Theoretical investigation on the dissociation of (R)-benzoin catalyzed by benzaldehyde lyase

Abstract

Benzaldehyde lyase (BAL) is a versatile thiamin diphosphate (THDP)‐dependent enzyme with widespread synthetic applications in industry. Besides lyase activity, BAL also performs the functions as carboligase and decarboxylase. Unlike many other THDP‐dependent enzymes, the active center of BAL is devoid of any acid‐base amino acid residues except Glu50 and His29, and therefore, the catalytic mechanism of BAL is unusual. In this article, the dissociation mechanism of (R)‐benzoin to benzaldehyde catalyzed by BAL has been studied by using density functional theory method. The calculation results indicate that the whole reaction consists of four elementary steps, and at least two steps contribute to rate‐limiting. A big difference with other THDP‐dependent enzymes is that, in the first stage of the reaction, the ligation of substrate and THDP ylide is not companied by proton transfer, and in the subsequent transition states and intermediates, the carbonyl oxygen always exists in the form of anion. Gln113, His29, and 4′‐amino group of THDP are found to have the function to stabilize the transition states and intermediates. His29 acts as the proton acceptor in step 2 and proton donor in step 3 using one water molecule as mediator. © 2013 Wiley Periodicals, Inc.

Computational characterization of enzyme-bound thiamin diphosphate reveals a surprisingly stable tricyclic state: implications for catalysis

“…Subsequently, a similar approach was used to characterize the nucleophilicity of the N1′ and N4′ centers [24]. In many cases, rather than simply focus on the cofactor, computational studies have been used to investigate full reaction mechanisms of ThDP enzymes, including pyruvate decarboxylase (PDC) [25–28], benzoylformate decarboxylase (BFDC) [29–30], acetohydroxy acid synthase [24,31–35], pyruvate dehydrogenase (PDH) [36], benzaldehyde lyase [37], cyclohexane dione hydrolase [38], oxalyl-CoA decarboxylase [39], DXP synthase [40] and transketolase [41–42].…”

A Theoretical Study of the Benzoylformate Decarboxylase Reaction Mechanism

“…The adopted methodology, called the cluster approach, has been very successful in elucidating reaction mechanisms of a wide variety of enzymes (Siegbahn and Himo, 2009 , 2011 ; Siegbahn and Blomberg, 2010 ; Blomberg et al, 2014 ; Himo, 2017 ). A number of previous theoretical studies using a variety of computational techniques have considered aspects of mechanism of a number of ThDP-dependent enzymes (Friedemann et al, 2004 ; Lie et al, 2005 ; Wang et al, 2005 ; Jaña et al, 2010 ; Topal et al, 2010 ; Xiong et al, 2010 ; Paramasivam et al, 2011 ; Alvarado et al, 2012 ; Hou et al, 2012 ; Jaña and Delgado, 2013 ; Sheng and Liu, 2013 ; Sheng et al, 2013 , 2014 ; Sánchez et al, 2014 ; Zhang et al, 2014 ; Zhu and Liu, 2014 ; Lizana et al, 2015 ; Nauton et al, 2016 ; White et al, 2016 ). Relevant results from these studies have been incorporated into the discussion of the BFDC mechanism below.…”

Enzymatic Stetter Reaction: Computational Study of the Reaction Mechanism of MenD

“…The relatively high energetic cost of forming Int2-Td is not entirely surprising as the formation of a tetrahedral post-decarboxylation ThDP intermediate previously had been found to be thermodynamically unfavorable unless the amino form could be recovered by reprotonation of N4′ by a neighboring residue. ,− Unusually, the MenD active site does not contain any ionizable residues in the vicinity of N4′ or C2α, so the recovery of the amino form requires that a proton comes from bulk solution (Scheme ). This is true regardless of whether protonation occurs at N4′ ( Int2-Td , Path A ) or C2α ( Int2 , Path B ).…”