The Eukaryotic Linear Motif resource for
Functional Sites in Proteins
Functional site class:
Motif which binds to the MATH domain of the TRAF4 K63 E3 ligase
Functional site description:
TRAF4 is considered unique among TRAF E3 ligase family members owing to differences in its domain organization and function. It was initially identified as a regulator of embryogenesis in mice and later found to be critical for cell migration, lipid binding and cancer progression. Unlike other TRAF family members, TRAF4 possesses nuclear localization signals (NLS) and does not interact with the canonical TRAF-binding receptors and hence is involved in different biological processes. The receptor-interacting surface residues in other TRAFs are not conserved in TRAF4 and account for its novel interaction mode. TRAF4-specific binding motifs have been identified in some platelet receptors.
ELM Description:
The TRAF4 MATH domain differs from other TRAF family members in primary sequence at the binding interface. So far, only two robust binding motifs have been defined in a pair of platelet receptors and a single structure solved in complex with a binding partner. So, there is uncertainty about the motif description. In the solved structure of the TRAF4/GPIbβ peptide complex (5YC1), the receptor binding area is demarcated by two hydrophobic pockets, major and minor, on the surface of TRAF4. The major pocket binds a deeply inserted Leu. The residues F408, Y436, and F434 form the major pocket and the residues W414 and F434 form the minor pocket on TRAF4. The hydrophobic pockets are marked by the acidic patches on the surface of the TRAF4 MATH domain. Importantly, TRAF4 variants (F434R, S357E, Y366R, Y436R, E406R, N355R) with residues belonging to these pockets have been shown to either reduce or disrupt the binding with receptor peptides in quantitative binding assays using SPR and ITC (Kim,2017). The serine triad present in other TRAFs is absent in TRAF4, and the region is replaced by W414 in TRAF4. The main interaction is between the conserved Leucine at the second position of the GPIbβ peptide and the major hydrophobic pocket. The alanine residue at the fourth position makes a non-covalent interaction with the minor hydrophobic pocket which likely fine-tunes the binding affinity. Alanine can be replaced with other residues, such as H or G, with reduced binding affinity. The arginine residues at the first (+1) and fifth (+5) positions form hydrogen bonds with the E406 and N355 side chains on TRAF4, respectively. Pro is excluded at the +3 and +5 positions due to β-augmentation H-bonding requirements.
Pattern: RL[^P].R
Pattern Probability: 0.0002695
Present in taxon: Vertebrata
Interaction Domain:
MATH/TRAF domain (IPR002083) Although apparently functionally unrelated, intracellular TRAFs and extracellular meprins share a conserved region of about 180 residues, the meprin and TRAF homology (MATH) domain (Stochiometry: 1 : 1)
o See 3 Instances for LIG_TRAF4_MATH_1
o Abstract
The Tumor necrosis factor Receptor-Associated Factors (TRAFs) are a family of seven Ring-type E3 ligases, most of which have a C-terminal MATH domain that interacts with substrates containing an appropriate SLiM (Yamamoto,2021). TRAF4 is unique among other TRAFs in different aspects. TRAF4 is the only member to possess three CART domains and two nuclear localization signal motifs. In the N-TRAF domain, the coiled coil domain is short compared to other TRAFs and thus involved in less heterotypic associations. More importantly, the hotspot residues that are important for the recognition of the TIM (TRAF Interaction Motif) in the TNF-receptors are not conserved in TRAF4 and thus they mediate a novel motif interaction in other types of transmembrane receptors (Kedinger,2007).
Peptides from the cytosolic tails of the platelet receptors GPIbβ and GPVI were shown to pull down TRAF4 as well as three proteins that it is found in complex with, Hic-5, Pyk2 and p47(phox) (Arthur,2011). In a single later structural and biochemical study (Kim,2017), a few TRAF4 binding motif candidates have been investigated, including the two platelet receptors (GPIbβ and GPVI) and peptides from TGF-β receptor 1 and 2 and in NOD2. The GPIbβ motif binds with low micromolar affinity (Kd =11 micromolar). On structural grounds, it is doubtful whether the TGFR motifs can be considered as plausible whereas the NOD2 peptides did not bind. The GPIbβ bound peptide (5YC1) sequence is RRLRARARARA, however only RLRAR could be modelled in the electron density. The Leu is a key interacting residue buried in a deep hydrophobic pocket. The Ala makes hydrophobic interactions but is solvent accessible. The three Arg residues are solvent accessible but the first and fifth still appear to make favourable electrostatic interactions, though the sidechain of the fifth residue (Arg) is present in two conformations. Interestingly, the main-chain conformation of the peptide is strongly conserved, highlighting the importance of contacts from the peptide backbone. The available information suggests a motif based on RLxxR. This motif would be expected to be revised as more interactions with biophysical data become available.

The TRAF4 binding to the platelet receptors, the GPIb-IX-V complex and GPVI leads to the generation of reactive oxygen species (ROS) at the site of thrombosis and is considered a potential site of action for antithrombotic drugs. Further, the TRAF4 binding to the TGF-β receptor is suggested to cause cancer initiation and progression, suggesting a site for developing anticancer drugs.
o 4 selected references:

o 9 GO-Terms:

o 3 Instances for LIG_TRAF4_MATH_1
(click table headers for sorting; Notes column: =Number of Switches, =Number of Interactions)
Acc., Gene-, NameStartEndSubsequenceLogic#Ev.OrganismNotes
P13224-2 GP1BB
382 386 LLLCRLRRLRARARARAAAR TP 3 Homo sapiens (Human)
297 301 DWHSRRKRLRHRGRAVQRPL TP 1 Homo sapiens (Human)
P37173 TGFBR2
546 550 SELEHLDRLSGRSCSEEKIP U 1 Homo sapiens (Human)
Please cite: The Eukaryotic Linear Motif resource: 2022 release. (PMID:34718738)

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