The Eukaryotic Linear Motif resource for
Functional Sites in Proteins
Functional site class:
Pex3-binding site
Functional site description:
Cytosolic import receptor Peroxin(Pex)19 (P40855) binds to the peroxisomal membrane proteins (PMPs) with its C-terminus. These PMPs are synthesized on free polyribosomes and are post-translationally inserted into peroxisomal membrane. The LxxLLxxxLxxF short linear motif at N-terminus of Pex19 interacts with N-terminal half of Pex3 at cytosolic side of peroxisomal membrane to import PMPs into the membrane. Pex3 (P56589) is a docking factor that is anchored to the peroxisomal membrane via its N-terminal 33 amino acid residues that are inserted into the membrane of peroxisome. This interaction is followed by release of PMPs into peroxisomal membrane and recycling of Pex19 into the cytosol for another round of PMPs import. Peroxisomes that lack either Pex3 or Pex19 lack detectable peroxisomal structures and mislocalise their PMPs to the cytosol where they are rapidly degraded.
ELMs with same tags:
ELM Description:
The disordered N-terminal region of Pex19 undergoes a disorder to order transition upon binding to N-terminal half of Pex3 (PF04882) and acquires an amphipathic alpha helical conformation. Human Pex19 contains a LxxLLxxxLxxF short linear motif consisting of leucine triad (LEU18, LEU21, LEU22) and phenylalanine at position 29 that are crucial for Pex3 binding (Sato,2010). Replacement of any leucines or phenylalanine significantly diminishes the binding activity of Pex19 to Pex3 (Sato,2010, Schmidt,2010). The docking surface of Pex3 for Pex19 (3AJB, Sato,2010) is a large tapered cavity that is complementary to the Pex19 alpha helical structure. The cavity is partially divided by TRP104 which protrudes from the cavity dividing it into wider surface area near the surface and narrower area deeper inside. Wider surface portion is occupied by the leucine triad and the narrower area is occupied by PHE29 (Sato,2010). TRP104 of Pex3 is a crucial residue for binding to Pex19. It interacts with following residues in Pex19: LEU22, ALA25, LEU26, and PHE29 (Sato,2008). Pex3 adopts a fold composed of 10 alpha helices and one short 3(10) helix. Long alpha3 helix of Pex3 forms the core of the crystal structure (3MK4, Schmidt,2010) with remaining 9 alpha helices and one 3(10) helix arranged circularly around it in five segments. This structure can be described as a large helical bundle. Pex19 alpha helix binds into the groove in Pex3 at the top of the helical bundle. One side of the groove consists of alpha2 and alpha3 helices whereas the other side is formed by the loop that connects helices alpha4 and alpha5, and by a portion of helix alpha8 (Schmidt,2010).
Pattern: L..LL...L..F
Pattern Probability: 5.240e-07
Present in taxon: Eukaryota
Interaction Domain:
Peroxin-3 (PF04882) Peroxin-3 (Stochiometry: 1 : 1)
o See 1 Instance for LIG_Pex3_1
o Abstract
Peroxisomes are single-membrane spherical subcellular organelles found in eukaryotes. Peroxisomes belong to microbody family along with glyoxysomes found in plants and glycosomes found in trypanosomes. The peroxisomal matrix contains enzymes involved in hydrogen peroxide metabolism, alpha and beta oxidation of long chain fatty acids, branched chain fatty acids, D-amino acids, and polyamines. Peroxisomes also synthesise cholesterol, bile acids, and ether lipids (plasmalogens) in mammals (Lanyon-Hogg,2010; Ma,2011).
Studies on peroxisome formation yielded conflicting results with two models of peroxisome formation (biogenesis) proposed. The early model of growth and division states that peroxisomes are autonomous organelles where peroxisomal membrane and matrix proteins are synthesized on free ribosomes and are post-translationally targeted from the cytoplasm to peroxisomes. Evidence for this model came from Reguenga,2001 where peroxisomal enzymes that are synthesised on free polyribosomes were imported post-translationally into peroxisome. Further evidence came from studies of PTS1 (TRG_PTS1) and PTS2 (TRG_PTS2) import signals that are present in peroxisomal matrix enzyme proteins. The second model is a recently proposed model of de novo biogenesis. First evidence for this model came from electron microscopy studies where peroxisomes are in close proximity to endoplasmic reticulum (Novikoff,1972). Further evidence came from reintroduction of corresponding wild-type gene in Pex3, Pex16, or Pex19 mutants that completely lack peroxisomal membrane structures regain peroxisomes after gene reintroduction. Pex3, Pex16, and Pex19 are three peroxins involved in peroxisome membrane biogenesis and absence of either one of these results in termination of peroxisomal biogenesis. Reintroduction of Pex3 gene into Pex3 deficient cells resulted in insertion of Pex3 into endoplasmic reticulum and subsequent release of vesicles from endoplasmic reticulum (ER) that later matured into peroxisomes by fusion of pre-peroxisomal vesicles that bud off from ER. Integral membrane Pex proteins were shown to enter ER with subsequent detachment of ER membrane and formation of pre-peroxisomal compartment (Tabak,2003). ER involvement in peroxisome formation has been shown but many questions still remain unanswered. It is unclear whether de novo biogenesis operates continuously or only switches on when cells lack peroxisomes (Ma,2009). In S. cerevisiae, ER-derived vesicles mature into peroxisomes only in cells lacking peroxisomes (Motley,2007) whereas in human fibroblasts both types of peroxisomal biogenesis occur simultaneously (Kim,2006).
Endoplasmic reticulum to peroxisome pathway can be divided into four steps: PMP targeting to endoplasmic reticulum, segregation of PMPs from secretory and endoplasmic reticulum proteins, incorporation of PMPs from endoplasmic reticulum into vesicles, fusion of endoplasmic-derived pre-peroxisomal vesicles with either pre-existing peroxisomes (growth and division model) or with other ER-derived pre-peroxisomal vesicles (de novo biogenesis model) followed by maturation of these pre-peroxisomal vesicles into mature peroxisomes.
Pex19 functions as an import receptor for newly synthesized class I PMPs. Class I PMPs contain peroxisomal membrane targeting sequence (mPTS). mPTS contains a Pex19-binding sequence and a sequence for PMP integration into the peroxisomal membrane. N-terminal domain of Pex19 contains Pex3-binding motif, LxxLLxxxLxxF that is responsible for docking to Pex3 whereas C-terminal half of Pex19 is required for binding to class I PMPs in the cytosol. Pex19 is also believed to function as a PMP-specific chaperone that binds and stabilizes PMPs by the formation of a soluble complex preventing aggregation of PMPs. The vast majority of Pex19 is cytosolic with 10% of Pex19 located in peroxisome. Pex19 proteins from multiple species including human, Chinese hamster, and S. cerevisiae are farnesylated at a conserved C-terminal CaaX motif (James,1994, Kammerer,1997, Gotte,1998). This post-translational modification is not necessary for Pex19 function since the deletion of the entire CaaX sequence in S. cerevisiae Pex19 did not prevent it from complementing the Pex19 deficient cells (Snyder,1999). The purpose of farnesylation of Pex19 is to increases its affinity to PMPs such as Pex10 and Pex13. Upon binding to Pex3, Pex19 forms tertiary complexes with integral membrane proteins, Pex16 and Pex26 (Matsuzono,2006).
Pex3 and Pex19 are also required budding off of pre-peroxisomal vesicles from endoplasmic reticulum. Pex3 is located in the endoplasmic reticulum where it concentrates in foci that then bud off in a Pex19-dependent manner and forms pre-peroxisomal vesicle. Pre-peroxisomal vesicles fuse with each other to form larger structures. PMPs including import machinery for peroxisomal matrix proteins are delivered to peroxisomal membrane by Pex19 and incorporated into the membrane by the interaction of LxxLLxxxLxxF motif of Pex19 with Pex3 followed by the import of matrix proteins that marks the completion of the peroxisome maturation process. Without Pex19, Pex3 is trapped in the endoplasmic reticulum and no pre-peroxisomal vesicle is formed. Lack of Pex3 results in Pex19 inability to dock to endoplasmic reticulum and bring PMPs to the membrane. Cells that contain peroxisomes recruit their membrane directly from the endoplasmic reticulum and in cells lacking peroxisomes, peroxisomes can be restored by de novo biogenesis (Hoepfner,2005).
There are two classes of PMPs, class I and class II. Class I PMPs are diverse group of proteins that include metabolite transporters such as PMP22, PMP32, and PMP70, peroxins involved in peroxisome division such as Pex11, peroxins involved in peroxisomal matrix protein import such as Pex2, Pex13, and Pex26, and one peroxin involved in peroxisome membrane synthesis, Pex16. This class of PMP import is dependent on Pex19 and Pex3 proteins for their import into peroxisomal membrane. Class II PMP import is independent of Pex19 and Pex3 and includes Pex3, Pex4, and Pex22 as a cargo (Schmidt,2012).
o 10 selected references:

o 11 GO-Terms:

o 1 Instance for LIG_Pex3_1
(click table headers for sorting; Notes column: =Number of Switches, =Number of Interactions)
Acc., Gene-, NameStartEndSubsequenceLogic#Ev.OrganismNotes
P40855 PEX19
18 29 ADRELEELLESALDDFDKAK TP 0 Homo sapiens (Human)
Please cite: The Eukaryotic Linear Motif resource: 2022 release. (PMID:34718738)

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