The Eukaryotic Linear Motif resource for
Functional Sites in Proteins
Functional site class:
UFM1 interacting motif
Functional site description:
Protein ufmylation is a recently identified post-translation modification in which an ubiquitin-like protein, UFM1 (Ubiquitin-fold modifier 1) is conjugated to the target proteins by a three-step enzymatic reaction. Ufm1 is activated by the E1 enzyme UBA5. This interaction is mediated by a UFM1-interacting motif in UBA5. This region of UBA5 is also capable of binding different UBL proteins in the LC3/GABARAP group that have different biological functions. The LIR/UFIM switching motif is conserved in UBA5 proteins from multicellular organisms and regulates several cellular activities including the endoplasmic reticulum stress response, hematopoiesis and fatty acid metabolism. The deregulation of the ufmylation system appears to be of therapeutic importance, being associated with different tumor types, ischemic heart diseases, diabetes, atherosclerosis, hip dysplasia.
ELM Description:
The dual binding mechanism of UBA5 (an E1 enzyme) to distinct UBL proteins UFM1 and the LC3/GABARAP is mediated by a short linear sequence present in the C-terminal IDP segment of UBA5. The core of the LIR/UFIM motif consists of four amino acids which comprise one aromatic and three aliphatic residues with one intermediate residue between the aromatic and the aliphatic residues. The binding modes of both UBLs are very similar but have unique properties.
W341 and V346 residues of UBA5 are important for binding both UBLs with W341A having the greatest effect and which contributes to the dual binding property of the UFIM. In UFM1, a hydrophobic patch (HP) similar to HP2 in GABARAP-type proteins is mainly involved in the interaction. A key residue I-343 binds to this hydrophobic pocket formed by the residues of L21, V23, V32, and F35. W341 does not intercalate with the hydrophobic core but it covers a part of the UFM1 surface and makes non-polar interactions with the P28 residue and thereby stabilizes the complex. V346 and L345 are both engaged in hydrophobic interactions with the side chains of UFM1. A salt bridge formation between the side chains of E344 and K3 in UFM1 further stabilizes the complex. The antiparallel mode of binding is mainly contributed by the hydrogen bond between S22 in UFM1 and E344 in UFIM, as well as between the V20 in UFM1 and V346 UFIM (5HKH).
All GABARAP-type proteins and LC3 proteins bind to the UBA5 UFIM region. Their mode of interaction is similar to the canonical LIR which have two intermediate residues between the aromatic and the aliphatic residues. UFIM utilizes two hydrophobic spots HP1 and HP2 in GABARAP-type proteins as the interaction site, making the interaction tighter compared to UFM1. Among GABARAP-type proteins, GABARAPL2 has the highest affinity and it could efficiently out-compete the UFM1-UBA5 interaction. In contrast, LC3 proteins displayed an invariably low affinity. The pattern in ELM is based on sequence alignments as well as the structure of the complex.
Pattern: [ND].WGI.[LIV][VMLI].{0,1}[ED]
Pattern Probability: 7.651e-09
Present in taxon: Eukaryota
Not represented in taxon: Fungi
Interaction Domain:
Ufm1 (PF03671) Ubiquitin fold modifier 1 protein (Stochiometry: 1 : 1)
o See 1 Instance for LIG_UFM1_UFIM_1
o Abstract
As with classical ubiquitination, ubiquitin-like proteins are also conjugated to their target proteins through a three-step enzymatic process. The key players of the protein ufmylation process include UFM1, UBA5, UFC1, UFL1, and UFSP1,2 (Wei,2016). UFM1 is activated by the E1 enzyme UBA5, which forms a high-energy thioester bond between its catalytic cysteine and the exposed C-terminal glycine of UFM1. The E2 ligase UFC1 then binds to UBA5 and the activated UFM1 is transferred to UFC1. Finally, the UFM1-specific ligase 1 (UFL1) acts as the E3 to recognize its substrate, transfer and ligate the UFM1 from E2 to the substrate. The reversal of ufmylation is carried out by the two UFM1-specific proteases, UFSP1 and UFSP2.
The UFM1 interaction is mediated by a short linear sequence, UFM1-interacting motif (UFIM) present in the C-terminal IDP segment of UBA5. This interaction allows UFM1 to occupy the activation site near the ATP-binding site in the adenylation domain with higher efficiency. As well as UFM1, UBA5 is also capable of binding a different family of UBLs, the autophagy-specific UBLs (LC3/GABARAP) using the UFIM peptide. The UFIM motif has some resemblance towards the canonical LIR (LC3 interacting region) motif present in proteins like selective autophagy receptors p62/SQSTM1 and Optineurin, hence the name non-canonical LIR (Rogov,2014). The UFIM motif does also interact with LC3. Though they have a similar mode of interaction, UFIM is different from the canonical LIR in the spacing between the aromatic and aliphatic residues and its unique antiparallel orientation (Habisov,2016). The dual binding modes exhibited by the LIR/UFIM peptide is so far purely based on in vitro experiments. At time of writing, in-cell experimental evidence is lacking for the interaction between UBA5 and LC3/GABARAPs and the role played by these interactions on protein ufmylation and vesicle trafficking have still to be delineated. The UFM1 core components are located at the cytosolic side of the ER membrane and play an important role in ER homeostasis. Therefore they are often associated with endoplasmic stress response associated diseases like type 2 diabetes and ischemic heart diseases (Wei,2016).
o 3 selected references:

o 7 GO-Terms:

o 1 Instance for LIG_UFM1_UFIM_1
(click table headers for sorting; Notes column: =Number of Switches, =Number of Interactions)
Acc., Gene-, NameStartEndSubsequenceLogic#Ev.OrganismNotes
339 348 IIHEDNEWGIELVSEVSEEE TP 7 Homo sapiens (Human)
Please cite: The Eukaryotic Linear Motif resource: 2022 release. (PMID:34718738)

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