structural Studies of Wnts and identification of an LRP6 binding site

Abstract

Wnts are secreted growth factors that have critical roles in cell fate determination and stem cell renewal. The Wnt/β-catenin pathway is initiated by binding of a Wnt protein to a Frizzled (Fzd) receptor and a coreceptor, LDL receptor-related protein 5 or 6 (LRP5/6). We report the 2.1 Å resolution crystal structure of a Drosophila WntD fragment encompassing the N-terminal domain and the linker that connects it to the C-terminal domain. Differences in the structures of WntD and Xenopus Wnt8, including the positions of a receptor-binding β hairpin and a large solvent-filled cavity in the helical core, indicate conformational plasticity in the N-terminal domain that may be important for Wnt-Frizzled specificity. Structure-based mutational analysis of mouse Wnt3a shows that the linker between the N- and C-terminal domains is required for LRP6 binding. These findings provide important insights into Wnt function and evolution.

Figure 1. Crystal structure of the Drosophila WntD NTD-linker

(A) Primary structures of WntD and Wnt3a. SS, signal sequence. An attempt to produce a C-terminal truncated Wnt3a construct (Wnt3a NTD-linker) equivalent to the dominant negative mutants of mouse Wnt1 or Xenopus Wnt8 was not successful (see also Figure S1), probably due to the unpaired Cys281 forms a disulfide bond in the full-length protein. Truncating Wnt3a just before Cys281 yielded a secreted protein that could be purified (see also Figures S2B and S4A). The Wnt3a linker peptide used in this study is also shown. WntD Cys232 is a conserved cysteine normally forms a disulfide bond with another conserved cysteine Cys269 within the Wnt CTD, but is unpaired in the crystallized WntD NTD-linker construct. (B) Two orthogonal views of the WntD NTD-linker structure. α-helices A to F are shown in blue and the β-hairpin in yellow. The five disulfide bridges are depicted as yellow sticks. The Cys51–Cys62 disulfide pair and the free Cys232 at the C-terminus are labeled. The inset shows the tip of the β-hairpin that contains the conserved acylated serine in other Wnt family members, but is a glutamine in WntD (Glu171). A fist-like structure of the tip of β-hairpin is observed in WntD (dark grey) and is stabilized by a hydrogen bond (dashed line) between Gln171 and Glu177 (sticks), as evidenced by the visible electron density (grey mesh, 2F_o-F_c map contoured at 0.9 σ).

Figure 2. Comparison of Drosophila WntD and Xenopus Wnt8 crystal structures

(A) Superposition of WntD (blue) and the XWnt8 (magenta)–Fzd8 CRD (green) complex. The crystal structure of WntD in the present study contains the N-terminal domain and the linker that connects it to the C-terminal domain, which ends at Cys232 (blue stick). The lipid at Ser187 of XWnt8 that makes extensive contact with Fzd8 CRD is labeled as Palmitoleic Acid Modification (PAM, red stick). (B) Cylinder representation of superimposed NTD-linker regions of WntD (blue) and XWnt8 (magenta) viewed from the side and the top. The root mean square deviation between the two structures is 2.0 Å for 168 Cα atoms. The less compact core of WntD is evident by the outward displacement of helices A, C, D and E relative to those of XWnt8. Helix B of the two structures also differ by a rotation of ~58°. (C) Conformations of the β-hairpins. The tip of the XWnt8 hairpin that connects helices E and F adopts an extended conformation with the lipid-modified Ser187 (magenta stick with red lipid, labeled PAM) extending from the tip, whereas the equivalent loop of WntD adopts a fist-like structure. WntD Gln171, the equivalent residue of XWnt8 Ser187, is shown in light-grey stick, and its interacting residue WntD Glu177 is depicted as yellow stick. The 4 Å displacement of the anti-parallel β-strands relative to those of XWnt8 is highlighted. XWnt8 contains a second β-hairpin between helices C and D (XWnt8 C–D hairpin, red, residues 108–135), whereas the equivalent loop in WntD (WntD C–D loop, cyan, residues 105–113, 120–124) is much shorter and partially disordered in the structure (dotted cyan line). (D) Linker region between the N-terminal and C-terminal domains of Wnts. The loop that connects the interface motifs is partially disordered in XWnt8 (dotted red line), but includes helix G (XWnt8 linker, red, residues 216–221, 235–260). The equivalent loop of WntD is well ordered (WntD linker, cyan, residues 200–232) and follows a similar path as that of XWnt8 towards to C-terminus, but does not contain the α-helix G. The last residue of WntD NTD-linker Cys232 and the equivalent Cys260 of XWnt8 are shown in sticks.

Figure 3. A large solvent-accessible cavity in WntD

(A) Surface representation (grey) of cavities inside the NTD α-helical cores of WntD (blue, top figure) and XWnt8 (magenta, bottom figure) as viewed from the side and the top. The water molecules and a glycerol molecule in the large cavity of WntD are shown in red spheres and green sticks, respectively. A Zn²⁺ (cyan sphere) is present on the top of the small cavity of XWnt8. (B) Closeup of the solvent molecules in the large solvent-filled cavity of WntD. The hydrogen bond network within the WntD cavity is shown with dashed lines and the side chains and backbones of the water/glycerol-interacting residues are depicted as sticks. The entry paths of the solvent molecules are gated by three pairs of polar residues (sticks): Asn71/Tyr132, Glu76/Arg147 and Lys70/Asp83.

Figure 4. The NTD-CTD linker is required for Wnt3a activity and LRP6 binding

(A) The effects of charge-reversal mutations on autocrine Wnt 3a reporter activity in HEK293T cells. Cells were transfected with 25 ng plasmid of the indicated mutants. Error bars denote standard deviation. (B) Effect of Wnt3a linker mutations on paracrine Wnt3a reporter activity in LS/L reporter cells. Cells were treated with indicated concentration of purified mutants. Error bars denote standard deviation. (C) Mutations in the linker affect Wnt3a binding to LRP6(1-4). Wnt3a mutants at indicated concentration were incubated with 40 nM LRP6(1-4), run on native PAGE, and analyzed by western blot with anti-His₆ (top) and anti-Wnt3a antibodies (middle). The highly basic Wnt3a protein or linker peptide (Fig. 4D) cannot enter the gel unless it is bound to LRP6(1-4). The amount of input Wnt3a mutants in the gels was shown by running the same samples on a separate reducing SDS-PAGE, and analyzed by western blot with anti-Wnt3a antibody (bottom). (D) Biotinylated Wnt3a linker peptide at the indicated concentration incubated with 80 nM LRP6(1-4), run on native PAGE, and analyzed by western blot with NeutrAvidin (top) and anti-His₆ antibody (bottom). (E) Full-length Dkk1 and Dkk1_C, but not Dkk1_N can displace the peptide from LRP6(1-4). 8 μM Wnt3a peptide was incubated with 80 nM LRP6(1-4) and full-length Dkk1, Dkk1_N or Dkk1_C at the indicated concentration, run on native PAGE, and analyzed by western blot with NeutrAvidin (top) and anti-His₆ antibody (middle). The amount of input Dkk1 proteins in the gels was shown by running the same samples on a separate reducing SDS-PAGE, and analyzed by western blot with anti-His₆ antibody (bottom).