Trends in Biochemical Sciences
Understanding nature's catalytic toolkit
Section snippets
Mechanisms of enzyme catalysis
Enzymes, and the principles by which they perform catalysis, have been the subject of intense study for over a hundred years, in which time the mechanisms of many different enzymes have been investigated in great detail. Serine proteases, for example, have been the focus of countless structural [1], kinetic [2] and theoretical 3, 4 studies. Even now, however, when the general principles that govern enzyme catalysis seem to be well understood [5], new theories continue to be proposed to explain
A data set of catalytic interactions
We have compiled from the literature a set of 191 enzymes to study (listed in the Supplementary Material). The set is non-redundant: that is, no two enzymes are evolutionarily related, as defined by sequence and structure comparisons in the CATH database [15]. The catalytic mechanism for each enzyme is extracted from the Catalytic Site Atlas [7] and the crystal structure is taken from the Protein Data Bank (PDB) [16]. All of the structures are high quality (resolution, 2 Å; R-factor, 0.3) and
The functions of secondary residues
The simplest of the functions performed by secondary interactions is orientation. Making bonds between residues restricts their motion and ensures that they are positioned correctly relative to the substrate. Because restricting motion reduces entropy, there is an energetic cost to this orientation. By pre-arranging the active site, this entropic cost is paid for when the enzyme folds or the substrate binds 18, 19, 20, rather than during catalysis, and thus it is beneficial to the enzyme. The
The contents of nature's toolkit
Before we look at the interactions between catalytic residues, it is helpful to see which residues are used most often in catalytic sites. Figure 1 shows the numbers of each residue that are catalytic in our data set and the catalytic propensity of each residue. The catalytic propensity of a residue is defined as the percentage of catalytic residues constituted by a particular reaction type, divided by the percentage of all residues in the data set constituted by that particular residue type [8]
Arginine–arginine
The eight catalytic arginine–arginine interactions in the data set come from five different enzymes: arginine kinase, flavocytochrome c, phytase, undecaprenyl pyrophosphate synthase and adenylate kinase. Four of these five enzymes catalyse reactions involving phosphate chemistry. In each case, the arginines form bonds to the phosphate oxygens and polarize the phosphate, making it a better leaving group. Figure 3a shows the arrangement of arginines around a substrate analogue in adenylate kinase
The roles of catalytic interactions
Previous studies have shown that ∼40% of catalytic residues are involved in either transition state stabilization or substrate activation [8] – processes that generally involve simply providing the appropriate charged groups or hydrogen-bonding partners around the substrate. Given this, it is not surprising that most catalytic residues interact directly with the substrate, rather than with each other. Interactions with other groups are not required for most residues to fulfil these types of
Concluding remarks
With the advent of structural genomics [38], the ability to predict function including catalytic mechanisms from enzyme structures [39] is increasingly important. In addition, the design or redesign of enzymes to bind new substrates or to perform new reactions is being actively pursued 34, 40. The catalytic units that we have described here provide a useful framework for understanding the chemistry performed by enzymes and might help to develop techniques for predicting and designing the
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