title: 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 × 107s-1·m-1) than for protocatechuate (PCA; 6 ± 1 × 102s-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.
authors.affiliation: Genome Science and Technology Program, The University of British Columbia, Vancouver, BC, Canada.
authors.forename: Eugene
authors.initials: E
authors.lastname: Kuatsjah
authors.affiliation: Department of Chemistry, The University of British Columbia, Vancouver, BC, Canada.
authors.forename: Hong-Ming
authors.initials: HM
authors.lastname: Chen
authors.affiliation: Genome Science and Technology Program, The University of British Columbia, Vancouver, BC, Canada.|Department of Chemistry, The University of British Columbia, Vancouver, BC, Canada.|Department of Biochemistry, Life Sciences Institute, The University of British Columbia, Vancouver, BC, Canada.
authors.forename: Stephen G
authors.initials: SG
authors.lastname: Withers
authors.affiliation: Genome Science and Technology Program, The University of British Columbia, Vancouver, BC, Canada.|Department of Biochemistry, Life Sciences Institute, The University of British Columbia, Vancouver, BC, Canada.|Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, BC, Canada.
authors.forename: Lindsay D
authors.initials: LD
authors.lastname: Eltis
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism*; D055162:Biocatalysis; D001713:Biphenyl Compounds / Q000737:chemistry / Q000378:metabolism*; D005231:Fatty Acids, Unsaturated / Q000737:chemistry / Q000378:metabolism; D006863:Hydrogen-Ion Concentration; D006867:Hydrolases / Q000235:genetics / Q000378:metabolism; D062385:Hydroxybenzoates / Q000378:metabolism; D007700:Kinetics; D008031:Lignin / Q000737:chemistry / Q000378:metabolism*; D008956:Models, Chemical; D015394:Molecular Structure; D010105:Oxygenases / Q000235:genetics / Q000378:metabolism*; D011994:Recombinant Proteins / Q000378:metabolism; D042301:Sphingomonadaceae / Q000201:enzymology / Q000235:genetics / Q000378:metabolism*; D013379:Substrate Specificity
chemical_list: D001426:Bacterial Proteins; D001713:Biphenyl Compounds; D005231:Fatty Acids, Unsaturated; D062385:Hydroxybenzoates; D011994:Recombinant Proteins; C009091:protocatechuic acid; C018971:2-hydroxy-6-oxo-6-phenyl-2,4-hexadienoic acid; D008031:Lignin; C113517:2,2',3-trihydroxy-3'-methoxy-5,5'-dicarboxybiphenyl oxygenase; D010105:Oxygenases; C439587:extradiol dioxygenase; D006867:Hydrolases; C120989:LigY hydrolase, bacteria
keywords: aromatic compound; bacterial catabolism; lignin