Characterization of an extradiol dioxygenase involved in the catabolism of lignin-derived biphenyl

Abstract

In the catabolism of lignin-derived biphenyl by Sphingobium sp. SYK-6, LigZ catalyzes the cleavage of 2,2′,3-trihydroxy-3′-methoxy-5,5′-dicarboxybiphenyl (OH-DDVA) to a meta-cleavage product (MCP) identified here as 4,11-dicarboxy-8-hydroxy-9-methoxy-2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate (DCHM-HOPDA). DCHM-HOPDA is transformed nonenzymatically, likely to a lactone (k = 0.13 ± 0.01 min−1, pH 7.5). This is hydrolyzed to the dienolate at alkaline pH (apparent pKa ~ 11.3). Only the dienolate is a substrate for LigY, the putative MCP hydrolase. LigZ has higher specificity for OH-DDVA (kcat/Km = 2.20 ± 0.02 × 107 s−1·m−1) than for protocatechuate (PCA; 6 ± 1 × 102 s−1·m−1). PCA also inactivates LigZ (partition ratio of 50), but at rates too low to be physiologically relevant. This study provides insight into the bacterial catabolism of lignin and facilitates the study of downstream catabolic enzymes.