Characterization of Thiamine Diphosphate-Dependent 4-Hydroxybenzoylformate Decarboxylase Enzymes from Rhodococcus jostii RHA1 and Pseudomonas fluorescens Pf-5 Involved in Degradation of Aryl C2 Lignin Degradation Fragments

Biochemistry. 2019 Dec 31;58(52):5281-5293. doi: 10.1021/acs.biochem.9b00177. Epub 2019 May 24.


A thiamine diphosphate-dependent enzyme annotated as a benzoylformate decarboxylase is encoded by gene cluster ro02984-ro02986 in Rhodococcus jostii RHA1 previously shown to generate vanillin and 4-hydroxybenzaldehyde from lignin oxidation, and a closely related gene cluster is also found in the genome of Pseudomonas fluorescens Pf-5. Two hypotheses for possible pathways involving a thiamine diphosphate-dependent cleavage, either C-C cleavage of a ketol or diketone aryl C3 substrate or decarboxylation of an aryl C2 substrate, were investigated by expression and purification of the recombinant enzymes and expression of dehydrogenase and oxidase enzymes also found in the gene clusters. The ThDP-dependent enzymes showed no activity for cleavage of aryl C3 ketol or diketone substrates but showed activity for decarboxylation of benzoylformate and 4-hydroxybenzoylformate. A flavin-dependent oxidase encoded by gene ro02984 was found to oxidize either mandelic acid or phenylglyoxal. The crystal structure of the P. fluorescens decarboxylase enzyme was determined at 1.69 Å resolution, showing similarity to structures of known benzoylformate decarboxylase enzymes. The P. fluorescens decarboxylase enzyme showed enhanced carboligase activity between vanillin and acetaldehyde, rationalized by the presence of alanine versus serine at residue 73 in the enzyme active site, which was investigated further by site-directed mutagenesis of this residue. A hypothesis for a pathway for degradation of aryl C2 fragments arising from oxidative cleavage of phenylcoumaran and diarylpropane structures in lignin is proposed.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Carboxy-Lyases / chemistry
  • Carboxy-Lyases / genetics
  • Carboxy-Lyases / metabolism*
  • Catalytic Domain
  • Computational Biology
  • Crystallography, X-Ray
  • Lignin / chemistry
  • Lignin / metabolism*
  • Models, Molecular
  • Multigene Family / genetics
  • Pseudomonas fluorescens / enzymology*
  • Pseudomonas fluorescens / genetics
  • Rhodococcus / enzymology*
  • Rhodococcus / genetics
  • Thiamine Pyrophosphate / metabolism*


  • Lignin
  • Carboxy-Lyases
  • benzoylformate decarboxylase
  • Thiamine Pyrophosphate

Supplementary concepts

  • Rhodococcus jostii