The Eukaryotic Linear Motif resource for
Functional Sites in Proteins
Functional site class:
PUB domain ligand (PIM motif)
Functional site description:
The PUB-interacting motif, also known as the PIM motif, is recognised by proteins containing the PUB domain. The best studied interactor of PIM motifs is the E3 ubiquitin-protein ligase RNF31 (RNF31, also known as HOIP), a component of the LUBAC complex, which forms linear ubiquitin chains that play an important role in immune and inflammatory processes by controlling the NF-κB signalling pathway and programmed cell death. The N-terminal region of HOIP/RNF31 contains a PUB domain that has been shown to bind to PIM motifs (xD[LM]Yx) present in Ubiquitin thioesterase otulin (OTULIN), Spermatogenesis-associated protein 2 (SPATA2) and Transitional endoplasmic reticulum ATPase (TERA, VCP or p97). These interactions regulate the assembly of linear ubiquitination linkages. The PIM motif in p97/VCP also binds the PUB domain of Peptide-N(4)-(N-acetyl-beta-glucosaminyl)asparagine amidase (NGLY1, also known as PNGase) and UBX domain-containing protein 6 (UBXN6).
ELM Description:
The consensus of the PIM motif is xD[LM]Yx. The key residues of the PIM motif have been structurally characterised in several complexes, the PIM-p97/VCP and PUB-HOIP (4P0A), PIM-OTULIN and PUB-HOIP (4P0B), and PIM-SPATA2 and PUB-HOIP (5LJN). The interaction between the PIM motif and the PUB domain is mostly mediated by the hydrophobic L/M and Y positions of the PIM sequence and a hydrophobic pocket on the PUB domain, and this interaction can be modulated by PTMs. The phosphorylation or mutation of the tyrosine in the PIM motif completely abolishes binding to the PUB domain (Schaeffer,2014). Also, mutation of the leucine (p97/VCP) or methionine (OTULIN) abrogates the binding, while the mutation of the preceding Asp decreases HOIP binding (Elliott,2014).
The PIM motif of p97/VCP is the only instance that can bind a PUB domain in proteins other than HOIP. The core of the binding pocket slightly differs between the PUB domain of HOIP and UBXD1/PNGase. The key residues in the UBXD1/PNGase pocket are YxxNx{9}Y, where the N contacts the PIM tyrosine, and in HOIP the pocket is – YxxNx{6}PxY, where a proline is a key residue for binding the PIM tyrosine (Blueggel,2019). Furthermore, the PIM motif in p97/VCP is directly C-terminal, while the PIM motifs in OTULIN and SPATA2 occur in internal part of proteins. Furthermore, the PIM motifs in OTULIN and SPATA2 bind to the HOIP protein with higher affinity than to the motif in p97/VCP (Elliott,2014; Blueggel,2019).
Pattern: .D[LM]Y.
Pattern Probability: 0.0000654
Present in taxon: Eukaryota
Interaction Domain:
PUB domain (IPR018997) The PUB (also known as PUG) domain is found in peptide N-glycanase where it functions as a AAA ATPase binding domain (Stochiometry: 1 : 1)
o See 2 Instances for DOC_PUB_PIM_1
o Abstract
The PUB domain (IPR018997) occurs in some proteins linked to the regulation of ubiquitination. The first PUB domain characterised in PNGase was shown to bind the p97/VCP/TERA protein and remove oligosaccharide chains from misfolded proteins prior to degradation (Allen,2006; Zhao,2007). Next, the PUB domain HOIP/RNF31 protein (Q96EP0) was described to interact with the OTULIN deubiquitinating enzyme controlling the assembly of linear ubiquitination chains (Elliott,2014; Elliott,2016). The HOIP/RNF31 E3 ligase is a part of the linear ubiquitin chain assembly complex (LUBAC) composed of three core proteins: E3 ubiquitin ligases HOIP and HOIL-1, and SHARPIN. To date, HOIP/RNF31 is the only known E3 ubiquitin ligase that can generate linear (Met1-linked) ubiquitin chains on the target protein. These chains formed by the LUBAC complex play an important role in immune and inflammatory processes and programmed cell death. For example, the complex regulates NF-κB signalling in response to TNF activation by attaching ubiquitin chains to the target proteins. Conversely, both CYLD and OTULIN are known LUBAC deubiquitinases (DUBs) which eliminate the ubiquitin linkages and inhibit NF-κB activation (Dittmar,2019). The E3 ligase HOIP contains a PUB domain in the N-terminal part of the protein that directly binds proteins containing a PIM sequence (xD[LM]Yx). PUB-HOIP interacts with the deubiquitinase OTULIN (Q96BN8) via a PIM motif and through this interaction eliminates the linear ubiquitin linkages on the target protein protecting against cell death (Elliott,2014). Another DUB that cleaves the ubiquitin chains is CYLD (Q9NQC7). The mechanism of CYLD-HOIP interaction differs from OTULIN, as SPATA2 contains the PIM sequence which directly binds HOIP. Next, the PUB domain of SPATA2 recruits the USP domain of CYLD in a PIM motif independent manner, so SPATA2 serves as a bridge between CYLD and HOIP (Kupka,2016). Both OTULIN and CYLD DUBs, regulate the activity of the LUBAC-mediated linear ubiquitination by restricting the formation of ubiquitination chains on target proteins. The PUB domain of HOIP also recognises the PIM motif in p97/VCP (P55072; Schaeffer,2014). p97/VCP recruits HOIP to protein aggregates and together with other components of the LUBAC complex attaches linear ubiquitin chains to target proteins, promoting the removal of misfolded proteins thereby decreasing their toxic effect (van Well,2019). Phosphorylation of the tyrosine within the PIM sequence in OTULIN, SPATA2 and p97 proteins abolishes the interaction with HOIP. This PTM switch mechanism can modulate the poly-ubiquitination activity of the LUBAC complex, however, the regulation and dynamics of the phosphorylation remained uncharacterised when this entry was prepared.
o 5 selected references:

o 7 GO-Terms:

o 2 Instances for DOC_PUB_PIM_1
(click table headers for sorting; Notes column: =Number of Switches, =Number of Interactions)
Acc., Gene-, NameStartEndSubsequenceLogic#Ev.OrganismNotes
335 339 YFSTQDDVDLYTDSEPRATY TP 8 Homo sapiens (Human)
53 57 QCPAEHEEDMYRAADEIEKE TP 5 Homo sapiens (Human)
Please cite: The Eukaryotic Linear Motif resource: 2022 release. (PMID:34718738)

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