Mechanism of Benzaldehyde Lyase Studied via Thiamin Diphosphate-Bound Intermediates and Kinetic Isotope Effects

• Published in: Biochemistry (Easton) Vol. 47; no. 12; pp. 3800 - 3809
• Main Authors: Chakraborty, Sumit, Nemeria, Natalia, Yep, Alejandra, McLeish, Michael J, Kenyon, George L, Jordan, Frank
• Format: Journal Article
• Language: English
• Published: United States American Chemical Society 25.03.2008
• Subjects: Acrolein - analogs & derivatives; Acrolein - metabolism; Aldehyde-Lyases - metabolism; Benzaldehydes - metabolism; Benzoin - metabolism; Butyrates - metabolism; Circular Dichroism; Deuterium Exchange Measurement; Glyoxylates - metabolism; Kinetics; Mandelic Acids - metabolism; Models, Chemical; Phenylpyruvic Acids - metabolism; Pseudomonas fluorescens - enzymology; Pyridines - metabolism; Thiamine Pyrophosphate - metabolism
• ISSN: 0006-2960; 1520-4995
• DOI: 10.1021/bi702302u

Direct spectroscopic observation of thiamin diphosphate-bound intermediates was achieved on the enzyme benzaldehyde lyase, which carries out reversible and highly enantiospecific conversion of (R)-benzoin to benzaldehyde. The key enamine intermediate could be observed at λmax 393 nm in the benzoin breakdown direction and in the decarboxylase reaction starting with benzoylformate. With benzaldehyde as substrate, no intermediates could be detected, only formation of benzoin at 314 nm. To probe the rate-limiting step in the direction of (R)-benzoin synthesis, the 1H/2H kinetic isotope effect was determined for benzaldehyde labeled at the aldehyde position and found to be small (1.14 ± 0.03), indicating that ionization of the C2αH from C2α-hydroxybenzylthiamin diphosphate is not rate limiting. Use of the alternate substrates benzoylformic and phenylpyruvic acids (motivated by the observation that while a carboligase, benzaldehyde lyase could also catalyze the slow decarboxylation of 2-oxo acids) enabled the observation of the substrate-thiamin covalent intermediate via the 1′,4′-iminopyrimidine tautomer, characteristic of all intermediates with a tetrahedral C2 substituent on ThDP. The reaction of benzaldehyde lyase with the chromophoric substrate analogue (E)-2-oxo-4(pyridin-3-yl)-3-butenoic acid and its decarboxylated product (E)-3-(pyridine-3-yl)acrylaldehyde enabled the detection of covalent adducts with both. Neither adduct underwent further reaction. An important finding of the studies is that all thiamin-related intermediates are in a chiral environment on benzaldehyde lyase as reflected by their circular dichroism signatures.