Pyruvate formate lyase mechanism

Knappe, J., Elbert, S., Frey, M., and Wagner, A. F. V., 1993, Pyruvate formate-lyase mechanism involving the protein-based glycyl radical. Biochem. Soc. Trans. 21 731n734. 

Benzylsuccinate synthase has an amino acid sequence homologous to that of pyruvate formate lyase (p. 799 -801), contains a glycyl radical, and is activated in a manner similar to activation of pyruvate formate lyase. Propose a mechanism for formation of benzylsuccinate. See Krieger et al.383... 

We have in the present chapter shown results from theoretical model system studies of the catalytic reaction mechanisms of three radical enzymes Galatose oxidase. Pyruvate formate-lyase and Ribonucleotide reductase. It is concluded that small models of the key parts of the active sites in combination with the DPT hybrid functional B3LYP and large basis sets provides a good description of the catalytic machineries, with low barriers for the rate determining steps and moderate overall exothermicity. The models employed are furthermore able to reproduce all the observed features in terms of spin distributions and reactive intermediates. 

In Pyruvate formate-lyase, the active site contains a stable glycyl radical and two catalyticaUy active cysteines. Two different proposed reaction mechanisms were tested, and it was concluded that the mechanism as suggested... 

In this respect the enzyme resembles pyruvate formate-lyase (Eq. 15-40). As with other enzymes using Pe4S4 clusters as radical generators, S-adenosylmethionine is also required. All ribonucleohde reductases may operate by similar radical mechanisms. ... 

Studies on three different iron—sulfur enzyme systems which all require S-adenosylmethionine (SAM) — lysine 2,3-aminomutase, pyruvate-formate lyase, and anaerobic ribonucleotide reductase — have led to the identification of SAM as a major source of free radicals in living cells (for a recent review, see Atta et ak, 2010). As in the dehydratases, these systems have a [4Fe—4S] centre chelated by only three cysteines with one accessible coordination site. The cluster is active only in the reduced state [4Fe—4S] and appears to combine the two roles described previously, serving both as a ligand for substrate binding and as a redox catalyst (Figure 13.19). Their mechanism again requires that the exposed iron atom of the cluster shifts towards octahedral geometry as it binds... 

Scheme 38. Possible heterolytic mechanism for the PFL-mediated cleavage of pyruvate by pyruvate formate-lyase.

S-Adenosylmethionine may also affect the activity of enzymes not related to the methionine biosynthetic pathway. For example, this compound is a component of the pyruvate formate-lyase system of E. coli (Knappe et al, 1965) participating by a mechanism which has yet to be fully clarified (Chase and Rabinowitz, 1968 Knappe et al., 1969). 

Benzoylformate decarboxylase (BFD EC 4.1.1.7) belongs to the class of thiamine diphosphate (ThDP)-dependent enzymes. ThDP is the cofactor for a large number of enzymes, including pyruvate decarboxylase (PDC), benzaldehyde lyase (BAL), cyclohexane-1,2-dione hydrolase (CDH), acetohydroxyacid synthase (AHAS), and (lR,6] )-2-succinyl-6-hydroxy-2,4-cyclohexadiene-l-carboxylate synthase (SHCHC), which all catalyze the cleavage and formation of C-C bonds [1]. The underlying catalytic mechanism is summarized elsewhere [2] (see also Chapter 2.2.3). 

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