Structure of enzyme—substrate complexes

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. 

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. 

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 ... 

The preceding summary and Fig. 20 present a frame-by-frame account of the pathway for ribonuclease catalysis, based predominandy on knowledge of the structures of the various intermediates and transition states involved. The ability to carry out such a study is dependent on three critical features (1) crystals of the enzyme which diffract sufficiently well to permit structural resolution to at least 2 A (2) compatibility of the enzyme, its crystals, and its catalytic kinetic parameters with cryoenzymology so as to permit the accumulation and stabilization of enzyme-substrate complexes and intermediates at subzero temperatures in fluid cryosolvents with crystalline enzyme and (3) the availability of suitable transition state analogs to mimic the actual transition states which are, of course, inaccessible due to their very short lifetimes. The results from this investigation demonstrate that this approach is feasible and can provide unparalleled information about an enzyme at work. 

In many organisms the immediate biosynthetic precursor of L-lysine is a,e-diaminopimelic acid (structure below). What type of enzyme would catalyze this reaction what coenzyme would be required and what type of enzyme-substrate complex would be formed ... 

G. F. Terp, I. T. Christensen, F. S. Jorgensen, Structural differences of matrix metalloproteinases. Homology modeling and energy minimizahon of enzyme-substrate complexes,/. Biomol. Struct. Dynam. 2000, 37, 933-946. 

The rapid technological progress in X-ray crystallography has enabled the structural analysis of numerous enzymes involved in coenzyme biosynthesis. Complete sets of structures that cover all enzymes of a given pathway are available in certain cases such as riboflavin, tetrahydrobiopterin, and folic acid biosynthesis. Stmctures of orthologs from different taxonomic groups have been reported in certain cases. X-ray structures of enzymes in complex with substrates, products, and analogs of substrates, products, or intermediates have been essential for the elucidation of the reaction mechanisms. Structures of some coenzyme biosynthesis enzymes have been obtained by NMR-structure analysis. 

A detailed kinetic analysis and the modeling of enzyme-substrate complexes with the aid of the 3D structure have led to the suggestion of the reaction mechanism detailed... 

In order to understand mechanisms of enzyme catalysis not only are the tertiary structures of enzymes of interest hut so too are the tertiary structures of enzyme-suhstrate complexes. There was, however, a problem As incredibly efficient catalysts, enzymes turn over substrate molecules in fractions of a second, while (40 years ago) collection of crystallographic data took days. The answer to the problem was to study complexes of exceedingly sluggish substrates, unreactive model substrates, as well as strongly bound inhibitors that compete for the active site. 

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