The Eukaryotic Linear Motif resource for
Functional Sites in Proteins
Accession:
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) binds tightly to the barbed end of actin filaments and limits polymerization. Its regulatory CPI motif was first characterized in CARMIL proteins. Later, other actin regulators were found to employ the same mechanism for the modulation of capping protein activity (Hernandez-Valladares,2010). Structural studies revealed that the CPI motif wraps around the stalk of the mushroom-shaped CP heterodimer (Hernandez-Valladares,2010; Takeda,2010). This relatively long motif makes numerous side-chain and main-chain contacts with the two subunits of CP, especially the β-subunit (Hernandez-Valladares,2010). Binding of the CPI motifs of different families of negative regulators to CP induces subtle, but functionally significant conformational changes in CP that disfavour actin binding, therefore they can allosterically down-regulate capping activity to different extents, depending on the potency of their CPIs (Hernandez-Valladares,2010; Takeda,2010; McConnell,2020; Takeda,2021).
The LIG_ActinCP_CPI_1 motif pattern covers all the experimentally validated instances of the motif and their evolutionary conservation patterns (McConnell,2020). It spans the core CPI, but it does not include family-specific motif extensions, like the CARMIL-specific interaction (CSI) motif (Hernandez-Valladares,2010). Also, compared to published CPI patterns, this pattern encodes the co-dependency of the 3rd and 5th residue positions, the variable length of the second half of the motif, the need for positively charged residues preceding the final well-defined position (predominantly a proline), and the fact that proline is disfavoured in the position following this final proline residue due to H-bonding constraints. The optimal motif approximates LxHxTxxRPKxxxRxxPS. The motif pattern does not cover the highly diverged twinfilin-type CPI motif due to its opposite functional effect (Johnston,2018), partially overlapping but distinctly different binding surface on CP (Takeda,2021), and dissimilar sequence pattern (Takeda,2021; McConnell,2020).
Pattern: L.(([H].[TQVG])|([SC].N)|(D.R))..R[PAVT][KRHM][^DEN].{1,5}((R.)|(.[RK]))..[PAS][^P]
Pattern Probability: 0.0007251
Present in taxon: Eukaryota
Interaction Domains:
o See 15 Instances for LIG_ActinCP_CPI_1
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 15 Instances for LIG_ActinCP_CPI_1
(click table headers for sorting; Notes column: =Number of Switches, =Number of Interactions)
Acc., Gene-, NameStartEndSubsequenceLogic#Ev.OrganismNotes
Q9Y5K6 CD2AP
CD2AP_HUMAN
486 503 NLLHLTANRPKMPGRRLPGR TP 18 Homo sapiens (Human)
8 
Q53GL0 PLEKHO1
PKHO1_HUMAN
150 168 LAHPTRDRAKIQHSRRPPTR TP 22 Homo sapiens (Human)
6 
Q552E2 washc2
WASC2_DICDI
1201 1218 ELTHATASRPKSGGRRPPTR TP 3 Dictyostelium discoideum
2 
P90630 Myosin-I binding protein Acan125
P90630_ACACA
1091 1108 NLTHMTKDRPMGPQRRRPQR TP 2 Acanthamoeba castellanii
2 
Q641Q2 WASHC2A
WAC2A_HUMAN
1024 1041 TLHSANKSRVKMRGKRRPQT TP 6 Homo sapiens (Human)
6 
Q95VZ3 carmil
CARML_DICDI
1023 1041 LTHVTASRPHIASKRKPPTR TP 3 Dictyostelium discoideum
2 
Q6F5E8 CARMIL2
CARL2_HUMAN
1016 1037 LRHPTRARPRPRRQHHHRPPPG TP 5 Homo sapiens (Human)
4 
Q9Y4E1 WASHC2C
WAC2C_HUMAN
1003 1020 TLHSANKSRVKMRGKRRPQT TP 5 Homo sapiens (Human)
4 
Q6EDY6 Carmil1
CARL1_MOUSE
986 1003 RLEHFTKLRPKRNKKQQPTQ TP 14 Mus musculus (House mouse)
4 
Q5VZK9 CARMIL1
CARL1_HUMAN
982 999 KLEHFTKLRPKRNKKQQPTQ TP 13 Homo sapiens (Human)
8 
Q8ND23 CARMIL3
CARL3_HUMAN
971 988 KLRHQTQGRPRPPRTTPPGP TP 3 Homo sapiens (Human)
2 
Q9VA36 cindr
Q9VA36_DROME
591 610 LTDMRQGRVKAPKRRPPSAA TP 3 Drosophila melanogaster (Fruit fly)
2 
Q96B97 SH3KBP1
SH3K1_HUMAN
476 494 LSHPTTSRPKATGRRPPSQS TP 5 Homo sapiens (Human)
6 
Q6JBY9 RCSD1
CPZIP_HUMAN
153 172 LPCYNKVRTRGSIKRRPPSR TP 4 Homo sapiens (Human)
4 
Q9JIY0 Plekho1
PKHO1_MOUSE
149 167 LAHPTRDRAKIQHSRRPPTR TP 1 Mus musculus (House mouse)
2 
Please cite: ELM — the eukaryotic linear motif resource in 2020. (PMID:31680160)

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