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. 2023 Jan 24;120(4):e2212246120.
doi: 10.1073/pnas.2212246120. Epub 2023 Jan 18.

Biochemical and structural characterization of a sphingomonad diarylpropane lyase for cofactorless deformylation

Affiliations

Biochemical and structural characterization of a sphingomonad diarylpropane lyase for cofactorless deformylation

Eugene Kuatsjah et al. Proc Natl Acad Sci U S A. .

Abstract

Lignin valorization is being intensely pursued via tandem catalytic depolymerization and biological funneling to produce single products. In many lignin depolymerization processes, aromatic dimers and oligomers linked by carbon-carbon bonds remain intact, necessitating the development of enzymes capable of cleaving these compounds to monomers. Recently, the catabolism of erythro-1,2-diguaiacylpropane-1,3-diol (erythro-DGPD), a ring-opened lignin-derived β-1 dimer, was reported in Novosphingobium aromaticivorans. The first enzyme in this pathway, LdpA (formerly LsdE), is a member of the nuclear transport factor 2 (NTF-2)-like structural superfamily that converts erythro-DGPD to lignostilbene through a heretofore unknown mechanism. In this study, we performed biochemical, structural, and mechanistic characterization of the N. aromaticivorans LdpA and another homolog identified in Sphingobium sp. SYK-6, for which activity was confirmed in vivo. For both enzymes, we first demonstrated that formaldehyde is the C1 reaction product, and we further demonstrated that both enantiomers of erythro-DGPD were transformed simultaneously, suggesting that LdpA, while diastereomerically specific, lacks enantioselectivity. We also show that LdpA is subject to a severe competitive product inhibition by lignostilbene. Three-dimensional structures of LdpA were determined using X-ray crystallography, including substrate-bound complexes, revealing several residues that were shown to be catalytically essential. We used density functional theory to validate a proposed mechanism that proceeds via dehydroxylation and formation of a quinone methide intermediate that serves as an electron sink for the ensuing deformylation. Overall, this study expands the range of chemistry catalyzed by the NTF-2-like protein family to a prevalent lignin dimer through a cofactorless deformylation reaction.

Keywords: NTF-2; Novosphingobium aromaticivorans; Sphingobium sp. SYK-6; aromatic catabolism; lignin.

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Conflict of interest statement

The authors declare no competing interest.

Figures

Scheme 1.
Scheme 1.
Reactions catalyzed by NTF-2-like protein family scaffold.
Fig. 1.
Fig. 1.
In vivo transformation of erythro-DGPD by SpLdpA in Sphingobium sp. SYK-6. (A) HPLC traces comparing the erythro-DGPD depletion when incubated with WT and ΔSpldpA SYK-6 cell extracts. Metabolites corresponding to erythro-DGPD [retention time (tR) 1.1 min; gray], vanillate (tR 1.3 min; pink), and vanillin (tR 1.8 min; blue) are labeled. (B) Growth of WT (blue) and ΔSpldpA (orange) SYK-6 strains on erythro-DGPD as the sole carbon source.
Fig. 2.
Fig. 2.
Simultaneous consumption of erythro-DGPD enantiomers by LdpA. The depletion of erythro-DGPD enantiomers as followed by chiral chromatography. The reaction was sampled following 0, 25, 50, 75, and 100 μM oxygen consumption in a mixture containing 100 μM racemic erythro-DGPD, NaLdpA, and NOV2. The green and orange traces represent the individual enantiomers, and the black trace represents the total erythro-DGPD. The measurements were an average of three replicates and the error bars are the SD. The numerical data are provided in the SI Appendix, Table S2.
Fig. 3.
Fig. 3.
Lineweaver–Burk plot of the inhibition of LdpA-catalyzed erythro-DGPD deformylation by lignostilbene. Experiments for NaLdpA (A) and SpLdpA (B) were performed in MOPS (I = 0.1 M, pH 7.0), 25 °C, and 0 (gray), 1 (blue), 2 (green), 4 (red), and 10 (yellow) μM lignostilbene. The lines represent a best fit of an equation describing competitive inhibition to the data, NaLdpA, kcat = 2.36 ± 0.06 s−1; KM = 15 ± 1 μM; Kic = 0.33 ± 0.03 μM, and SpLdpA, kcat = 2.11 ± 0.06 s−1; KM = 16 ± 1 μM; Kic = 0.26 ± 0.02 μM. The numerical data used to determine these kinetic parameters are provided in the SI Appendix, Table S4.
Fig. 4.
Fig. 4.
Structural architecture of LdpA and substrate interactions. (A) Superposition of SpLdpA (magenta) with NaLdpA (teal). (B) Side view of the SpLdpA trimer. Two protein chains are shown as surfaces (yellow and green) and one protein chain is shown in cartoon mode (red) with bound substrate erythro-DGPD (light blue). (C) Top view of the SpLdpA trimer. (D) Pseudo-stereoscopic view of the interaction of SpLdpA with the erythro-DGPD enantiomers (αS, βR) (Left) and (αR, βS) (Right). When viewed in stereo, alternating eye switching results in an optimal impression of the binding modes of the two diastereomer substrates. (E) Omit electron density map for the (αS, βR)- and (αR, βS)-erythro-DGPD enantiomers bound to SpLdpA at 2.5 σ level. (F) Pseudo-stereoscopic view of the interaction of SpLdpA with the threo-DGPD enantiomers (αS, βS) (Left) and (αR, βR) (Right). (G) Omit electron density map for the (αS, βS)- and (αR, βR)-threo-DGPD enantiomers bound to SpLdpA at 2.5 σ level. A version of D and F with annotated polar distances is provided in the SI Appendix, Fig. S12.
Fig. 5.
Fig. 5.
Summary of LdpA mutational analysis. A diagram of the erythro-DGPD-bound LdpA complex. The amino acid residues are in black and erythro-DGPD is in pink. The residues numbering from NaLdpA and SpLdpA are labeled in blue and green, respectively. The dashed lines represent polar interactions ≤3 Å. The activity of the NaLdpA variants presented is normalized to the activity of the WT enzyme and labeled in orange. The two catalytic motifs are noted by shaded regions. Numerical data are provided in the SI Appendix, Table S7.
Fig. 6.
Fig. 6.
Molecular mechanism of LdpA. (A) Proposed catalytic mechanism of LdpA. The amino acid side chain numberings for NaLdpA and SpLdpA are highlighted in blue and green, respectively. The atoms highlighted in pink are frozen in the DFT computations and are only shown for the IN0. The oxygen atoms for the Cα and Cγ-hydroxyl groups are in green and pink, respectively. The Cα -phenolic proton is in orange. The partial bonds in transition states are denoted in dotted line. (B) Free energy profiles associated with the different intermediates and transition states associated with the different enantiomeric form of DGPD. All energies are in kcal/mol. DFT methods: B3LYP-D3(BJ)/6-31G(d,p), SCRF = (CPCM, Solvent = water), with Grimme correction for entropy and Head–Gordon correction for enthalpy. The numerical data are provided in the SI Appendix, Table S9.

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