The Eukaryotic Linear Motif resource for
Functional Sites in Proteins
Functional site class:
MAPK docking motifs
Functional site description:
The MAPK-docking motif, also known as D-motif or kinase interaction motif (KIM) consists of one or more basic and two to four hydrophobic residues in adjacent groups. These residues bind to the MAPK-docking groove in various MAPKs. The basic-hydrophobic pattern can be present either in N- to C-terminal or C- to N-Terminal orientation. A linker region of variable length intersects the basic and hydrophobic residues. This linker region may build secondary structures, like helices, and therefore can add some additional order to the motif bound state. The docking motif patterns vary according to which MAPKs are to be bound. Some docking motifs are quite specific while others are more general.

The binding site of the D-motifs is distinct from another MAPK docking motif class (the FxFP-type), thus they can act in a combinatorial manner.
ELM Description:
The sixth and rarest class of classical MAPK docking motifs was first identified in an intracellular parasite secreted protein. Toxoplasma gondii uses the GRA24 protein to tamper with cellular signalling of its mammalian host, utilizing its twin high-affinity MAPK docking motifs (Braun,2013). These motifs combine the DCC-type (partly polyproline II helix-like) geometry on their hydrophobic segment with a distinctly HePTP-like, helical N-terminus (Pellegrini,2016). Similarly to the DCC class, GRA24-type motifs also contact the MAPK docking groove with three hydrophobic contact points (ϕL = Leu/Ile/Val/Pro, ϕA = Leu/Ile/Val and ϕB = Leu/Ile/Val/Met/Phe), with two intervening residues in between ϕL and ϕA. (unlike MEF2A-type or HePTP-type motifs). It is also likely that (as with the ordinary DCC-type motifs) either one of these two intervening positions must be a proline to help maintain a polyproline II helix-like geometry. On the other hand, the N-termini of GRA24 motifs posess an alpha-helical geometry with one hydrophobic and two charged residues (ϕU-x-x-θ-θ-G), in an arrangement that is essentially identical to the D-motif of HePTP itself. Since currently there are only two well-known examples of this motif type, it is difficult to give an an approriately inclusive motif definition. In particular, it is still unclear how many more subtle structural variants could exist for this class (as already noted for the HePTP type motifs).
Pattern: [LIV][^P][^P][RK][RK]G.{3,6}[LIVP]P.[LIV].[LIVMF]|[LIV][^P][^P][RK][RK]G.{3,6}[LIVP].P[LIV].[LIVMF]
Pattern Probability: 6.636e-07
Present in taxon: Eukaryota
Interaction Domain:
Pkinase (PF00069) Protein kinase domain (Stochiometry: 1 : 1)
o See 2 Instances for DOC_MAPK_GRA24_9
o Abstract
Classical mitogen-activated protein kinase (MAPK) signalling systems typically consist of three-tiered kinase pathways, with each member activated through phosphorylation by kinases from the preceding layer. These pathways respond to a variety of extracellular challenges involving growth factors, morphogenic signals, biotic and abiotic stress stimuli. Eukaryotic organisms frequently contain multiple MAPK pathways, each responsive for eliciting a specific response to particular upstream signals. Multicellular animals (Metazoa) possess four different groups of classical MAPKs: The ERK1/2 family is responsible for cell cycle progression, growth and differentiation of cells in response to growth factors, also being a key player in the formation of most cancers (Dhillon,2007). In contrast, the JNK and p38 MAPK families are primarily activated by diverse stressors (hyperosmosis, oxidative stress, DNA damage, inflammation, etc.) as well as morphogenes (Cargnello,2011). The single ERK5 protein forms a family of its own, controlling the development of specialized organs (such as the heart and blood vessels Nithianandarajah-Jones,2012). All known MAPKs are serine/threonine kinases, targeting sites followed by a proline ([ST]P consensus). As such sites are extremely common (found in ~80% of all proteins), additional interactions are required to direct the kinase activity towards the correct substrates (Ubersax,2007, Bardwell,2006).
The interacting molecules are kinase substrates, MAPK activators, phosphatases, regulators and adapters (bringing the kinase and the substrate together). One way by which the MAPKs ensure their interaction partner specificity is by interaction through docking motifs, short amino acid stretches located on MAPK-interacting proteins (Bardwell,2003, Bardwell,2001, Sharrocks,2000).
The surface of MAPK kinase domain harbours special binding sites, distinct from the catalytic site, that serve to recruit docking motifs of interaction molecules. The major docking site of MAPKs consists of the hydrophobic docking groove and the adjacent, negatively charged CD (complementary docking) helix, extended by the also negatively charged ED or top site in p38 (Tanoue,2001). Together they recognize the so called D-motifs (named after the D-domain of Elk1, and the δ-domain of c-Jun) of partner proteins, also known as KIMs (kinase interacting motifs Kallunki,1996). D-motifs are intrinsically unstructured linear motifs, typically consisting of one or more positively charged amino acids, followed by a linker and finally three alternating hydrophobic residues. The length and composition of internal linkers is a key determinant in specific interactions of D-motifs with particular MAPKs (Garai,2012). Due to the topography of MAPKs, D-motifs of substrates must be separated from the phosphorylation site by a minimum distance (suggested are ~9 amino acids) for efficient coupling (Fernandes,2007). These docking motifs are most commonly found upstream (N-terminally) from the target phosphorylation sites by approximately 10-100 amino acids, but can be located virtually anywhere in the substrate proteins (Garai,2012, Zeke,2015). Certain interacting molecules do not even possess docking motifs on their own, relying on heterologous interactions with a D-motif containing partner in order to receive phosphorylation from a MAPK.

D-motifs or KIMs are not the only type of MAPK docking motifs. A second docking site of MAPKs (located below the activation loop of the kinase) can recruit the so-called FxFP motifs of substrate proteins. Due to their positioning relative to the catalytic site on the kinase, FxFP motifs are typically found downstream (C-terminally) of phosphorylation sites, often in relative proximity to the target site (5-20 amino acids downstream). Since the FxFP motifs bind to a different surface on the MAPK, they can combine with D-motifs in the same substrate, and act synergistically to enhance phosphorylation. A single substrate protein may contain a D-motif (KIM) or an FxFP motif or both (Galanis,2001, Jacobs,1999).

o 4 selected references:

o 10 GO-Terms:

o 2 Instances for DOC_MAPK_GRA24_9
(click table headers for sorting; Notes column: =Number of Switches, =Number of Interactions)
Acc., Gene-, NameStartEndSubsequenceLogic#Ev.OrganismNotes
S7WIN8 TGGT1_230180
520 534 TGLLERRGVSELPPLRIVKP TP 5 Toxoplasma gondii GT1
S7WIN8 TGGT1_230180
441 455 TGLLERRGVSELPPLYIPRP TP 7 Toxoplasma gondii GT1
Please cite: The Eukaryotic Linear Motif resource: 2022 release. (PMID:34718738)

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