Covalent Catalysis is one of the four strategies that an enzyme will use to catalyze a specific reaction, which involves the formation of a transient covalent bond between a substrate and a residues in the enzyme active site or with a cofactor. In covalent catalysis, an additional covalent intermediate is added to the reaction, and helps to reduce the energy of transition states in the later stages of the reaction. The most common covalent bonds are formed as a result of the attack by an enzyme nucleophilic group on an electrophilic moiety of the substrate that is bound at the active site.

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In an enzymatic reaction, covalent catalysis occurs when the substrate become temporarily covalently attached to the enzyme during the catalytic reaction. In this reaction, the enzyme contains a reactive group, usually a nucleophilic residue or an electrophilic residue, which reacts with the substrate through a nucleophilic or electrophilic attack. The nucleophilic groups can be either RCOO-, RNH, ROH that are present on the side-chains of amino acid residues, or the nitrogen atoms of the imidazole ring of histidine residues. The electrophilic moieties of substrates may be acyl, phosphoryl, or glycosyl groups, so the covalent intermediates would be acyl-, phosphoryl-, and glycosyl-enzyme complexes. Enzyme molecules are poor in electrophilic groups, but electrophilic catalysis does occur with those enzymes that contain metals or prosthetic groups that act as electron sinks during catalysis. The charge loss in the reaction during transitional state will then accelerate the hydrolysis.

Figure 1. Mechanism of covalent catalysis.

Rather than lowering the activation energy for a reaction pathway, covalent catalysis provides an alternative pathway for the reaction (via to the covalent intermediate) and so is distinct from true catalysis. A true proposal of a covalent catalysis would require, for example, a partial covalent bond to the transition state by an enzyme group, and such effects do not contribute significantly to catalysis.

Covalent Intermediates Formed by Substrates and Cofactors

Some enzymes utilize non-amino acid cofactors such as pyridoxal phosphate (PLP) or thiamine pyrophosphate (TPP) to form covalent intermediates with reactant molecules. Such covalent intermediates function to reduce the energy of later transition states, similar to how covalent intermediates formed with active site amino acid residues allow stabilization, but the capabilities of cofactors allow enzymes to carryout reactions that amino acid side residues alone could not. Enzymes utilizing such cofactors include the PLP-dependent enzyme aspartate transaminase and the TPP-dependent enzyme pyruvate dehydrogenase.

Catalytic Triad of Enzymes

At a later stage in covalent catalysis, the covalent bond must be broken to regenerate the enzyme. This mechanism is utilized by the catalytic triad of enzymes such as proteases like chymotrypsin and trypsin, where an acyl-enzyme intermediate is formed. Chymotrypsin is a degradative protease of the digestive system. It catalyzes the cleavage of peptide bonds that are adjacent to large aromatic or nonpolar residues. It cleaves the peptide bond on the carboxyl terminus side of the protein. The chymotrypsin has three main catalytic residues termed as the catalytic triad. These are His57, Asp102 and Ser195. The nucleophile is the hydroxyl group on the serine. Upon deprotonation the serine residue becomes a powerful nucleophile due to its alkoxide that will attack the relatively unreactive carbon of the carbonyl in the protein.

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