Covalently bound intermediates, catalytic

The topologically defined region(s) on an enzyme responsible for the binding of substrate(s), coenzymes, metal ions, and protons that directly participate in the chemical transformation catalyzed by an enzyme, ribo-zyme, or catalytic antibody. Active sites need not be part of the same protein subunit, and covalently bound intermediates may interact with several regions on different subunits of a multisubunit enzyme complex. See Lambda (A) Isomers of Metal Ion-Nucleotide Complexes Lock and Key Model of Enzyme Action Low-Barrier Hydrogen Bonds Role in Catalysis Yaga-Ozav /a Plot Yonetani-Theorell Plot Induced-Fit Model Allosteric Interaction... 

A catalytic cycle is composed of a series of elementary processes involving either ionic or nonionic intermediates. Formation of covalently bound species in the reaction with surface atoms may be a demanding process. In contrast to this, the formation of ionic species on the surface is a facile process. In fact, the isomerization reaction, the hydrogenation reaction, and the H2-D2 equilibration reaction via ionic intermediates such as alkyl cation, alkylallyl anion, and (H2D)+ or (HD2)+ are structure-nonrequirement type reactions, while these reactions via covalently bound intermediates are catalyzed by specific sites that fulfill the prerequisites for the formation of covalently bound species. Accordingly, the reactions via ionic intermediates are controlled by the thermodynamic activity of the protons on the surface and the proton affinity of the reactant molecules. On the other hand, the reactions via covalently bound intermediates are regulated by the structures of active sites. 

By virtue of being involved in a catalytic mechanism, a covalently bound intermediate is only transient. In such cases, it has often proved possible to change conditions so that decay... 

Fig. 1 Catalytic mechanism of CALB showing an acylation and deacylation step and the formation of a covalently bound acyl-enzyme intermediate bottom right) [16]...

Palm, G. J., Lubkowski, J., Derst, C., Schleper, S., Rohm, K. H. and Wlodawer, A. (1996). A covalently bound catalytic intermediate in Escherichia coli asparaginase crystal structure of a Thr-89-Val mutant. FEBS Lett. 390 (2), 211-216. 

The catalytic mechanisms and molecular recognition properties of peptide synthetases have been studied for several decades [169]. Nonribosomal peptides are assembled on a polyenzyme-protein template, first postulated by Lipmann [170]. The polyenzyme model was refined into the thiotemplate mechanism (Fig. 11) in which the amino acid substrates are covalently bound via thioester linkages to active site sulfhydryls of the enzyme and condensed via a processive mechanism involving a 4 -phosphopantetheine carrier [171-173].The presence of a covalently attached pantetheine cofactor was first established in a cell-free system that catalyzed enzymatic synthesis of the decapeptides gramicidin S and tyrocidine. As in the case of fatty acid synthesis, its role in binding and translocating the intermediate peptides was analyzed [174,175]. 

The use of stoichiometric, covalently bound chiral auxiliaries as a method of asymmetric synthesis is generally impractical and cannot compete with catalytic methods on a commercial scale. However, at the laboratory scale, the oxathiane method provides a predictable method to obtain a desired enantiomer with high selectivity. Since the intermediate compounds prior to hydrolysis are diastereomeric, they are easily separated (often by crystallization) and thus enantiomerically pure compounds are readily obtained. 

This chapter will concentrate on examples of templated synthesis where the template takes the form of a temporary, covalent tether. The intermediate molecule containing both reacting species is in all cases isolable (or potentially so). This distinguishes this intra molecularization approach from substrate-directed stereoselective synthesis. In this case, the template, most frequently a metal, is used in a much more transient sense allowing the potential for developing catalytic systems, which is obviously not possible using a covalently bound template. 

---