Aldolases structures

Mavridis, I.M., et al. Structure of 2-keto-3-deoxy-6-phosphogluconate aldolase at 2.8 A resolution. 

The structure of human muscle fructose-1,6-bisphosphate aldolase, as determined by X-ray crystallography and downloaded from the Protein Data Bank. (PDB ID 1ALD Gamblin, S. J., Davies, G. J., Grimes, J. M., Jackson, R. M., Littlechild, J. A., Watson, H. C. Activity and specificity of human aldolases. J. Mol. Biol. v219, pp. 573-576, 1991.)... 

Several dozens of aldolases have been identified so far in nature [23,24], and many of these enzymes are commercially available at a scale sufficient for preparative applications. Enzyme catalysis is more attractive for the synthesis and modification of biologically relevant classes of organic compounds that are typically complex, multifunctional, and water soluble. Typical examples are those structurally related to amino acids [5-10] or carbohydrates [25-28], which are difficult to prepare and to handle by conventional methods of chemical synthesis and mandate the laborious manipulation of protective groups. 

A number of mechanistically distinct enzymes can likewise be employed for the synthesis of product structures identical to those accessible from aldolase catalysis. Such alternative cofactor-dependent enzymes (e.g. transketolase) are emerging as useful catalysts in organic synthesis. As these operations often extend and/or... 

Figure 10.21 Aldolase-catalyzed asymmetric synthesis of uncommon L-configured sugars (a), and selected examples of carbohydrate-related product structures that are accessible by enzymatic aldolization (b).

Phosphonate analogs to phosphate esters, in which the P—0 bond is formally replaced by a P—C bond, have attracted attention due to their stability toward the hydrolytic action of phosphatases, which renders them potential inhibitors or regulators of metabolic processes. Two alternative pathways, in fact, may achieve introduction of the phosphonate moiety by enzyme catalysis. The first employs the bioisosteric methylene phosphonate analog (39), which yields products related to sugar 1-phosphates such as (71)/(72) (Figure 10.28) [102,107]. This strategy is rather effective because of the inherent stability of (39) as a replacement for (25), but depends on the individual tolerance of the aldolase for structural modification close... 

Aldehydes up to a chain length of four nonhydrogen atoms are tolerated as acceptors. 2-Hydroxyaldehydes are relatively good acceptors, and the D-isomers are preferred over the t-isomers [180]. Reactions that lead to thermodynamically unfavorable structures may proceed with low stereoselectivity at the reaction center [181]. Recently, a single-point mutant aldolase was found 2.5 times more effective than the wild type in accepting unphosphorylated glyceraldehyde [182,183]. 

Sakakibara, M., Mukai, T., Yatsuki, H and Hori, K Human aldolase isozyme gene The structure of multispecies aldolase B mRNAs. Nucleic Acids Res. 13,5055-5069 (1985). 

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 cholesterol-lowering drug atorvastatin, marketed as Lipitor, is an example where biocatalysis research has been applied extensively and is in industrial use. The enzyme 2-deoxyribose-5-phosphate aldolase (DERA) has been a target of directed evolution for the production of atorvastatin intermediates [8,9,71]. DeSantis and coworkers [8,9] used structure-based... 

DeSantis, G., Liu, J., Clark, D.R et al. (2003) Structure-based mutagenesis approaches toward expanding the substrate specificity of D-2-deoxyribose-5-phosphate aldolase. Bioorganic and Medicinal Chemistry, 11, 43-52. 

Directed evolution methods, as well as rational structure-based mutagenesis approaches, have been successful in broadening the substrate tolerance of aldolases. A common goal is to... 

The essentially nonreversible formation of D-fructose 1-phosphate in the muscle-aldolase system is probably attributable to thermodynamic stabilization. D-Fructose 1-phosphate can form a stable pyranose structure, whereas D-fructose 1,6-diphosphate can exist only in the less stable furanose or acyclic forms.72(,) Only when the cleavage products are removed is the monophosphate effectively split under the influence of aldolase. 

Dihydroneopterin aldolase (Table 1, entry 8) Inhibitors (such as 33) of dihydro-neopterin aldolase were identified using high throughput X-ray-based fragment screening of a 10,000 member random library [43]. Structure-guided optimisation gave potent leads such as 35. 

Antibodies produced by this procedure were screened for their ability to react with the hapten to form the vinylogous amide 6, which has a convenient UV chromophore near 318nm, clear of the main protein absorption. Two antibodies selected in this way catalysed the expected aldol reaction of acetone with aldehyde 7 by way of the enamine 8 (Scheme 3) the remainder did not. These two effective aldolase mimics have been studied in some detail, and a crystal structure is available for (a Fab fragment of) one of them.126,281... 

Small molecules that act as collisional quenchers may penetrate into the internal structure of proteins, diffuse, and cause quenching upon collision with the aromatic groups. Lakowicz and Weber(53) have shown that the interaction of oxygen molecules with buried tryptophan residues in proteins leads to quenching with unexpectedly high rate constants—from 2 x 109 to 7 x 109 M l s 1. Acrylamide is also capable of quenching the fluorescence of buried tryptophan residues, as was shown for aldolase and ribonuclease 7V(54) A more hydrophobic quencher, trichloroethanol, is a considerably more efficient quencher of internal chromophore groups in proteins.(55)... 

Differences between the spectra of fluorescence and phosphorescence are immediately obvious. For all tryptophans in proteins the phosphorescence spectrum, even at room temperature, is structured, while the fluorescence emission is not. (Even at low temperatures the fluorescence emission spectrum is usually not structured. The notable exceptions include a-amylase and aldolase, 26 protease, azurin 27,28 and ribonuclease 7, staphylococcal endonuclease, elastase, tobacco mosaic virus coat protein, and Drosophila alcohol dehydrogenase 12. )... 

Espelt, L., Parella, T., Bujons, J., Solans, C., Joglar, J., Delgado, A. and, Clapes, P., Stereoselective aldol additions catalyzed hy dihydroxyacetone phosphate-dependent aldolases in emulsion systems preparation and structural characterization of linear and cyclic iminopolyols from aminoaldehydes. Chem. Eur. J., 2003, 9, 4887. 

The stereochemistry of the aldol reaction is highly predictable since it is generally controlled by the enzyme and does not depend on the structure or stereochemistry of the substrates. Aldolases generally show a very strict specificity for the donor substrate (the ketone), but tolerate a broad range of acceptor substrates (the aldehyde). Thus, they can be functionally classified on the base of the donor substrate accepted by the enzyme. 

DHAP-dependent aldolases produce 2-keto-3,4-dihydroxy adducts with high control of the configuration of the two newly formed stereogenic centers. However, while it can be assumed that the absolute configuration at C3 is independent on the acceptor used in the reaction, the configuration of the stereocenter generated from the addition to the aldehyde (C4 position) in some cases may depend on the structure and stereochemistry of the acceptor [6]. 

In an interesting extension of this work, the Neu5Ac aldolase from E. coli was subjected to directed evolution to expand its catalytic activity for enantiomeric forms of the usual substrates to include A -acetyl-L-mannosamine and L-arabinose with formation of the synthetically important products L-sialic add and L-3-deoxy-L-manno-oct-2-ulosonic add (l-KDO) (163). The evolved Neu5Ac aldolases were characterized by sequence analysis, kinetics, stereoselectivity, and in one case even by an X-ray structure analysis. Again, remote mutations were identified. It is significant... 

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