This substrate is an oligosaccharide of six sugars, The fnal products are an oligosaccharide of four sugars labeled A through F. Only sugars D and E are shown in detail. (left) and a disaccharide (right), produced by hydrolysis.
In the enzyme–substrate complex (ES), the The Asp52 has formed a covalent bond between enzyme forces sugar D into a strained the enzyme and the C1 carbon atom of sugar D. conformation. The Glu35 in the enzyme is The Glu35 then polarizes a water molecule (red ), positioned to serve as an acid that attacks the so that its oxygen can readily attack the C1 adjacent sugar–sugar bond by donating a proton carbon atom and displace Asp52. (H+) to sugar E; Asp52 is poised to attack the C1 carbon atom.
atoms that speed up a reaction by using charged groups to alter the distribution of electrons in the substrates (Figure 3–52B). And as we have also seen, when a substrate binds to an enzyme, bonds in the substrate are often distorted, changing the substrate shape. These changes, along with mechanical forces, drive a substrate toward a particular transition state (Figure 3–52C). Finally, like lysozyme, many enzymes participate intimately in the reaction by transiently forming a covalent bond between the substrate and a side chain of the enzyme. Subsequent steps in the reaction restore the side chain to its original state, so that the enzyme remains unchanged after the reaction (see also Figure 2–48).
Tightly Bound Small Molecules Add Extra Functions to Proteins
Although we have emphasized the versatility of enzymes—and proteins in general—as chains of amino acids that perform remarkable functions, there are many instances in which the amino acids by themselves are not enough. Just as humans
The reaction of the water molecule (red) completes the hydrolysis and returns the enzyme to its initial state, forming the fnal enzyme– product complex (EP).
Figure 3–51 events at the active site of lysozyme. The top left and top right drawings show the free substrate and the free products, respectively, whereas the other three drawings show the sequential events at the enzyme active site. Note the change in the conformation of sugar D in the enzyme–substrate complex; this shape change stabilizes the oxocarbenium ion-like transition states required for formation and hydrolysis of the covalent intermediate shown in the middle panel. It is also possible that a carbonium ion intermediate forms in step 2, but the covalent intermediate shown in the middle panel has been detected with a synthetic substrate (Movie 3.9). (See D.J. Vocadlo et al., Nature 412:835–838, 2001.)
Figure 3–52 Some general strategies of enzyme catalysis. (A) Holding substrates (A) enzyme binds to two (B) binding of substrate (C) enzyme strains the together in a precise alignment. (B) Charge substrate molecules and to enzyme rearranges bound substrate stabilization of reaction intermediates.
orients them precisely to electrons in the substrate, molecule, forcing it encourage a reaction to creating partial negative toward a transition (C) Applying forces that distort bonds in the occur between them and positive charges state to favor a reaction substrate to increase the rate of a particular that favor a reaction reaction.