Aldolase, class function

Two classes of aldolases are used by organisms for catalysis of the retro-aldol reaction. In fungi, algae, and some bacteria, the retro-aldol reaction is catalyzed by class 11 aldolases, which function by coordination of the fmctose carbonyl group with as Lewis acid. In plants and animals, the reaction is catalyzed by class 1 aldolases and does not take place on the free ketone. Instead, fmctose... 

Functionally related to FruA is the novel class I fructose 6-phosphate aldolase (FSA) from E. coli, which catalyzes the reversible cleavage of fructose 6-phosphate (30) to give dihydroxyacetone (31) and d-(18) [90]. It is the only known enzyme that does not require the expensive phosphorylated nucleophile DHAP for synthetic purpose. 

Kimura and co-workers have synthesized a series of alkoxide complexes with the alcohol functionality as a pendent arm.447 674 737 A zinc complex of l-(4-bromophenacyl)-l, 4,7,10-tetraaza-cyclododecane was also synthesized by the same workers to mimic the active site of class II aldolases. The X-ray structure shows a six-coordinate zinc center with five donors from the ligand and a water molecule bound. The ketone is bound with a Zn—O distance of 2.159(3) A (Figure 12). Potentiometric titration indicated formation of a mixture of the hydroxide and the enolate. Enolate formation was also independently carried out by reaction with sodium methoxide, allowing full characterization.738... 

The most important chemical function of Zn2+ in enzymes is probably that of a Lewis acid providing a concentrated center of positive charge at a nucleophilic site on the substrate/ This role for Zn2+ is discussed for carboxypeptidases (Fig.12-16) and thermolysin, alkaline phosphatase (Fig. 12-23),h RNA polymerases, DNA polymerases, carbonic anhydrase (Fig. 13-1),1 class II aldolases (Fig. 13-7), some alcohol dehydrogenases (Fig. 15-5), and superoxide dismutases (Fig.16-22). Zinc ions in enzymes can often be replaced by Mn2+, Co2+, and other ions with substantial retention of catalytic activity/ ... 

Functionally and mechanistically reminiscent of the pyruvate lyases, the 2-deoxy-D-ribose 5-phosphate (121) aldolase (RibA EC 4.1.2.4) [363] is involved in the deoxynucleotide metabolism where it catalyzes the addition of acetaldehyde (122) to D-glyceraldehyde 3-phosphate (12) via the transient formation of a lysine Schiff base intermediate (class I). Hence, it is a unique aldolase in that it uses two aldehydic substrates both as the aldol donor and acceptor components. RibA enzymes from several microbial and animal sources have been purified [363-365], and those from Lactobacillus plantarum and E. coli could be induced to crystallization [365-367]. In addition, the E. coli RibA has been cloned [368] and overexpressed. It has a usefully high specific activity [369] of 58 Umg-1 and high affinity for acetaldehyde as the natural aldol donor component (Km = 1.7 mM) [370]. The equilibrium constant for the formation of 121 of 2 x 10M does not strongly favor synthesis. Interestingly, the enzyme s relaxed acceptor specificity allows for substitution of both cosubstrates propional-dehyde 111, acetone 123, or fluoroacetone 124 can replace 122 as the donor [370,371], and a number of aldehydes up to a chain length of 4 non-hydrogen atoms are tolerated as the acceptor moiety (Table 6). 

Antibody Catalysis. Recent advances in biocatalysis have led to the generation of catalytic antibodies exhibiting aldolase activity by Lemer and Barbas. The antibody-catalyzed aldol addition reactions display remarkable enantioselectivity and substrate scope [18]. The requisite antibodies were produced through the process of reactive immunization wherein antibodies were raised against a [Tdiketone hapten. During the selection process, the presence of a suitably oriented lysine leads to the condensation of the -amine with the hapten. The formation of enaminone at the active site results in a molecular imprint that leads to the production of antibodies that function as aldol catalysts via a lysine-dependent class I aldolase mechanism (Eq. 8B2.12). 

Although the transition state analog approach is suitable for enzymes that bind their transition state noncovalendy, many natural enzymes achieve rate accelerations through covalent catalysis. For example, in the mechanism of most esterases and amidases, a functional group (e.g., a serine hydroxyl) of the protein covalently interacts with the substrate to form a protein bound intermediate. Furthermore, nature s most fundamental carbon-carbon bond-forming enzymes, class I aldolases, use... 

In our original hapten design for aldolase antibodies, the /3-diketone functionality of hapten 4 was used as a reactive immunogen to trap a chemically reactive lysine residue in the active site of an antibody as a stable enaminone. The chemical mechanism leading up to the stabilized enaminone should match that of Class I aldolases over this portion of the reaction coordinate. 

Initial evidence for the structural diversification of the /fa-barrel fold by circular permutation was found in sequence alignments of members of the a-amylase superfamily [31]. More recently, analysis of crystallographic data of transaldolase B from E. coli suggested that the enzyme was derived from circular permutation of a class I aldolase [32]. In either case, the shift of the two N-terminal /fa-repeats (plus the /(-strand of the third subunit for amylases) onto the C-terminus resulted in no apparent functional changes. 

Lorentzen E, Siebers B, Hensel R, Pohl E. Stracture, function and evolution of the Archaeal class 1 fructose-1,6-bisphosphate aldolase. Biochem. Soc. Trans. 2004 32(2) 259—263. 

However, (26) should bind strongly to class II aldolases on account of its chelating ability and this has been found to be the case with rabbit muscle fructose diphosphate aldolase where (26) functions as a competitive inhibitor. Triose phosphate isomerase is also strongly inhibited by (26) this may be due to its similarity to the cw-eriediolate (28), which is an intermediate in the reaction pathway of this enzyme. Acyldihydroxyacetone phosphates are important intermediates in the biosynthesis of glycerolipids and the acyl... 

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. 

Mechanistic pathways for both classes of aldolases have been substantiated by several recent crystal structures of liganded enzymes that altogether provide a detailed insight into the catalytic cycles and the individual function of active site residues in the stereochemically determining events. 

The fructose 6-phosphate aldolase (ESA) from E. coli is a novel class I aldolase that catalyzes the reversible formation of fructose 6-phosphate from dihydroxyacetone and o-glyceraldehyde 3-phosphate it is, therefore, functionally related to transaldolases [245]. Recent determination of the crystal structure of the enzyme sho ved that it also shares the mechanistic machinery [246]. The enzyme has been sho vn to accept several aldehydes as acceptor components for preparative synthesis. In addition to dihydroxyacetone it also utilizes hydroxyacetone as an alternative donor to generate 1-deoxysugars, for example 118, regioselectively (Eigure 5.52) [247]. 

Class I aldolases function as Nature s most fundamental carbon-carbon bond forming enzymes. Designer catalysts - aldolase antibodies - that mimic the aldolases have been created by using a reaction-based selection strategy with 1,3-diketones. The covalent reaction mechanism is a fundamental part of the selection. Broad scope, enhanced catalytic activity, and defined chemical mechanism are three features of these aldolase antibodies that distinguish them from traditional antibody catalysts. The substrate specificities of aldolase antibodies are different from those of naturally existing... 

A wide range of small organic molecules, mainly secondary amines such as proline derivatives, promote asymmetric aldol reactions through enamine catalysis [6]. List, Reymond, Gong, and others reported the first examples of peptidic catalysts for aldol reactions [7]. In their report, Reymond and coworkers [7a] developed two classes of peptides, following two different designs. In the first peptide class a primary amine is present as a side chain residue (similar to the natural type I aldolase) or as free N-terminus in the second a secondary amine or a proHne residue is present at the N-terminus of the peptide, which incorporated at least one free carboxyhc function (Figure 5.3). 

Class 1 aldolase mimics consist of amino acid catalysts that presumably activate the donor via enamine formation and the acceptor through a hydrogen bond with an acid functionality. Repotted hrst by Wiechert et al. and then by Hajos and Parrish,-proline was found to catalyze intramolecular asymmetric aldol reactions. However, the... 

The simple primary-tertiary diamine salts can be successfully applied in the aldol reactions of a-hydroxyketones with good activity and excellent stereoselectivity. Notably, the catalyst enabled the reaction of dihydroxyacetone (DHA), a versatile C3-building block in the chemical and enzymatic synthesis of carbonhydrates. By employing either free or protected DHA, syn- or anh-diols could be selectively formed with excellent enantioselectivity (Scheme 5.7). Since enantiomers of diamine 26 and 29 are readily available, this class of chiral primary amine catalysts thus functionally mimics four types of DHA aldolases in nature [17b]. Later, simple chiral primary-tertiary diamine 27 derived from amino acid was also found to be a viable catalyst for the iyn-selective aldol reactions of hydroxyacetone and free DHA (Scheme 5.7) [18]. 

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