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P28328

- PEX2_HUMAN

UniProt

P28328 - PEX2_HUMAN

Protein

Peroxisome biogenesis factor 2

Gene

PEX2

Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 148 (01 Oct 2014)
      Sequence version 2 (15 Dec 2009)
      Previous versions | rss
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    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. protein binding Source: UniProtKB
    2. 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

    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

    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

    Keywords - Cellular componenti

    Membrane, Peroxisome

    Pathology & Biotechi

    Involvement in diseasei

    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.1 Publication
    Note: The disease is caused by mutations affecting the gene represented in this entry.
    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.1 Publication
    Note: The disease is caused by mutations affecting the gene represented in this entry.
    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

    ArrayExpressiP28328.
    BgeeiP28328.
    CleanExiHS_PAF1.
    HS_PXMP3.
    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 239-290.
    ModBaseiSearch...
    MobiDBiSearch...

    Transmembrane

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

    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.
    HOGENOMiHOG000294074.
    HOVERGENiHBG000416.
    InParanoidiP28328.
    KOiK06664.
    OMAiTQCFHGF.
    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

    MASRKENAKS ANRVLRISQL DALELNKALE QLVWSQFTQC FHGFKPGLLA    50
    RFEPEVKACL WVFLWRFTIY SKNATVGQSV LNIKYKNDFS PNLRYQPPSK 100
    NQKIWYAVCT IGGRWLEERC YDLFRNHHLA SFGKVKQCVN FVIGLLKLGG 150
    LINFLIFLQR GKFATLTERL LGIHSVFCKP QNICEVGFEY MNRELLWHGF 200
    AEFLIFLLPL INVQKLKAKL SSWCIPLTGA PNSDNTLATS GKECALCGEW 250
    PTMPHTIGCE HIFCYFCAKS SFLFDVYFTC PKCGTEVHSL QPLKSGIEMS 300
    EVNAL 305
    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:
    EMBL
    GenBank
    DDBJ
    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:
    EMBL
    GenBank
    DDBJ
    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 .
    CCDSi CCDS6221.1.
    PIRi A41812.
    RefSeqi NP_000309.1. NM_000318.2.
    NP_001073336.1. NM_001079867.1.
    NP_001165557.1. NM_001172086.1.
    NP_001165558.1. NM_001172087.1.
    UniGenei Hs.437966.

    3D structure databases

    ProteinModelPortali P28328.
    SMRi P28328. Positions 239-290.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 111786. 6 interactions.
    IntActi P28328. 8 interactions.
    MINTi MINT-1377091.

    Protein family/group databases

    TCDBi 3.A.20.1.1. the peroxisomal protein importer (ppi) family.

    PTM databases

    PhosphoSitei P28328.

    Polymorphism databases

    DMDMi 281185478.

    Proteomic databases

    MaxQBi P28328.
    PaxDbi P28328.
    PRIDEi P28328.

    Protocols and materials databases

    DNASUi 5828.
    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENST00000357039 ; ENSP00000349543 ; ENSG00000164751 .
    ENST00000520103 ; ENSP00000428590 ; ENSG00000164751 .
    ENST00000522527 ; ENSP00000428638 ; ENSG00000164751 .
    GeneIDi 5828.
    KEGGi hsa:5828.
    UCSCi uc003yax.3. human.

    Organism-specific databases

    CTDi 5828.
    GeneCardsi GC08M077892.
    GeneReviewsi PEX2.
    HGNCi HGNC:9717. PEX2.
    HPAi HPA011410.
    HPA027729.
    MIMi 170993. gene.
    614866. phenotype.
    614867. phenotype.
    neXtProti NX_P28328.
    Orphaneti 772. Infantile Refsum disease.
    44. Neonatal adrenoleukodystrophy.
    912. Zellweger syndrome.
    PharmGKBi PA34060.
    GenAtlasi Search...

    Phylogenomic databases

    eggNOGi NOG245402.
    HOGENOMi HOG000294074.
    HOVERGENi HBG000416.
    InParanoidi P28328.
    KOi K06664.
    OMAi TQCFHGF.
    OrthoDBi EOG7SR4NB.
    PhylomeDBi P28328.
    TreeFami TF105312.

    Miscellaneous databases

    ChiTaRSi PEX2. human.
    GeneWikii PXMP3.
    GenomeRNAii 5828.
    NextBioi 22704.
    PROi P28328.
    SOURCEi Search...

    Gene expression databases

    ArrayExpressi P28328.
    Bgeei P28328.
    CleanExi HS_PAF1.
    HS_PXMP3.
    Genevestigatori P28328.

    Family and domain databases

    Gene3Di 3.30.40.10. 1 hit.
    InterProi IPR006845. Pex_N.
    IPR018957. Znf_C3HC4_RING-type.
    IPR001841. Znf_RING.
    IPR013083. Znf_RING/FYVE/PHD.
    IPR017907. Znf_RING_CS.
    [Graphical view ]
    Pfami PF04757. Pex2_Pex12. 1 hit.
    PF00097. zf-C3HC4. 1 hit.
    [Graphical view ]
    SMARTi SM00184. RING. 1 hit.
    [Graphical view ]
    PROSITEi PS00518. ZF_RING_1. 1 hit.
    PS50089. ZF_RING_2. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    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: October 1, 2014
    This is version 148 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