions.
IntActiP28328. 8 interactions.
MINTiMINT-1377091.

Structurei

3D structure databases

ProteinModelPortaliP28328.
SMRiP28328. Positions 239-289.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the pex2/pex10/pex12 family.Curated
Contains 1 RING-type zinc finger.PROSITE-ProRule annotation

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri244 – 28441RING-typePROSITE-ProRule annotationAdd
BLAST

Keywords - Domaini

Transmembrane, Transmembrane helix, Zinc-finger

Phylogenomic databases

eggNOGiNOG245402.
GeneTreeiENSGT00390000001846.
HOGENOMiHOG000294074.
HOVERGENiHBG000416.
InParanoidiP28328.
KOiK06664.
OMAiRNRHLAS.
OrthoDBiEOG7SR4NB.
PhylomeDBiP28328.
TreeFamiTF105312.

Family and domain databases

Gene3Di3.30.40.10. 1 hit.
InterProiIPR006845. Pex_N.
IPR018957. Znf_C3HC4_RING-type.
IPR001841. Znf_RING.
IPR013083. Znf_RING/FYVE/PHD.
IPR017907. Znf_RING_CS.
[Graphical view]
PfamiPF04757. Pex2_Pex12. 1 hit.
PF00097. zf-C3HC4. 1 hit.
[Graphical view]
SMARTiSM00184. RING. 1 hit.
[Graphical view]
PROSITEiPS00518. ZF_RING_1. 1 hit.
PS50089. ZF_RING_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P28328-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MASRKENAKS ANRVLRISQL DALELNKALE QLVWSQFTQC FHGFKPGLLA
60 70 80 90 100
RFEPEVKACL WVFLWRFTIY SKNATVGQSV LNIKYKNDFS PNLRYQPPSK
110 120 130 140 150
NQKIWYAVCT IGGRWLEERC YDLFRNHHLA SFGKVKQCVN FVIGLLKLGG
160 170 180 190 200
LINFLIFLQR GKFATLTERL LGIHSVFCKP QNICEVGFEY MNRELLWHGF
210 220 230 240 250
AEFLIFLLPL INVQKLKAKL SSWCIPLTGA PNSDNTLATS GKECALCGEW
260 270 280 290 300
PTMPHTIGCE HIFCYFCAKS SFLFDVYFTC PKCGTEVHSL QPLKSGIEMS

EVNAL
Length:305
Mass (Da):34,843
Last modified:December 15, 2009 - v2
Checksum:iF624F93C613FF2DB
GO

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti55 – 551E → K in PBD5B; infantile Refsum disease. 1 Publication
VAR_011389
Natural varianti184 – 1841C → R.4 Publications
Corresponds to variant rs10087163 [ dbSNP | Ensembl ].
VAR_060784

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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.
CCDSiCCDS6221.1.
PIRiA41812.
RefSeqiNP_000309.1. NM_000318.2.
NP_001073336.1. NM_001079867.1.
NP_001165557.1. NM_001172086.1.
NP_001165558.1. NM_001172087.1.
UniGeneiHs.437966.

Genome annotation databases

EnsembliENST00000357039; ENSP00000349543; ENSG00000164751.
ENST00000520103; ENSP00000428590; ENSG00000164751.
ENST00000522527; ENSP00000428638; ENSG00000164751.
GeneIDi5828.
KEGGihsa:5828.
UCSCiuc003yax.3. human.

Polymorphism databases

DMDMi281185478.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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.
CCDSiCCDS6221.1.
PIRiA41812.
RefSeqiNP_000309.1. NM_000318.2.
NP_001073336.1. NM_001079867.1.
NP_001165557.1. NM_001172086.1.
NP_001165558.1. NM_001172087.1.
UniGeneiHs.437966.

3D structure databases

ProteinModelPortaliP28328.
SMRiP28328. Positions 239-289.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi111786. 6 interactions.
IntActiP28328. 8 interactions.
MINTiMINT-1377091.

Protein family/group databases

TCDBi3.A.20.1.1. the peroxisomal protein importer (ppi) family.

PTM databases

PhosphoSiteiP28328.

Polymorphism databases

DMDMi281185478.

Proteomic databases

MaxQBiP28328.
PaxDbiP28328.
PRIDEiP28328.

Protocols and materials databases

DNASUi5828.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000357039; ENSP00000349543; ENSG00000164751.
ENST00000520103; ENSP00000428590; ENSG00000164751.
ENST00000522527; ENSP00000428638; ENSG00000164751.
GeneIDi5828.
KEGGihsa:5828.
UCSCiuc003yax.3. human.

Organism-specific databases

CTDi5828.
GeneCardsiGC08M077892.
GeneReviewsiPEX2.
HGNCiHGNC:9717. PEX2.
HPAiHPA011410.
HPA027729.
MIMi170993. gene.
614866. phenotype.
614867. phenotype.
neXtProtiNX_P28328.
Orphaneti772. Infantile Refsum disease.
44. Neonatal adrenoleukodystrophy.
912. Zellweger syndrome.
PharmGKBiPA34060.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiNOG245402.
GeneTreeiENSGT00390000001846.
HOGENOMiHOG000294074.
HOVERGENiHBG000416.
InParanoidiP28328.
KOiK06664.
OMAiRNRHLAS.
OrthoDBiEOG7SR4NB.
PhylomeDBiP28328.
TreeFamiTF105312.

Miscellaneous databases

ChiTaRSiPEX2. human.
GeneWikiiPXMP3.
GenomeRNAii5828.
NextBioi22704.
PROiP28328.
SOURCEiSearch...

Gene expression databases

BgeeiP28328.
CleanExiHS_PAF1.
HS_PXMP3.
ExpressionAtlasiP28328. baseline and differential.
GenevestigatoriP28328.

Family and domain databases

Gene3Di3.30.40.10. 1 hit.
InterProiIPR006845. Pex_N.
IPR018957. Znf_C3HC4_RING-type.
IPR001841. Znf_RING.
IPR013083. Znf_RING/FYVE/PHD.
IPR017907. Znf_RING_CS.
[Graphical view]
PfamiPF04757. Pex2_Pex12. 1 hit.
PF00097. zf-C3HC4. 1 hit.
[Graphical view]
SMARTiSM00184. RING. 1 hit.
[Graphical view]
PROSITEiPS00518. ZF_RING_1. 1 hit.
PS50089. ZF_RING_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  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.
    , 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.

Entry informationi

Entry nameiPEX2_HUMAN
AccessioniPrimary (citable) accession number: P28328
Secondary accession number(s): Q567S6, Q9BW41
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 1, 1992
Last sequence update: December 15, 2009
Last modified: January 7, 2015
This is version 150 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (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.

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Human chromosome 8
    Human chromosome 8: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. 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.