Structure of enzyme—substrate

Zuegg, J., Gruber, K., Gugganig, M. et al. (1999) Three-dimensional structures of enzyme-substrate complexes of the hydroxynitrile lyase from Hevea brasiliensis. Protein Science A Publication of the Protein Society, 8, 1990-2000. 

Laskowski M, Qasim MA. What can the structures of enzyme-inhibitor complexes tell us about the structures of enzyme substrate complexes Biochim Biophys Acta 2000 1477 324-337. 

H. A. Scheraga, M. R. Pincus, and K. E. Burke, in Structure of Complexes between Biopolymers and Low Molecular Weight Molecules, W. Bartmann and G. Snatzke, Eds., pp. 53-76, John Wiley Sons, Chichester, 1983. Calculations of Structures of Enzyme-Substrate Complexes. 

However, since the structures of enzyme-substrate complexes have not been widely investigated yet, these mechanistic proposals have to be considered with care. 

With these introductory remarks, we may now consider the low-energy structures of enzyme-substrate complexes. In this section, we describe results for a-chymotrypsin and, in the next section, results for lysozyme. Further details may be found in a paper by Scheraga et al. [44]. 

All of these calculations are based on the use of ECEPP potentials [1,4], which have been obtained from crystal and gas-phase data. These potentials are ideally suited for computation of the structures of enzyme-substrate complexes because the interactions between enzymes and substrates are the same as those between the molecules of a crystal. They may therefore be employed (as we have done in the case of chymotrypsin and lysozyme) to identify the crucial interactions that lead to recognition. Once these interactions are known they may be used to construct, from theoretical considerations alone, substrates and inhibitors that can bind with the highest affinities to the active site of the enzyme. 

With respect to X-ray crystallography, improvements in instrumentation are now enabling organic chemists to carry out their own measurements to ascertain structures, for example, of synthetic intermediates. The most exciting advance, however, is seen in the field of biopolymers, where entire structures of enzyme-substrate complexes, clusters of proteins and reactive centers, etc., have been elucidated. In most cases, such achievements lead to quantum jumps in our understanding of intricate biochemical processes by defining the three-dimensional structures of all molecules involved. 

Pincus, M. R., Zimmerman, S. S., and Scheraga, H. A., 1976b, Prediction of three-dimensional structures of enzyme-substrate and enzyme-inhibitor complexes of lysozyme, Proc. Natl. Acad. Sci. USA 73 4261. 

Fumaric acid is converted to L-malic acid by hydration in the presence of the enzyme fumamse. From the structure of the substrate and the configuration of the product, it is apparent that the hydroxyl group has been added to the si fiice of one of the carbon atoms of the double bond. Each of the trigonal carbon atoms of an alkene has its fiice specified separately. The molecule of fumaric acid shown below is viewed fixjm the re-re fiice. 

In this chapter, DKRs will be categorized according to the racemization method employed, as being catalyzed by (i) a metal, (ii) a base, (hi) an acid, (iv) an aldehyde, or (v) an enzyme. Also racemizations that take place through continuous cleavage/ formation of the substrate, or through 5 2 displacement, among other methods, will be discussed. In most cases, the racemization method of choice depends on the structure of the substrate. In all cases, the KR is catalyzed by an enzyme. 

This represents an acceleration of at least lO u over the rate of the spontaneous reaction (4). Another striking and biochemically important aspect of enzyme catalyzed reactions is their specificity for the reaction catalyzed and the structure of the substrate utilized. 

As described above, simple mutation, regardless of rational or random, sometimes changes the function of enzymes in a drastic manner. Especially, in the case of enzymes belonging to enolase superfamily, including decarboxylases, consideration of the reaction mechanism is important because the apparently different transformations proceed via a similar key intermediate. Thus, the well-designed mutation and structure of the substrates will lead to a successful expansion of the application of enzymes in organic synthesis. 

Attempts have been made to apply the structure-activity concept (Hansch and Leo 1995) to environmental problems, and this has been successfully applied to the rates of hydrolysis of carbamate pesticides (Wolfe et al. 1978), and of esters of chlorinated carboxylic acids (Paris et al. 1984). This has been extended to correlating rates of biotransformation with the structure of the substrates and has been illustrated with a number of single-stage reactions. Clearly, this approach can be refined with the increased understanding of the structure and function of the relevant degradative enzymes. Some examples illustrate the application of this procedure ... 

Advances in the technology of x-ray diffraction have made it possible to achieve three-dimensional structures of enzymes together bound, in many cases, to their substrates. 

Khan H, T Barna, RJ Harris, NC Bruce, I Barsukov, AW Munro, PCE Moody, NS Scrutton (2004) Atomic resolution structures and solution behavior of enzyme-substrate complexes of Enterobacter cloacae PB2 pentaerythritol tetranitrate reductase. J Biol Chem 279 30563-30572. 

The specificity of substrate utilization depends on the well-defined arrangement of atoms in the enzyme active site that in some way complements the structure of the substrate molecule. 

We have just discussed several common strategies that enzymes can use to stabilize the transition state of chemical reactions. These strategies are most often used in concert with one another to lead to optimal stabilization of the binary enzyme-transition state complex. What is most critical to our discussion is the fact that the structures of enzyme active sites have evolved to best stabilize the reaction transition state over other structural forms of the reactant and product molecules. That is, the active-site structure (in terms of shape and electronics) is most complementary to the structure of the substrate in its transition state, as opposed to its ground state structure. One would thus expect that enzyme active sites would bind substrate transition state species with much greater affinity than the ground state substrate molecule. This expectation is consistent with transition state theory as applied to enzymatic catalysis. 

This is the oldest model for how an enzyme works. It makes a nice, easy picture that describes enzyme specificity. Only if the key fits will the lock be opened. It accounts for why the enzyme only works on certain substrates, but it does not tell us why the reaction of the correct substrates happens so fast. It doesn t tell us the mechanism of the lock. A problem arises because the structure of the substrate changes as it is converted to product. So what is the enzyme complementary to—the substrate, the product, or what The answer is often the transition state (Fig. 7-2). 

If amylases are to be used as tools for the detailed study of the breakdown and structure of their substrates it is obviously important to separate them from other enzymes and from other naturally associated constituents which may influence the results. It is then equally important to study the properties of the purified amylase and to supply it with the chemical environment necessary to protect it from inactivation and to enable it to act efficiently. With beta amylases this ideal has often been approached. Beta amylases from several sources have been prepared by selective inactivation of other enzymes that accompany them in nature23 and highly active products have been obtained by extensive purification.20 24-26 Balls and his associates have recently reported the crystallization of beta amylase from sweet potato.27... 

When the inhibitor and substrate are structurally similar, the inhibitor forms a complex or associate with enzyme and decrease the rate of enzyme catalyzed reaction by reducing the proportion of enzyme-substrate complex as follows ... 

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