Molecular Basis of C-N Bond Cleavage by the Glycyl Radical Enzyme Choline Trimethylamine-Lyase

Abstract

Deamination of choline catalyzed by the glycyl radical enzyme choline trimethylamine-lyase (CutC) has emerged as an important route for the production of trimethylamine, a microbial metabolite associated with both human disease and biological methane production. Here, we have determined five high-resolution X-ray structures of wild-type CutC and mechanistically informative mutants in the presence of choline. Within an unexpectedly polar active site, CutC orients choline through hydrogen bonding with a putative general base, and through close interactions between phenolic and carboxylate oxygen atoms of the protein scaffold and the polarized methyl groups of the trimethylammonium moiety. These structural data, along with biochemical analysis of active site mutants, support a mechanism that involves direct elimination of trimethylamine. This work broadens our understanding of radical-based enzyme catalysis and will aid in the rational design of inhibitors of bacterial trimethylamine production.

Figure 1. Anaerobic metabolism of choline into trimethylamine (TMA) is a disease-associated microbial activity that utilizes the glycyl radical enzyme (GRE) CutC

(A) Anaerobic microbes generate TMA from choline in the human gut and in the environment. TMA is further metabolized to the greenhouse gas methane by archaea, or to the disease-associated metabolite trimethylamine N-oxide by a human liver monooxygenase. (B) General mechanistic hypothesis for GRE function: the 5′-deoxyadenosyl radical (Ado•) is used by an AdoMet radical enzyme to produce a stable glycyl radical within GREs. A thiyl radical is proposed to serve as the active oxidant in all GREs and would be generated transiently within the active site. S = substrate, P = product. Following initial hydrogen atom abstraction to form an α-hydroxy radical, (C) CutC may perform base-catalyzed direct elimination of TMA. (D) Alternately, choline cleavage could involve a 1,2-migration of the trimethylammonium moiety followed by decomposition of the resulting carbinolamine.

Figure 2. Overall structure of CutC from D. alaskensis G20

(A) CutC crystallizes as a dimer of dimers; the dimeric unit is shown below rotated 90°. (B) Within a single monomer, the active site cavity is found at the center of the (β/α)₁₀ barrel (solid ribbon), above the Cys loop. Residues Cys489 (location of putative, transient thiyl radical) and Gly821 (location of the stable glycyl radical) are shown in spheres. The glycyl radical domain (yellow) harbors the active site glycyl radical on the Gly loop in post-translationally modified proteins. (C) Cross-section of the CutC active site displaying a ring of aromatic residues (sticks) at the top of the active site, including two residues on a helix that caps the top of the barrel (gray). Choline is shown in the active site (cyan sticks). See Figure S1 for structural comparisons.

Figure 3. CutC binds substrate in a pocket above the Cys loop

(A) Stereoimage of CutC bound to its substrate, choline (cyan). The proposed hydrogen atom transfer pathway from Gly821 to Cys489 to C1 of choline is marked (red dashes). Hydrogen bonds (2.5–3.2 Å) are shown for residues within the active site (black dashes). The average HO–C1–C2–N(Me₃) dihedral angle is 61°. (B) Stereoimage of the CH---O hydrogen bonds (yellow dashes) present in the CutC-choline complex. (C) Diagram of protein and water interactions with the trimethylammonium moiety of choline with CH–O and hydrogen bond distances (Å). CH---O hydrogen bonds are indicated for C to O distances of 3.8 Å or less (yellow). Hydrogen bonds (black) and presumed cation-π interactions (gray) are shown between protein and substrate atoms. Distances (Å) are given in the diagram. The maximum-likelihood-estimated coordinate error is 0.20 Å. (D) Comparison of CutC (green) and GDH (magenta) active site residues involved in binding C1 and C2 (sticks). The Cys loop GCVEP motif is conserved between the two enzymes. An aromatic residue contributed from β3 coordinates C2 of choline (gray dashes). The proposed hydrogen transfer pathways (red dashes) between the active site Gly, Cys, and C1 are virtually identical in the two structures. See Figure S2 for sequence alignments and Figure S3 for additional CH---O hydrogen bonding analysis.

Figure 4. Structures of mutant CutC enzymes

(A,B,C,D) Composite omit density (light blue) is contoured at 1.5σ around active site residues with changes to each mutant structure highlighted (yellow). Hydrogen bonds (black dashes), steric clashes (pink dashes), and hydrogen-atom transfer pathways (red dashes) are indicated. Crystals were grown in the presence of 10 mM choline. (A) CutC-Y208F (1.90-Å resolution) closely resembles the wild-type enzyme, with the only difference being the generation of a new partially-occupied water binding site (HOH*). (B) E491A at 1.90-Å resolution contains active site density consistent with disordered water and/or partial occupancy of choline. (C) The E491Q mutant (1.60-Å resolution) has no density for choline. Instead, two new water molecules are bound in the active site (HOH*). The orientation of the side chain amide is deduced based on the contacts to hydrogen bond donors within the Cys loop. (D) T502A at 1.85-Å resolution is virtually identical to the wild-type CutC structure. See Table 1 for activity data on mutant proteins.

Figure 5. Putative hydrogen bonding networks in wild-type and mutant CutC enzymes

The orientation is shifted ~90° around the y-axis from Figure 4. Tyr506 and the Gly loop are not shown for clarity. Polar hydrogen atoms are shown within the networks based on inferred position given the available donor and acceptor groups, and considering that the pH of the crystallization was 8.0. Riding hydrogen atoms were added to the model during the final rounds of refinement. (A) In wild-type CutC, two networks of hydrogen bonds are highlighted (black dashes). Interactions between Glu491 and Thr502 and a backbone amide suggest that it is deprotonated and able to act as a general base to accept a proton from choline (cyan). Asp216 is also likely to be deprotonated, sharing a single proton in a hydrogen bond (O–O distance of 2.7 Å) with Tyr208. A proposed connection (white dashes) between Thr502-Asp216 would be possible if either of these residues were to change conformation. CH---O hydrogen bonds to Tyr208 and Aps216 are shown as yellow dashes. (B) In CutC-E491Q, the side chain carbonyl of Gln491 is likely to be pointing down toward the backbone amide, leaving the side chain nitrogen to point toward Thr502. (C) In CutC-T502A, no connection is available between Glu491 and Asp216. See Figure S4 and Table 1 for activity data on mutant CutC proteins.

Figure 6

Mechanistic proposal for choline cleavage by CutC.