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Protein

Peroxisomal biogenesis factor 3

Gene

PEX3

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

Functioni

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.2 Publications

GO - Molecular functioni

  • lipid binding Source: UniProtKB
  • protein dimerization activity Source: UniProtKB

GO - Biological processi

  • peroxisome membrane biogenesis Source: Ensembl
  • peroxisome organization Source: UniProtKB
  • protein import into peroxisome membrane Source: UniProtKB
  • transmembrane transport Source: Reactome

Keywordsi

Biological processPeroxisome biogenesis

Enzyme and pathway databases

ReactomeiR-HSA-1369062 ABC transporters in lipid homeostasis
SIGNORiP56589

Protein family/group databases

TCDBi9.A.17.1.2 the integral membrane peroxisomal protein importer-2 (ppi2) family

Names & Taxonomyi

Protein namesi
Recommended name:
Peroxisomal biogenesis factor 3
Alternative name(s):
Peroxin-3
Peroxisomal assembly protein PEX3
Gene namesi
Name:PEX3
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 6

Organism-specific databases

EuPathDBiHostDB:ENSG00000034693.14
HGNCiHGNC:8858 PEX3
MIMi603164 gene
neXtProtiNX_P56589

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Topological domaini1 – 15CytoplasmicSequence analysisAdd BLAST15
Transmembranei16 – 36HelicalSequence analysisAdd BLAST21
Topological domaini37 – 116PeroxisomalSequence analysisAdd BLAST80
Transmembranei117 – 140HelicalSequence analysisAdd BLAST24
Topological domaini141 – 373CytoplasmicSequence analysisAdd BLAST233

Keywords - Cellular componenti

Membrane, Peroxisome

Pathology & Biotechi

Involvement in diseasei

Peroxisome biogenesis disorder complementation group 12 (PBD-CG12)1 Publication
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:614882
Peroxisome biogenesis disorder 10A (PBD10A)2 Publications
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:614882
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_009304138G → E in PBD10A. 1 Publication1
Peroxisome biogenesis disorder 10B (PBD10B)1 Publication
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionA moderately severe peroxisome biogenesis disorder belonging to the Zellweger disease spectrum. PBD10B is characterized by neonatal jaundice, dysmorphic features, delayed psychomotor development, axial hypotonia that can progress to severe spastic paraparesis with hyperreflexia, nephrocalcinosis, neurogenic bladder, nystagmus, and cataracts. Laboratory studies show increased levels of very long-chain fatty acids. Inheritance is autosomal recessive.
See also OMIM:617370
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_078657331G → R in PBD10B. 1 Publication1

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi125L → P: Abolishes binding to PEX19 without affecting targeting to peroxisomes; when associated with D-134. 1 Publication1
Mutagenesisi134N → D: Abolishes binding to PEX19 without affecting targeting to peroxisomes; when associated with P-125. 1 Publication1

Keywords - Diseasei

Disease mutation, Peroxisome biogenesis disorder, Zellweger syndrome

Organism-specific databases

DisGeNETi8504
GeneReviewsiPEX3
MalaCardsiPEX3
MIMi614882 phenotype
617370 phenotype
OpenTargetsiENSG00000034693
Orphaneti772 Infantile Refsum disease
44 Neonatal adrenoleukodystrophy
912 Zellweger syndrome
PharmGKBiPA33200

Polymorphism and mutation databases

BioMutaiPEX3
DMDMi3914303

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002087371 – 373Peroxisomal biogenesis factor 3Add BLAST373

Proteomic databases

EPDiP56589
PaxDbiP56589
PeptideAtlasiP56589
PRIDEiP56589
ProteomicsDBi56929

PTM databases

iPTMnetiP56589
PhosphoSitePlusiP56589

Expressioni

Tissue specificityi

Found in all examined tissues.

Gene expression databases

BgeeiENSG00000034693
CleanExiHS_PEX3
ExpressionAtlasiP56589 baseline and differential
GenevisibleiP56589 HS

Organism-specific databases

HPAiHPA042830
HPA058006

Interactioni

Subunit structurei

Interacts with PEX19.4 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
PEX19P4085527EBI-594885,EBI-594747

GO - Molecular functioni

  • protein dimerization activity Source: UniProtKB

Protein-protein interaction databases

BioGridi114076, 8 interactors
ELMiP56589
IntActiP56589, 5 interactors
MINTiP56589
STRINGi9606.ENSP00000356563

Structurei

Secondary structure

1373
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi41 – 83Combined sources43
Helixi86 – 93Combined sources8
Helixi100 – 142Combined sources43
Beta strandi147 – 151Combined sources5
Helixi158 – 165Combined sources8
Helixi166 – 168Combined sources3
Helixi169 – 172Combined sources4
Helixi174 – 191Combined sources18
Beta strandi199 – 201Combined sources3
Helixi202 – 217Combined sources16
Helixi234 – 237Combined sources4
Helixi246 – 248Combined sources3
Helixi255 – 271Combined sources17
Helixi274 – 296Combined sources23
Beta strandi319 – 321Combined sources3
Helixi322 – 330Combined sources9
Helixi333 – 336Combined sources4
Turni339 – 341Combined sources3
Helixi344 – 349Combined sources6
Helixi352 – 366Combined sources15

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3AJBX-ray2.50A49-373[»]
3MK4X-ray2.42A41-373[»]
ProteinModelPortaliP56589
SMRiP56589
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP56589

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni1 – 45Targeting to peroxisomesAdd BLAST45
Regioni120 – 136Interaction with PEX19Add BLAST17

Sequence similaritiesi

Belongs to the peroxin-3 family.Curated

Keywords - Domaini

Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiKOG4444 Eukaryota
ENOG41101IY LUCA
GeneTreeiENSGT00390000008481
HOGENOMiHOG000007212
HOVERGENiHBG000467
InParanoidiP56589
KOiK13336
OMAiWSLQMAI
OrthoDBiEOG091G1027
PhylomeDBiP56589
TreeFamiTF352826

Family and domain databases

InterProiView protein in InterPro
IPR006966 Peroxin-3
PANTHERiPTHR28080 PTHR28080, 1 hit
PfamiView protein in Pfam
PF04882 Peroxin-3, 2 hits

Sequencei

Sequence statusi: Complete.

P56589-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MLRSVWNFLK RHKKKCIFLG TVLGGVYILG KYGQKKIREI QEREAAEYIA
60 70 80 90 100
QARRQYHFES NQRTCNMTVL SMLPTLREAL MQQLNSESLT ALLKNRPSNK
110 120 130 140 150
LEIWEDLKII SFTRSTVAVY STCMLVVLLR VQLNIIGGYI YLDNAAVGKN
160 170 180 190 200
GTTILAPPDV QQQYLSSIQH LLGDGLTELI TVIKQAVQKV LGSVSLKHSL
210 220 230 240 250
SLLDLEQKLK EIRNLVEQHK SSSWINKDGS KPLLCHYMMP DEETPLAVQA
260 270 280 290 300
CGLSPRDITT IKLLNETRDM LESPDFSTVL NTCLNRGFSR LLDNMAEFFR
310 320 330 340 350
PTEQDLQHGN SMNSLSSVSL PLAKIIPIVN GQIHSVCSET PSHFVQDLLT
360 370
MEQVKDFAAN VYEAFSTPQQ LEK
Length:373
Mass (Da):42,140
Last modified:December 15, 1998 - v1
Checksum:i3515A1F29656B7CC
GO

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_05357282Q → R. Corresponds to variant dbSNP:rs35220041EnsemblClinVar.1
Natural variantiVAR_009304138G → E in PBD10A. 1 Publication1
Natural variantiVAR_078657331G → R in PBD10B. 1 Publication1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ001625 mRNA Translation: CAA04879.1
AJ131389 mRNA Translation: CAA10362.1
AJ009866
, 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 No translation available.
CH471051 Genomic DNA Translation: EAW47866.1
BC014551 mRNA Translation: AAH14551.1
BC015506 mRNA Translation: AAH15506.1
CCDSiCCDS5199.1
RefSeqiNP_003621.1, NM_003630.2
UniGeneiHs.592832
Hs.7277

Genome annotation databases

EnsembliENST00000367591; ENSP00000356563; ENSG00000034693
GeneIDi8504
KEGGihsa:8504
UCSCiuc003qjl.4 human

Keywords - Coding sequence diversityi

Polymorphism

Similar proteinsi

Entry informationi

Entry nameiPEX3_HUMAN
AccessioniPrimary (citable) accession number: P56589
Secondary accession number(s): Q6FGP5
Entry historyiIntegrated into UniProtKB/Swiss-Prot: December 15, 1998
Last sequence update: December 15, 1998
Last modified: June 20, 2018
This is version 159 of the entry and version 1 of the sequence. See 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

3D-structure, Complete proteome, Reference proteome

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