Trends in Biochemical Sciences
Catalytic triads and their relatives
Section snippets
The architecture of the classical triad in serine proteases
The first protease catalytic site, revealed by David Blow and colleagues[4]about 30 years ago using X-ray crystallography, was that of α-chymotrypsin. Their analysis showed initially that two residues were directly involved in catalysis: Ser195 and His57. Chemical evidence for the involvement of Ser195 and His57 in the catalytic reaction already existed, and the crystal structure revealed that the catalytic serine residue was indeed near enough to His57 to form a hydrogen bond. However, the
Variations in the `serine' catalytic triad
No real variation (but see below) in the chemical make-up of the catalytic sites of the serine-protease families has been observed; the three active residues all sit at the same location in their respective structures. An equivalent alignment of the active atoms in the aspartate, histidine and serine side chains occurs in the αμβ-hydrolase family (e.g. the lipases16, 17; see Fig. 2d) and in a recently discovered esterase family[18]. The catalytic triad of brain acetyl hydrolase (a member of
Variations at the hydrogen-bond-acceptor/acid component
Some years ago, lipases were also shown to contain the Asp–His–Ser catalytic triad22, 23; this provided another example of convergent evolution of this catalytic triad. The chirality of the catalytic clusters in lipases and other αμβ hydrolases, however, differs from that of the serine proteases: the positions of the attacking and leaving atoms are reversed. Analysis of the many other lipase structures and some related enzymes has revealed other interesting variations in the catalytic triad17,
Variations at the base
The enzymes that break open the β-lactam ring in penicillin, and the enzyme penicillin acylase, which removes the side group, also exploit serine residues for nucleophilic attack. The other components of the catalytic structure, however, vary. The structural chemistry of these enzymes is discussed below because there are changes in the base and, in the case of the penicillin acylase, other important changes as well.
In β-lactamase enzymes, a lysine residue replaces the histidine base (Fig. 2e).
Variations at the nucleophile
The use of a threonine residue as the nucleophile in asparaginases (Fig. 2h) is not surprising[37]. There are no significant chemical differences between the Oγ atoms of threonine and serine residues, but these residues do different significantly in conformation and bulk. The relatively simple structure of the substrate (the side-chain amide group of asparagine or glutamine residues) might permit a threonine residue to present the catalytic Oγ correctly. The threonine side chain might have an
Catalytic economy in Ntn-hydrolases
Another class of hydrolytic enzymes, the so-called Ntn-hydrolases, has been recognized recently[40]; two such enzymes are penicillin acylase and the prokaryotic proteasome catalytic subunit. In these two enzymes (Fig. 2i,j), the side chain that provides the nucleophile is an N-terminal residue whose α-amino nitrogen atom acts as a base. Thus, nucleophile and base exist in the same amino acid. There is no acid component—a property that is shared by β-lactamase and some esterases. Although only
Summary
The catalytic triad first observed as Ser–His–Asp in serine proteases exists in a variety of forms and evolved a number of times independently. The comparisons between the different catalytic systems that led to the recognition of these chemical and structural relationships were made possible by the availability of results from many crystallographic analyses. There is little doubt in our minds that other discoveries of relationships in catalytic chemistry and in protein function will be made in
Acknowledgements
We thank the many individuals, including Rod Hubbard and Janet Thornton, who are interested in these ideas for discussions, and thank Richard Coxon and John Olive for their help in designing and producing the figures. We also thank Michael James and Zygmunt Derewenda for providing us with coordinates. This work was supported by the BBSRC, as well as by the National Cancer Institute, DHHS, under contract with ABL. The contents of this publication do not necessarily reflect the views or policies
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