The Eukaryotic Linear Motif resource for
Functional Sites in Proteins
Functional site class:
Actin capping protein regulatory motif
Functional site description:
Actin-capping protein (CP) is a heterodimer of α- and β-subunits that binds free actin filament barbed ends with high affinity, thereby restricting their further growth. CP is present in a range of cellular structures where actin filament elongation must be tightly controlled, such as the sarcomeres, lamellipodia, invadopodia, podosomes and adherent junctions of eukaryotic cells. A diverse set of unrelated proteins employ the Capping Protein-Interaction (CPI) linear motif to allosterically down-regulate the actin-capping activity of CP and thereby fine-tune actin assembly dynamics. These include CARMIL proteins, CD2AP, CIN85, CKIP1, FAM21 and CapZIP. In contrast, by binding to actin and CP simultaneously, twinfilins help to maintain the dynamic capping/de-capping exchange cycle of CP and restrict its localization to the leading edge of actin filaments. Twinfilins carry a highly diverged CPI-like motif that binds a partially overlapping surface on CP, thereby protecting CP from its negative regulators.
ELMs with same func. site: LIG_ActinCP_CPI_1  LIG_ActinCP_TwfCPI_2 
ELM Description:
The actin capping protein (CP) heterodimer binds tightly to the barbed end of actin filaments and limits polymerization. The CP regulatory CPI motif was initially characterized in allosteric negative regulators of CP, like CARMIL proteins, but later the only known pro-capping regulators of CP, twinfilins also turned out to employ a highly diverged CPI-like motif for CP binding (Johnston,2018). Structural and competition studies revealed that the twinfilin-type TwfCPI motif binds a surface on CP that mostly overlaps with the one that the CPIs of negative regulators bind. In particular, the central two positive residues of the two motif types bind similarly, and accordingly, have similar sequence constraints: KPk in human twinfilins 1 and 2 and RP[KR] in human CARMILs (Johnston,2018; Hakala,2021; Edwards,2014). The conserved residues preceding and following the central positive residues of the two motif types differ significantly (McConnell,2020), therefore a unified CPI pattern could not be derived. The situation is further complicated by the observation that the phosphoinositide- and capping protein-binding sites in the C-terminal tail of twinfilin were reported to overlap, implying that membrane and CP binding are mutually exclusive (Hakala,2018). In many eukaryotes, the protein sequence terminates after the TwfCPI, defining the C-terminal boundary. However, in metazoans, the C-terminus is extended and the TwfCPI is part of a larger IDD (Intrinsically Disordered Domain). The current motif pattern describes the core motif, without the extension that is specific to multicellular metazoans. An optimal TwfCPI motif would be FxKPKxPxxK.
Pattern: F.[KR]P..[PAS].{0,3}[RK]
Pattern Probability: 0.0000295
Present in taxon: Eukaryota
Interaction Domains:
o See 4 Instances for LIG_ActinCP_TwfCPI_2
o Abstract
Actin filament networks are crucial for a number of cellular functions, including the determination of cell shape and many aspects of intracellular motility. Accordingly, precise control over actin filament growth is essential for eukaryotic cells. The filaments have a fast-growing barbed end (the plus end) and a slow growing pointed end (the minus end). Actin polymerization at the barbed ends of actin filaments can be dynamically regulated and this plays a key role in cell morphogenesis and cell motility through the formation of cellular structures, such as sarcomeres, lamellipodia, invadopodia, podosomes and adherent junctions, among others (Edwards,2014).
The heterodimeric actin capping protein (CP) is universally present in eukaryotes. It restricts actin filament elongation by binding to the barbed ends with high affinity and therefore serves as an essential signal integrator for regulating actin dynamics. While indirect regulators, such as formins and ENA/VASP proteins, compete with CP for binding to the barbed ends to control the organization and dynamics of cellular actin networks, other regulators inhibit its capping function more directly via steric or allosteric mechanisms (Takeda,2010;Edwards,2014).
Allosteric negative regulators of CP function typically employ the conserved Capping Protein-Interaction (CPI) motif for the spatiotemporal modulation of capping activity (Hernandez-Valladares,2010;Edwards,2014;McConnell,2020). A diverse set of otherwise unrelated proteins rely on this mechanism including CARMIL proteins (Q5VZK9; Q6F5E8 and Q8ND23), CD2AP (CD2-associated protein; Q9Y5K6), CIN85 (Cbl-interacting protein of 85 kDa; Q96B97), CKIP1 (CK2-interacting protein 1; or PLEKHO1; Q53GL0), FAM21 (Q641Q2) and CapZIP (CapZ-interacting protein; Q6JBY9) (Hernandez-Valladares,2010; Edwards,2014). These proteins typically localize at the interface between actin filament barbed ends and cellular membranes and modulate actin assembly dynamics to promote membrane protrusions/deformations that drive changes in cell shape (Edwards,2015; Edwards,2014).
CP is a heterodimer of α- and β-subunits (P52907; P47756). Structural studies revealed that the CPI motif binds the stalk of the mushroom-shaped CP heterodimer (at a site distant from the actin-binding interface), adopting an extended conformation (3LK2; 3LK4; Hernandez-Valladares,2010; Takeda,2010). Therefore, the motif does not directly compete with actin binding, but it is an allosteric regulator that enforces a conformation on the CP heterodimer that is less favourable for actin capping. Also, the motif binds into a cleft contributed by both capping protein subunits (most interactions are with the β-subunit); therefore, it can only bind to the fully assembled heterodimeric CP (Hernandez-Valladares,2010). The CPI is a relatively long linear motif, where specificity-determining residues are interspersed with residues that do not seem to be important for the interaction. Different families of the listed allosteric negative regulators show different residue preferences at certain specificity-determining positions and also at seemingly neutral sites of the motif (McConnell,2020). Based on phylogenetic analyses, the CPI motif turned out to be widely conserved among CARMIL proteins of Metazoa and in species belonging to the Amoebozoa clade, such as Dictyostelium discoideum and Acanthamoeba castellanii (Edwards,2014; McConnell,2020). The LIG_ActinCP_CPI_1 motif class introduced here only includes the core CPI that is present in all the different negative regulators, but it does not cover family-specific motif extensions, like the CARMIL-specific interaction (CSI) motif (Hernandez-Valladares,2010).
A highly diverged version of the CPI motif is also employed by the only known positive (pro-capping) regulators of CP function, twinfilins (Johnston,2018; Takeda,2021;McConnell,2020;LIG_ActinCP_TwfCPI_2). Twinfilins are unique members of the Actin Depolymerization Factor-Homology (ADF-H) domain family, containing two ADF-H domains joined by a small linker sequence and followed by a short C-terminal tail harbouring the CP-binding motif and the overlapping membrane attachment site (Hakala,2018). Twinfilins help to maintain the dynamic capping/de-capping exchange cycle of CP through a processive filament end-attachment mechanism and restrict its localization to the leading edge of actin filaments (Hakala,2021). Also, they protect CP from barbed-end displacement by its negative regulators by direct competition, as their diverged CPI binds to a surface patch of CP that largely overlaps with the cleft bound by the CPIs of negative regulators (Johnston,2018; Takeda,2021).
o 8 selected references:

o 7 GO-Terms:

o 4 Instances for LIG_ActinCP_TwfCPI_2
(click table headers for sorting; Notes column: =Number of Switches, =Number of Interactions)
Acc., Gene-, NameStartEndSubsequenceLogic#Ev.OrganismNotes
Q9Z0P5 Twf2
323 333 FKQAFAKPKGPGGKRGHKRL TP 4 Mus musculus (House mouse)
P53250 TWF1
320 330 PNKSNLKFNKPKGPLRKRRT TP 8 Saccharomyces cerevisiae S288c
Q91YR1 Twf1
323 333 HKQSFAKPKGPAGKRGIRRL TP 21 Mus musculus (House mouse)
Q12792 TWF1
323 333 HKQSFAKPKGPAGKRGIRRL TP 1 Homo sapiens (Human)
Please cite: ELM — the eukaryotic linear motif resource in 2020. (PMID:31680160)

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