The Eukaryotic Linear Motif resource for
Functional Sites in Proteins
Functional site class:
Extracellular side LRP5 and -6 binding motif
Functional site description:
Wnt signaling can be inhibited by several antagonists that either bind directly to the Wnt ligands or to the outer modules of the Wnt receptors LRP5/6. The well known inhibitors of canonical Wnt signalling are Dickkopf family proteins, WISE and sclerostin (SOST). These proteins inhibit the signaling pathway by direct binding to LRP5/6 which sterically interferes with Wnt binding. Alternatively, their binding can also induce a conformational change on LRP6 which disrupts the Wnt binding sites. The latter inhibition is achieved via binding of a short ‘NxI’ motif present in the Wnt antagonists to the first (E1) β-propeller domain of LRP5/6. Mutations are known in the ligand-binding site of LRP5/6 that can disrupt the inhibition of Wnt signaling by SOST and DKK1 and hence result in diseases associated with disregulation of bone homeostasis. So these interactions have the potential to regulate bone deposition by modulating Wnt signaling and are a therapeutic target for bone related diseases.
ELM Description:
The binding of Wnt antagonists to the first β-propeller domain of LRP5/6 receptors is mediated by a short motif, ‘NxI’. The motif binds to the top center of the first β–propeller and abrogates the binding site for the Wnt ligand and thus inhibits the pathway. In the LRP6-DKK1 complex, the key residues involved in the interaction form a “handshake” interaction between the invariant N198 of the motif and the N185 of LRP6. The main chain oxygen from DKK1 N198 also forms a polar interaction with the R141 sidechain of LRP6. Further, a hydrophobic residue IIe is mostly present at the Asn+2 position of NxI. This Ile fits very well in the hydrophobic pocket present on LRP6. It is important to mention that the main chain oxygen of the residue next to Ile forms another polar contact with LRP6, which seems to act as a stabilizer of the motif interaction with LRP6. Moreover, in addition to the core motif, the side chain of a flexibly spaced basic residue (R/K) (within 6 aa positions C-terminally of the Ile), interacts with an acidic surface patch on the LRP6 but is not buried. This interaction might provide some additional affinity and specificity in the LRP6-DKK1 complex formation. Among the other key positions, hydrophobic/small amino acids are also present at -2 position from Asn of the motif. There is a variation on either side of the motif in the case of DKK and SOST. In SOST, the additional presence of Proline is observed at -1 position from the motif (NxI). Further, the motif is followed by a Glycine residue and the position of the basic residue can be variable up to six amino acids from the former residue. Overall, the motif is present in multiple DKK proteins, SOST and WISE and is well conserved in vertebrate proteins.
Pattern: ([VILA]..N.I[RK])|([VILA].PN.IG.{0,6}[RK])
Pattern Probability: 0.0000263
Present in taxon: Chordata
Interaction Domain:
Ldl_recept_b (PF00058) Low-density lipoprotein receptor repeat class B (Stochiometry: 1 : 1)
o See 3 Instances for LIG_LRP6_Inhibitor_1
o Abstract
Wnt signalling is antagonized on the external side of the plasma membrane through interactions between LRP5/6 co-receptors and secreted inhibitors of Wnt signalling. These interactions disrupt the Wnt–Frizzled–LRP5/6 receptor complex which is required for active signal transduction. There are many Wnt antagonists which negatively regulate the Wnt pathway either by directly binding to Wnt (secreted Frizzled-related protein and Wnt inhibitory factor) or to LRP5/6 (Dickkopf, WISE and sclerostin). For LRP5/6 inhibition, the focus of interest lies in the short ’NxI’ motif, which is present in several inhibitor proteins like Dickkopf family proteins, WISE and SOST. These proteins bind to the first β propeller domain of LRP5/6. The full-length LRP5/6 can be divided into the ectodomain (ECD), transmembrane domain, and cytoplasmic domain. The ECD contains four YWTD β-propeller domains, each of which is coupled to an epidermal growth factor (EGF)–like domain. These four β-propeller (P) and EGF like (E) domains (P1E1, P2E2, P3E3, P4E4) are followed by three low density lipoprotein receptor type A (LA) domains (Xu et al.,2011 ). All the Dickkopf family proteins except DKK3 bind the LRP5/6 with high affinity. DKK1 binds to LRP5/6 in a bipartite manner, the C-terminal region of DKK1 binds to P3E3, P4E4 while the N-terminal ‘NxI’ motif binds to P1E1. So DKK1 can inhibit a broad number of Wnt proteins that bind either E1E2 or E3E4 (Cochran et al., 2011), while the cystine knot-containing proteins SOST and WISE use only the first propeller domain of LRP5/6 for motif-binding and inhibit only a subset of Wnts (Mueller et al.,2013). Both DKK1 and SOST suppress new bone formation. The lack of, or low levels of, SOST leads to the development of a condition known as van Buchem disease or Sclerosteosis in human. Mutations in the ligand binding site of LRP5/6 lead to unusually high bone-mass density (Boyden et al., 2002). However these patients do not suffer from gross developmental abnormalities nor, apparently, an increased risk of cancer.
o 11 selected references:

o 11 GO-Terms:

o 3 Instances for LIG_LRP6_Inhibitor_1
(click table headers for sorting; Notes column: =Number of Switches, =Number of Interactions)
Acc., Gene-, NameStartEndSubsequenceLogic#Ev.OrganismNotes
109 121 PLPLLPNWIGGGYGTKYWSR TP 2 Gallus gallus (Chicken)
114 126 PARLLPNAIGRGKWWRPSGP TP 7 Homo sapiens (Human)
O94907 DKK1
37 43 ATLNSVLNSNAIKNLPPPLG TP 3 Homo sapiens (Human)
Please cite: The Eukaryotic Linear Motif resource: 2022 release. (PMID:34718738)

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