6QSI

Pseudomonas fluorescens Pf-5 thiamine diphosphate-dependent 4-hydroxybenzoylformate decarboxylase

Summary for 6QSI

• Entry DOI: 10.2210/pdb6qsi/pdb
• Descriptor: Benzoylformate decarboxylase, THIAMINE DIPHOSPHATE, SODIUM ION, ... (5 entities in total)
• Functional Keywords: benzoylformate decarboxylase, thaimine diphosphate, pseudomonas fluorescens pf-5, lignin degradation, oxidoreductase
• Biological source: Pseudomonas protegens Pf-5
• Total number of polymer chains: 2
• Total formula weight: 113004.26

Authors

Wilkinson, R.C.,Fulop, V. (deposition date: 2019-02-20, release date: 2020-01-08, Last modification date: 2024-05-15)

Primary citation

Wei, Z.,Wilkinson, R.C.,Rashid, G.M.M.,Brown, D.,Fulop, V.,Bugg, T.D.H.
Characterization of Thiamine Diphosphate-Dependent 4-Hydroxybenzoylformate Decarboxylase Enzymes fromRhodococcus jostiiRHA1 andPseudomonas fluorescensPf-5 Involved in Degradation of Aryl C2Lignin Degradation Fragments.
Biochemistry, 58:5281-5293, 2019

PubMed Abstract: A thiamine diphosphate-dependent enzyme annotated as a benzoylformate decarboxylase is encoded by gene cluster ro02984-ro02986 in 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 Pf-5. Two hypotheses for possible pathways involving a thiamine diphosphate-dependent cleavage, either C-C cleavage of a ketol or diketone aryl C substrate or decarboxylation of an aryl C 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 C 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 decarboxylase enzyme was determined at 1.69 Å resolution, showing similarity to structures of known benzoylformate decarboxylase enzymes. The 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 C fragments arising from oxidative cleavage of phenylcoumaran and diarylpropane structures in lignin is proposed.

PubMed: 30946572
DOI: 10.1021/acs.biochem.9b00177

Experimental method

X-RAY DIFFRACTION (1.69 Å)