Functional Annotation of LigU as a 1,3-Allylic Isomerase during the Degradation of Lignin in the Protocatechuate 4,5-Cleavage Pathway from the Soil Bacterium Sphingobium sp. SYK-6

Abstract

Sphingobium sp. SYK-6 is a Gram-negative soil bacterium that contributes to the degradation of lignin. Lignin provides structural support and protection to plants as a complex aromatic heteropolymer. The lignin degradation pathway of guaiacyl moieties leads to the intermediate, protocatechuate (PCA), which is further degraded via the 4,5-cleavage pathway in which PCA is ultimately metabolized to pyruvate and oxaloacetate. In this pathway, LigI has been shown to catalyze the hydrolysis of 2-pyrone-4,6-dicarboxylate to (4 E)-oxalomesaconate (OMA). Here we have demonstrated, using ¹H and ¹³C nuclear magnetic resonance spectroscopy, that LigU catalyzes the isomerization of the double bond between C4 and C5 in (4 E)-OMA to (3 Z)-2-keto-4-carboxy-3-hexenedioate (KCH), where the double bond has migrated to be between C3 and C4 via a 1,3-allylic isomerization. LigU is most closely related in amino acid sequence to methylaconitate isomerase (PrpF) from Shewanella oneidensis and methylitaconate-Δ-isomerase (Mii) from Eubacterium barkeri. The kinetic constants for the isomerization of OMA to KCH by LigU at pH 8.0 were determined to be 1300 ± 120 s^-1 and (7.7 ± 1.5) × 10⁶ M^-1 s^-1 for k_cat and k_cat/ K_m, respectively. We have also shown that the product of the LigU-catalyzed reaction is the preferred substrate for the LigJ hydratase. In this reaction, LigJ catalyzes the hydration of KCH to 4-carboxy-4-hydroxy-2-oxoadipate.