The Eukaryotic Linear Motif resource for
Functional Sites in Proteins
Functional site class:
MIT domain binding motif
Functional site description:
ESCRT (Endosomal sorting complex required for transport) machinery regulates several biological and membrane remodelling processes. These include endosomal sorting, intraluminal vesicle formation (ILV), budding of enveloped viruses (HIV-1), and abscission during cytokinesis. ESCRT complex proteins assist these functions. Many of these proteins have the MIT (microtubule interacting and trafficking) domain, which consists of a three-helix bundle, and it recognises MIM (MIT-Interacting Motifs) docking motifs (Takasu,2005; Guo,2015). Currently, five MIT-MIM interactions (MIM1-5) are known (Skalicky,2012; Guo,2015). MIM1 is an α-helical motif, MIM2 is a proline-rich region with random coil conformation (Kieffer,2008), MIM3-5 adopt helical conformations (Yang,2008; Yang,2012). MIM4 establishes more polar contacts than MIM1 (Solomons,2011). The MIM1 motif present in ESCRT-III subunits regulates the delay of cytokinetic abscission, turnover of the ESCRT-III proteins and endosomal sorting.
ELM Description:
MIM1 is a helical motif present at or near the C-terminus of ESCRT-III subunit proteins (CHMP1A, CHMP1B, CHMP2A, IST1, VPS2, DID2) and binds to the groove between α2 and α3 helices of the MIT domain (2V6X; 4U7Y). The core of the MIM1 motif is LxxR[FL]xxL, where x is a non-Pro residue. Charged residues in the flanking regions of the core form electrostatic interactions with the MIT domain.

IST1 MIM1 has a conserved Leu353 at +1 position that binds to the hydrophobic pocket on the VPS4 MIT domain (4U7Y). The central residue in the MIM1 docking motif is +4 Arg (IST1 - 356R; DID4 - 224R; CHMP1A - 190R) as it forms salt-bridges/H-bonds with surface residues of the MIT domain. Specifically, +4 Arg forms three, four, and five salt bridge interactions with MIT domains of VPS4 (Asp65 and Glu70), LIP5 (Asp65 and Glu68), and Spartin (Asn28, Asn32, Glu35), respectively. A strictly conserved Leu or Phe follows after the Arg (+4 site). Another Phe at the -3 position of IST1 MIM1 interacts deeply in the hydrophobic pocket formed by Tyr20, Phe24, and Thr84 on the Spartin MIT domain (4U7I).

The MIM1 from VPS2/DID4 forms similar hydrophobic and charged interactions. Here, Leu225 (+5 position) from MIM1 gets deeply buried into a hydrophobic pocket on the VPS4 protein. This pocket is formed by Leu37, Leu64, and Phe60 residues of the VPS4 MIT domain (2V6X). In VPS2-VPS4 and CHMP1A-VPS4 complexes, the N-terminus of the MIM1 motif contains D/E. These negatively charged residues are located within two residues upstream from the +1 Leu and form complementary salt bridges to the residues on the MIT domain. Specifically, VPS2-VPS4 interaction involves three salt bridges formed by Asp218 of VPS2 and Lys53, Arg57 of VPS4 MIT domain (2V6X). At the MIM1 C-terminus, a conserved Leu is present at +8 and forms hydrophobic interactions on the surface groove of the MIT domain. Arg/Lys at the +9 position is quite conserved, and in VPS2/DID4 (2V6X), forms a salt bridge with Asp38 on the VPS4 MIT domain.
Pattern: ((F[^P][^P])|([DE].{0,2}))L[^P][^P]R[FL][^P][^P]L[KR]{0,2}
Pattern Probability: 0.0000103
Present in taxon: Eukaryota
Interaction Domain:
MIT (PF04212) MIT (microtubule interacting and transport) domain (Stochiometry: 1 : 1)
o See 5 Instances for DOC_MIT_MIM_1
o Abstract
Cells in eukaryotes have complex endomembrane systems and sorting events that require membrane remodelling complexes. ESCRT (endosomal sorting complex required for transport) machinery performs membrane remodelling, sorting and scission events. This machinery consists of a series of protein complexes, including ESCRT-0, -I, -II, -III, and an AAA ATPase VPS4. VPS4 performs the sequential recruitment of ESCRT-III layers, turnover, and disassembly of subunits in an ATP-dependent manner (Pfitzner,2020; Mierzwa,2017). The ESCRT-III complex is responsible for the Intraluminal vesicle (ILVs) formation during the multivesicular body (MVB) formation (Katzmann,2002), cytokinetic abscission during the last stages of cytokinesis (Carlton,2007), reformation of the nuclear envelope and sealing (Vietri,2015), budding of virions (including HIV-1) in eukaryotes (Morita,2004), neuron pruning (Loncle,2015) and cortical constriction (Elia,2011). The metazoan ESCRT-III subunits (CHMP1-7, IST1) polymerise into spiral filaments to constrict the vesicle neck region during the egress of viruses via the secretory pathway or during the budding of intraluminal vesicles. This process is known as reverse topology membrane fission, which results in the budding away of the vesicle from the cytosolic surface of the membrane (Pfitzner,2020; Schoneberg,2017).

A number of ESCRT complex proteins (VPS4, Vta1, LIP5, Spartin, ULK3, AMSH, UBPY, MITD1, and Spastin) contain the MIT (microtubule interacting and trafficking) domain. The MIT domain is a three-helix bundle that interacts with proteins through different surface grooves formed by its three helices. MIMs (MIT Interacting Motifs) present in ESCRT-III subunits (CHMP1A, CHMP1B, CHMP2A, IST1, VPS2, DID2) dock to the MIT domain. Five types of MIMs (MIM1-5) have been reported to interact with different sites/surface grooves on the MIT domain. MIM1 is an α-helical motif, and its central Leu residues form hydrophobic contacts in the region between the α2 and α3 helix of the MIT domain. Polar residues flank the MIM1 motif core and engage with the MIT domain via H-bonds and salt bridge interactions (Guo,2015; Obita,2007; Stuchell-Brereton,2007). MIM2 contains at least two essential prolines and binds as a random coil between α1 and α3 of the MIT domain (Kieffer,2008; Vild,2014). MIM3 interacts as a helical structure in the same region, and its C-terminus is similar to MIM1 as observed in the CHMP1B - Spastin complex (Yang,2008). MIM4 also adopts a helical conformation and binds in the groove generated by helices 3 and 4/5 of the AMSH MIT domain (Solomons,2011). MIM5 forms two helices and interacts with MIT domain helices 1-3. A representative MIM5 interaction is observed in VPS60 (128–186) - Vta1 NTD (N-terminal Domain) complex (Yang,2012).

ESCRT–III protein IST1 (Increased sodium tolerance-1; P53990) is required for cytokinetic abscission and contains MIM1 and MIM2 docking motifs. Replacing key interacting residues (L375A/K376A) of IST1 MIM1 resulted in defective multinucleated phenotypes, indicating the importance of this region (Agromayor,2009; Bajorek,2009). Further, MIM1 and MIM2 motifs are employed by IST1 to bind MIT domain-containing protein kinase ULK3 (Unc-51-like kinase 3). This interaction results in IST1 phosphorylation by ULK3, thereby delaying cytokinetic abscission in response to lagging chromosomes in the mid-body during cell division (Caballe,2015). Interestingly, IST1 can bind in both MIM1, and MIM3 modes as the bulky side-chain of Phe357 provides sufficient binding energy while interacting with the MIT domain of VPS4 (4U7Y) and Spartin (4U7I), respectively (Guo,2015). Point mutations in the key MIT interacting residues of the IST1 MIM1 (L353A, R357E, L360A, L360A/K361A; P53990) abrogates the interaction with the MIT domain of Spartin, LIP5, VPS4B, VPS4, MITD1, UBPY (Guo,2015; Bajorek,2009; Agromayor,2009).

MIM1-MIT binding between MITD1 (MIT-domain containing protein 1) (Q8WV92) and ESCRT-III subunits (IST1, CHMP1A, CHMP1B, CHMP2A) allows the recruitment of MITD1 during cell division (Hadders,2012). MIM1,2-MIT interaction regulates both the recruitment and functioning of VPS4 ATPase (Han,2015; Shestakova,2010). Substituting the critical Leu and Arg residues (L221D, R224D, L225D, L228D) in the VPS2 MIM1 motif impedes its binding with VPS4 (Obita,2007).

MIM1 forms an amphipathic helix where one side of the alpha helix makes hydrophobic interactions with the MIT domain, whereas the other side engages in hydrophilic contacts. The former interactions happen via Leu residues in the MIM1 core region, whereas the latter interactions happen through aspartic acid, glutamic acid at N-terminus and Arg, Lys at the C terminus (2V6X; 2JQ9; 2JQK; 4WZX; 4U7E; 4U7I; 4U7Y).
o 10 selected references:

o 13 GO-Terms:

o 5 Instances for DOC_MIT_MIM_1
(click table headers for sorting; Notes column: =Number of Switches, =Number of Interactions)
Acc., Gene-, NameStartEndSubsequenceLogic#Ev.OrganismNotes
P69771 DID2
193 203 VNVDDEKEDKLAQRLRALRG TP 5 Saccharomyces cerevisiae S288c [new]
187 196 VASAEQDELSQRLARLRDQV TP 5 Homo sapiens (Human) [new]
185 195 ESSVRSQEDQLSRRLAALRN TP 7 Homo sapiens (Human) [new]
P36108 DID4
220 230 FHGNPDDDLQARLNTLKKQT TP 6 Saccharomyces cerevisiae S288c [new]
P53990 IST1
351 362 SEDIDFDDLSRRFEELKKKT TP 11 Homo sapiens (Human) [new]
Please cite: ELM — the eukaryotic linear motif resource in 2020. (PMID:31680160)

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