The Eukaryotic Linear Motif resource for
Functional Sites in Proteins
Functional site class:
Docking motif binding to N-terminal kinase domain of RSK family kinases
Functional site description:
The 90 kDa ribosomal S6 kinases (RSK) are downstream effectors of the Ras–extracellular signal-regulated kinase (ERK) and mitogen-activated protein kinase (MAPK) signaling cascade and regulate diverse cellular processes. In addition, activated RSK phosphorylates important translational regulators such as EIF4B, RPS6, and EIF4B. The DDVF peptide sequence was identified as an RSK N-terminal kinase domain (NTKD) binding motif that enables the phosphorylation of RSK substrates.
ELM Description:
The short, partly acidic [DE]-[DE]-V-F motif was first identified in the L protein of Theiler’s murine encephalomyelitis virus (TMEV). It is highly conserved and so far has been identified in a few viral and bacterial pathogens, e.g., ORF45 protein of Kaposi’s sarcoma-associated herpesvirus (KSHV) and YopM protein of Yersinia. Asp/Glu from +1 and +2 motif positions interact via H-bonds on the positively charged surface (encircled by Arg300, Lys304, Arg305, Asn306 and Lys284) around the deep hydrophobic pocket which is formed between the αG-αH loop and helix G on the RSK kinase domain. Both, +3 Val and +4 Phe are deeply buried in the hydrophobic pocket. Additional H-bond contacts are also observed from the main chain carbonyl atom of +1 Asp/Glu and +3 Val. In ORF45, the backbone carbonyl atom of the latter is engaged in β-augmentation with the kinase domain. An extra backbone contact stabilizing the β-augmentation is provided by the N-atom from the amino acid following +4 Phe. Further, the -1 position has a Proline residue, which provides the kink to the motif peptide for the interaction with the surface and the pocket afterward (7OPO). Mutation of the residues (F268S, L285A, L285W, M287W, R305F) involved in binding pocket formation on the kinase domain leads to ~100-1000-fold reduction in the binding affinity with the ORF45 motif. The KAKLGM motif is conserved across evolution in all RSK isoforms (RKS1-4) and is part of a surface-exposed loop at the base of an α-helix in the N-terminal kinase domain (NTKD). When the pathogens bind to this loop, it may indirectly stabilize the neighbouring kinase activation loop in an active conformation. This suggests that the physiological regulation of RSK may depend on cellular factors that interact with the kinase in a similar way.
Pattern: [DE][DE]VF
Pattern Probability: 0.0000161
Present in taxons: Bacteria Eukaryota Viruses
Interaction Domain:
Protein kinase domain (IPR000719) Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases (Stochiometry: 1 : 1)
o See 5 Instances for DOC_RSK_DDVF_1
o Abstract
The 90 kDa ribosomal S6 kinases (RSK) are highly conserved Ser/Thr kinases, which are downstream effectors of the Ras–extracellular signal-regulated kinase (ERK) and mitogen-activated protein kinase (MAPK) signaling cascade. Unusually, RSKs have two protein kinase phosphorylation domains. The human RSK family consists of four isoforms (RSK1–4) and regulates diverse cellular processes, such as cell growth, cell survival, and proliferation. In addition, the members of the RSK family phosphorylate translational regulators, including the eukaryotic initiation factor 4B (EIF4B, P23588), the 40S ribosomal protein S6 (RPS6, P62753), and the tumor suppressors Tuberin (TSC2, P49815) and Programmed cell death protein 4 (PDCD4, Q53EL6). There are accumulating data that SLiMs in pathogenic organisms often evolve to mimic and subvert functional host protein interfaces. Proteins from several unrelated viruses and bacteria, including the Theiler’s murine encephalomyelitis virus (TMEV) leader (L) protein, the PRF45 (Human herpesvirus 8), and the YopM of bacteria from the genus Yersinia, can recruit the cellular p90-ribosomal protein S6 kinases (RSKs) through a conserved DDVF motif located in an IDD region. The consequence of the protein-protein interactions is to maintain the RSK kinases in an active state and influence the phosphorylation of RSK downstream substrates (Sorgeloos,2022).
The molecular details of the interaction of the DDVF motif with the N-terminal kinase domain (NTKD) are more complex than is typical for Linear Motifs which mostly bind ordered surface pockets of the core folded domain. TMEV Leader Protein (L) (P13899), ORF45 (F5HDE4), and YopM (P17778) bind a conserved but surface-located loop located on the RSK N-terminal kinase domains, KAKLGM, as shown by cross-linking experiments, as well as crystallographic data of the RSK2 NTKD in complex with ORF45 (7OPO; Alexa,2022). While Val and Phe from ORF45 DDVF are deeply buried, the backbone atom of the following amino acid (after the Phe) and the Val from motif makes contact with the NTKD via β-augmentation. Interestingly, the β-strand which engages from the NTKD also forms additional contacts with the IDD region containing DDVF which is wrapped around the bulge on the kinase surface (formed by the mentioned β-strand on the NTKD). The long IDD region also helps dimerization of the kinase as it interacts with the N-terminal region of one RSK copy and C-terminus part of another RSK molecule (7OPO; Alexa,2022).
The L proteins from different TMEV virus strains (P08544 and P08545) have high sequence similarity to the canonical TMEV (P13899), and are likely to interact in a similar manner to the conserved loop of RSKs. The RSK KAKLGM motif is conserved in the N-terminal kinase domain (NTKD) of all human RSK isoforms and regulates RSK activity, likely acting as an allosteric regulation site.
The downstream consequences are various, e.g., YopM inhibits effector-triggered pyrin inflammasome activation (Ratner,2016), whereas, upon RSK recruitment and accumulation of c-Fos, ORF45 accelerates lytic replication of Kaposi's Sarcoma-Associated Herpesvirus (Li,2015). The RSK recruitment by cardiovirus L protein leads to the inhibition of the antiviral eukaryotic initiation factor 2 alpha kinase 2 (EIF2AK2) (Borghese,2019).
o 5 selected references:

o 7 GO-Terms:

o 5 Instances for DOC_RSK_DDVF_1
(click table headers for sorting; Notes column: =Number of Switches, =Number of Interactions)
Acc., Gene-, NameStartEndSubsequenceLogic#Ev.OrganismNotes
63 66 TVIDMSAPDDVFAEDTPSPP TP 2 Human herpesvirus 8 strain GK18
P17778 yopM
405 408 VDPYEFAHETTDKLEDDVFE TP 1 Yersinia pestis
P08545 Genome polyprotein
45 48 DLLCVDLDDDVFWPSDTSTQ TP 1 Theiler"s encephalomyelitis virus (STRAIN GDVII)
P08544 Genome polyprotein
45 48 DLLCVDLDDDVFWPSDTSNQ TP 1 Theiler"s encephalomyelitis virus (STRAIN BEAN 8386)
P13899 Genome polyprotein
45 48 DLLCVDLDDDVFWPSNSSNQ TP 1 Theiler"s encephalomyelitis virus (STRAIN DA)
Please cite: The Eukaryotic Linear Motif resource: 2022 release. (PMID:34718738)

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