Structural analysis of the GGDEF-EAL domain-containing c-di-GMP receptor FimX

Abstract

Bacterial pathogenesis involves social behavior including biofilm formation and swarming, processes that are regulated by the bacterially unique second messenger cyclic di-GMP (c-di-GMP). Diguanylate cyclases containing GGDEF and phosphodiesterases containing EAL domains have been identified as the enzymes controlling cellular c-di-GMP levels, yet less is known regarding signal transmission and the targets of c-di-GMP. FimX, a protein from Pseudomonas aeruginosa that governs twitching motility, belongs to a large subfamily containing both GGDEF and EAL domains. Biochemical and structural analyses reveals its function as a high-affinity receptor for c-di-GMP. A model for full-length FimX was generated combining solution scattering data and crystal structures of the degenerate GGDEF and EAL domains. Although FimX forms a dimer in solution via the N-terminal domains, a crystallographic EAL domain dimer suggests modes for the regulation of FimX by c-di-GMP binding. The results provide the structural basis for c-di-GMP sensing via degenerate phosphodiesterases.

Figure 1. Structure of the FimX^EAL

(A) Domain organization of FimX. Protein constructs used in this study are indicated. The sequence motifs of the putative inhibitory site (I-site), diguanylate active site, and phosphodiesterase active site are shown. (B) Crystal structure of apo-FimX^EAL. The structure of the isolated EAL domain of FimX from P. aeruginosa is shown as ribbon presentation in two orthogonal views, with the molecular surface shown as inset. The EAL motif (E⁴⁷⁵VL in FimX) is colored in yellow. The linker between the GGDEF and EAL domains of FimX forms a helix in this structure and is colored in blue.

Figure 2. Structural comparison between the c-di-GMP-bound form and the apo-state

(A) Crystal structure of FimX^EAL•c-di-GMP. The c-di-GMP-bound structure of FimX^EAL, (colored in grey) was superimposed onto the nucleotide-free structure (colored in red) shown in Figure 1. Although present in the construct, the linker helix (blue) is disordered in FimX^EAL•c-di-GMP. The bottom panel shows a close-up view of the nucleotide binding pocket, with residues involved in c-di-GMP binding shown as sticks. The (|Fo|-|Fc|) electron density map shown as calculated from a model prior to inclusion of nucleotide and is contoured at 3σ. (B) Comparison of the degenerate EAL domain of FimX and the EAL domain of YkuI. The c-di-GMP bound state of FimX^EAL (grey) and YkuI^EAL (PDB code 2w27; cyan) were superimposed. Nucleotide and magnesium coordinating residues are shown as sticks. Residue type and sequence position are indicated (left: FimX^EAL, right: YkuI^EAL). YkuI was crystallized in the presence of calcium (green sphere).

Figure 3. Isothermal titration calorimetry data for c-di-GMP binding to FimX

(A) Binding of c-di-GMP to FimX^EAL. Calorimetric titration for c-di-GMP (250 μM) titrated into FimX^EAL (25 μM) is shown. Derived values for K_d and stoichiometry (N) are shown. (B) Binding of c-di-GMP to full-length FimX. Calorimetric titration for c-di-GMP (250 μM) titrated into full-length FimX (25μM) is shown. Derived values for K_d and stoichiometry (N) are shown.

Figure 4. Structure of the degenerate GGDEF domain of FimX

(A) Crystal structure of FimX^GGDEF. The GGDEF domain of FimX is shown in green. The degenerate GGDEF motif (G³⁴⁶DSIF in FimX) at the active site is colored in orange. The right panel shows a superposition with the GGDEF domain of the active diguanylate cyclase PleD from Caulobacter crescentus (PDB code 1w25; grey). (B) Close-up view of the degenerate nucleotide binding site of FimX^GGDEF. The structures of nucleotide-free FimX^GGDEF (green) and the GGDEF domain of PleD bound to a nonhydrolyzable GTP analog (PDB code 2v0n; grey) were superimposed. The degenerate GDSIF motif of FimX is colored in organge. Nucleotide and magnesium (yellow sphere) coordinating residues are shown as sticks. Residue type and sequence position are indicated (left: FimX^GGDEF, right: PleD). (C) Cyclic di-GMP-incompatible active and I-sites of FimX^GGDEF. The structures of nucleotide-free FimX^GGDEF (green) and the GGDEF domain of PleD bound to c-di-GMP at the active (left panel) and I-site (right panel) (PDB code 2w25; grey) were superimposed. Cyclic di-GMP coordinating residues of PleD and corresponding residues of FimX are shown as sticks. (D) Sequence alignment of nucleotide binding motifs in GGDEF domain-containing proteins. GGDEF domain sequences from FimX, WspR, PleD and CC3396 were aligned using ClustalW. Sequence blocks spanning the nucleotide binding sites (colored residues) are shown. Residues involved in magnesium binding (filled arrows), GTP binding (open arrow and asterisks) are highlighted. The GGDEF motif and the I-site are colored in green and red, respectively.

Figure 5. Structure of an EAL domain dimer observed in FimX^dual crystals

(A) Crystal structure of a homodimeric EAL domain of FimX. In the structure of FimX^dual, the two EAL domains in the asymmetric unit (colored in red and grey) form a dimeric assembly. The inset (top left panel) shows a surface presentation of an EAL domain monomer. The nucleotide binding site is colored in blue. Two orthogonal views are shown. The N-termini of the EAL domain are colored in green (B) Blocked c-di-GMP binding in the dimer. The structures of FimX^EAL•c-di-GMP and FimX^dual were superimposed. Only the nucleotide of the c-di-GMP-bound structure is shown as sticks. The close-up view (right panel) shows clashes of c-di-GMP with the dimeric EAL domain.

Figure 6. Dimer interfaces in EAL domain-containing structures of FimX

(A) Conformational variation in FimX^EAL and FimX^dual domain dimers. A comparison of the EAL domain dimer observed in the crystal structure of FimX^dual (left panel) and the FimX dimer in apo-FimX^EAL (middle panel) crystals is shown. The structure of FimX^dual is colored as in Figure 4. The protomers of the FimX^EAL structure are colored in yellow and grey, with their N-termini shown as orange spheres. The right panel shows a superposition of the two dimers using a single EAL domain as reference. The inset is an orthogonal view highlighting the position of the N-termini in both dimers. (B) Mapping of dimer interfaces onto the surface of the EAL domain. The structure of FimX^EAL shown as ribbons (left panel) depicts the orientation of the surface presentations (middle and right panel). In the middle panel, interfacial residues of the apo-FimX^EAL dimer are colored orange. Additional residues contributing to dimerization in FimX^dual are colored in red. In the right panel, a dimer interface observed in structures of the EAL domain-containing protein tdEAL and YkuI is colored in cyan on the surface of the crystal structure of YkuI (PDB code 2w27).

Figure 7. Oligomerization state of FimX in solution

(A) Size exclusion chromatography. Standard proteins (arrows), FimX full-length and truncations were analyzed by size exclusion chromatography in gel filtration buffer. Standardization using elution times, molecular weights of the standard proteins, and column specifics yielded a standard curve for molecular weight estimations for FimX. (B) Analytical ultracentrifugation. FimX full-length and truncations were analyzed by sedimentation velocity analytical ultracentrifugation in gel filtration buffer. Molecular weights were analyzed by using the program SedFit.

Figure 8. Solution scattering analysis of FimX

Small-angle X-ray scattering curves and distance distribution functions of FimX^full-length (A), FimX^ΔEAL (B), FimX^dual (C), and FimX^EAL (D) are shown after averaging and subtraction of solvent background scattering. Theoretical scattering profiles calculated from the ab initio models with the lowest χ values are shown (black line; see Figure 8). The inset shows Guinier plots (including linear fits) at the low angle region (S_max*R_g<1.3). For constructs containing the EAL domain, experiments were also performed in the presence of c-di-GMP (dashed grey lines).

Figure 9. SAXS-based shape reconstruction of FimX

(A) SAXS-based shape reconstruction of FimX^EAL (red), FimX^dual (green), FimX^ΔEAL (blue), and FimX^full-length (orange) are shown after averaging of twenty independent models (grey envelopes) and filtering (colored enveloped). High-resolution crystal structures of the EAL and GGDEF domains were docked into the appropriate envelopes and are shown in cartoon presentation. (B) Model for full-length FimX. High-resolution crystal structures of the EAL and GGDEF domains, as well as models for the dimeric response receiver and PAS domains (PDB codes 3BRE and 1DRM, respectively; De et al., 2008; Gong et al., 1998) were docked into the envelopes modeled from the solution scattering of full-length FimX, and are shown in cartoon presentation. A superposition of solution envelopes for FimX^ΔEAL (blue) and FimX^full-length is shown. The circle highlights a region in the FimX^full-length envelope that is missing in the FimX^ΔEAL envelope.