Aldolase, class types

A specific type of lyase, the aldolase class of enzymes, catalyzes the formation of an asymmetric C-C bond, which is a most useful reaction to the synthetic... 

FDP Aldolase. The most extensively utilized class of enzymes for monosaccharide synthesis are the aldolases (E.C. sub-class 4.1.2.). This ubiquitous group of enzymes catalyzes reversible aldol reactions in vivo. Two major groups of aldolases exist type I aldolases, found primarily in higher plants and animals, catalyze aldol condensations by means of a Schiff base formed between an enzyme lysine e-amino group and the nucleophilic carbonyl group type II aldolases, found primarily in microorganisms, utilize a divalent zinc to activate the nucleophilic component (79). Approximately 25 aldolases have been identified to date (18),... 

There are two distinct groups of aldolases. Type I aldolases, found in higher plants and animals, require no metal cofactor and catalyze aldol addition via Schiff base formation between the lysiae S-amino group of the enzyme and a carbonyl group of the substrate. Class II aldolases are found primarily ia microorganisms and utilize a divalent ziac to activate the electrophilic component of the reaction. The most studied aldolases are fmctose-1,6-diphosphate (FDP) enzymes from rabbit muscle, rabbit muscle adolase (RAMA), and a Zn " -containing aldolase from E. coli. In vivo these enzymes catalyze the reversible reaction of D-glyceraldehyde-3-phosphate [591-57-1] (G-3-P) and dihydroxyacetone phosphate [57-04-5] (DHAP). 

Four DHAP converting aldolases are known, these can synthesize different diastereomers with complementary configurations D-fructose (FruA EC 4.1.2.13) and D-tagatose 1,6-bisphos-phate (TagA, F.C 4.1.2.-), L-fuculose (FucA EC 4.1.2.17) and L-rhamnulose 1-phosphate aldolase (RhuA EC 4.1.2.19)3. The synthetic application of the first (class 1 or 2) and the latter two types (class 2) has been examined. 

Aldolases are part of a large group of enzymes called lyases and are present in all organisms. They usually catalyze the reversible stereo-specific aldol addition of a donor ketone to an acceptor aldehyde. Mechanistically, two classes of aldolases can be recognized [4] (i) type I aldolases form a Schiff-base intermediate between the donor substrate and a highly conserved lysine residue in the active site of the enzyme, and (ii) type II aldolases are dependent of a metal cation as cofactor, mainly Zn, which acts as a Lewis acid in the activation of the donor substrate (Scheme 4.1). 

The Schiff-base-forming types (class I) are known only for the two former aldolases (FruA, TagA), which are found usually in mammalian or (as an exception) in specific microbial organisms, whereas the Zn2+-dependent type (class II) comprises all four DHAP aldolases which are commonly found in bacteria [43], Typically, type I FruA enzymes are tetrameric proteins composed of subunits of 40 kDa [191,192], while the type II FruA are dimers of 39 kDa subunits [193]. RhuA and FucA enzymes are homotetrameric with a subunit molecular weight of 25 kDa and 30 kDa respectively [194,195],... 

The transaldolase (EC 2.2.1.2) is an ubiquitous enzyme that is involved in the pentose phosphate pathway of carbohydrate metabolism. The class I lyase, which has been cloned from human [382] and microbial sources [383], transfers a dihydroxyacetone unit between several phosphorylated metabolites. Although yeast transaldolase is commercially available and several unphosphorylated aldehydes have been shown to be able to replace the acceptor component, preparative utilization has mostly been limited to microscale studies [384,385] because of the high enzyme costs and because of the fact that the equilibria usually are close to unity. Also, the stereochemistry of transaldolase products (e.g. 38, 40) [386] matches that of the products from the FruA-type DHAP aldolase which are more effortlessly obtained. 

Referring to a mechanistic classification of organocatalysts (Seayad and List 2005), currently the two most prominent classes are Brpnsted acid catalysts and Lewis base catalysts. Within the latter class chiral secondary amines (enamine, iminium, dienamine activation for a short review please refer to List 2006) play an important role and can be considered as—by now—already widely extended mimetics of type I aldolases, whereas acylation catalysts, for example, refer to hydrolases or peptidases (Spivey and McDaid 2007). Thiamine-dependent enzymes, a versatile class of C-C bond forming and destructing biocatalysts (Pohl et al. 2002) with their common catalytically active coenzyme thiamine (vitamin Bi), are understood to be the biomimetic roots ofcar-bene catalysis, a further class of nucleophilic, Lewis base catalysis with increasing importance in the last 5 years. 

Pyruvate-dependent aldolases have catabolic activity in vivo, whereas their counterparts utilizing phosphoenolpyruvate as the donor substrate are involved in the biosynthesis of keto acids. Both classes of enzymes have been used in synthesis to prepare similar a-keto acids. The enzymes catalzye this type of reaction in vivo and their stereoselectivity are presented together in this section (Schemes 5.27, 5.28). 

Like transketolase, transaldolase (TA, E.C. 2.2.1.2) is an enzyme in the oxidative pentose phosphate pathway. TA is a class one lyase that operates through a Schiff-base intermediate and catalyzes the transfer of the C(l)-C(3) aldol unit from D-sedoheptulose 7-phosphate to glyceraldehyde-3-phosphate (G3P) to produce D-Fru 6-P and D-erythrose 4-phosphate (Scheme 5.59). TA from human as well as microbial sources have been cloned.110 111 The crystal structure of the E. coliu and human112 transaldolases have been reported and its similarity to the aldolases is apparent, since it consists of an eight-stranded (o /(3)s or TIM barrel domain as is common to the aldolases. As well, the active site lysine residue that forms a Schiff base with the substrate was identified.14112 Thus, both structurally and mechanistically it is related to the type I class of aldolases. 

Kimura and his associates have been preeminent in exploiting the potential of Zn(II) complexes of pendant-arm polyaza macrocycles to act as models for the hydrolytic Zn(II)-containing enzymes. Collectively, their work in this area involves structurally unmodified macrocycles as well as pendant-arm macrocycles, and the reader is referred to a number of reviews 6-15) that summarize their work in its entirety. The particular object of this section is to examine how different types of pendant arm have been introduced onto a macrocyclic framework and how it has been possible to utilize their presence to elicit information of relevance to a particular group of enzymes. The enzyme groups studied using pendant-arm macrocycles have been the alkaline phosphatases and the class II aldolases. 

Two distinct types of aldolase are known. Class I aldolases occur in animals, plants, protozoans, and algae, and Class II, in bacteria, fungi,... 

An exhaustive review of all of the types of reactions that are catalyzed by metal-requiring enzymes and the specific functions of these metals, as currently understood, is beyond the scope of this chapter. To complicate this general area of investigation, even within a single group of enzymes, the metal ions may play different roles in the catalytic processes for reaction-related enzymes. Not all enzymes of a specific class necessarily require a cation for activity. In some cases, the roles of the cation may be substituted by specific amino acid residues in the protein. A classic example of such a case is the muscle and yeast fmctose-bisphosphate aldolases. The muscle enzyme catalyzes the aldol condensation using a Schiff base intermediate to activate the substrate, whereas the yeast enzyme is a Zn +-metalloenzyme (1). The cation appears to serve as the electrophile in the activation of the substrate for the same reaction. 

There are, however, clear stereomechanistic differences between these two classes of enzyme-catalyzed reactions. The Claisen-type condensations uniformly involve inversion of configuration at the a-carbon of the esteratic substrate, involving C-C bond formation at either the re or the si face of the ketonic or aldehydic substrate (Table VII) (196-211). Moreover, neither Schiff bases nor metal ions have been directly implicated in the catalytic mechanisms of these enzymes. Unlike the aldolases, these enzymes do not catalyze rapid enolization of the nucleophilic substrate in the absence of the second substrate. Inversion of configuration suggests that at least two catalytic groups, perhaps operating in concert, facilitate C-C bond formation. Physicochemical measurements on citrate synthase are consistent with this interpretation of inversion of configuration. 

One of the most classical reactions for the formation of C-C bonds is the aldolic condensation. In nature, such stereocontrolled reactions are catalyzed by enzymes of the class of lyases (EC 4). The majority of these enzymes can be found in the biosynthesis of carbohydrates, and are used for the synthesis of natural and unnatural carbohydrates. Aldolases (and transketolases) have been intensively investigated and their scope of applications has been evaluated and reviewed by the groups of Whitesides and Wong [16, 21,142-145] (see also Chapter B4 in [22]). Aldolases can be divided into three main types ... 

Figure 15.6. Complementary phylogenetic patterns. (A) The two classes of lysyl-tRNA synthetases. Note that both COGs include T. pallidum] it encodes an unusual class II enzyme that might not be involved in translation. (B) Two classes of fructose-1,6-bisphosphate aldolase. Note that E. coll and A. aeolicus encode both types of aldolases.

Pickl A, Johnsem U, Schonheit P. Fructose degradation in the haloarchaeon Haloferax volcanii involves a bacterial type phosphoenolpyravate-dependent phosphotransferase system, fractose-1-phosphatase kinase, and class II fractose-l,6-bisphosphate aldolase. J Bacteriol. 2012 194 3088-97. 

Paracatalytic enzyme modification is a new type of catalysis-linked and, hence, substrate-dependent enzyme modification. In all instances in which the substrate promotes inactivation of an enzyme by a chemical reagent, particularly by an oxidant, paracatalsrtic modification should he considered to be the underlying mechanism. In contrast to ligand-induced and syncatalytic modifications, paracatalytic modification involves a direct chemical interaction between enzyme-activated substrate and extrinsic reagent. In this respect, it is similar to the chemical trapping of covalent enzyme-substrate intermediates, e.g., the reduction of enzyme-substrate Schiff bases by sodium borohydride in class I fructose-l,6-bis-phosphate aldolases - or in acetoacetate decarboxylase. ... 

Other interesting organocatalysts of the aldol reaction, for example simple tertiary amine Bronsted bases and phase-transfer type quaternary ammonium salts [34-36]. Mechanistically related class I aldolases and catalytic antibodies have been fundamentally important in the development of the reactions described belotv and are discussed in another chapter of this book. 

For class I type enzymes, the (/ia)8-barrel structure of the class I fructose 1,6-bisphosphate aldolase (FruA, vide infra) from rabbit muscle was the first to be uncovered by X-ray crystal-structure analysis [33] this was followed by those from several other species [34-37]. A complex of the aldolase with non-covalently bound substrate DHAP (dihydroxyacetone phosphate) in the active site indicates a trajectory for the substrate traveling towards the nucleophilic Lys229 N [38, 39]. There, the proximity of side-chains Lysl46 and Glul87 is consistent with their participation as proton donors and acceptors in Schiff base formation (A, B) this was further supported by site-directed mutagenesis studies [40]. 

---