Catalytic triad, serine protease

Especially for enzymes, common mechanisms and associated active sites are often observed. This allows searching for appropriate 3D patterns in a database of structures and for checking models to contain such a pattern (for a well known example, see SER-HIS-ASP serine protease catalytic triad [262]). 

Another possibility is to search for constellations of amino acids that can confirm a similar function even when the proteins containing them adopt completely different folds. Probably the best known example of this type of similarity is the serine protease catalytic triad (Ser, His, Asp), which occurs in at least 10 different folds. Several approaches have been developed to search for these, including PINTS [42] (http //pints.embl.de), the Catalytic Site Adas [43] (http //www.ebi.ac.uk/thomton-srv/databases/CSA), and Spasm/Rigor [44]. For some protein structures these similarities can be very illuminating as to function by either finding a convergendy evolved site on a new fold [45] or confirming a prediction of function based on a weak similarity to a known fold [46,47]. 

After the nucleophilic attack by the hydroxyl function of the active serine on the carbonyl group of the lactone, the formation of the acyl-enzyme unmasks a reactive hydroxybenzyl derivative and then the corresponding QM. The cyclic structure of the inhibitor prevents the QM from rapidly diffusing out of the active center. Substitution of a second nucleophile leads to an irreversible inhibition. The second nucleophile was shown to be a histidine residue in a-chymotrypsin28 and in urokinase.39 Thus, the action of a functionalized dihydrocoumarin results in the cross-linking of two of the most important residues of the protease catalytic triad. 

Due to the similarity between the lipase and protease catalytic triads, the mechanism of lipase catalysis is similar to that of serine protease (Jaeger et al., 1999). a/p Hydrolases have a common catalytic mechanism of ester hydrolysis. First, serine is activated by deprotonation. Subsequently, the nucleophiUty of hydroxyl... 

Carter, P, Wells, J.A. Dissecting the catalytic triad of a serine protease. Nature 332 564-568, 1988. 

Until recently, the catalytic role of Asp ° in trypsin and the other serine proteases had been surmised on the basis of its proximity to His in structures obtained from X-ray diffraction studies, but it had never been demonstrated with certainty in physical or chemical studies. As can be seen in Figure 16.17, Asp ° is buried at the active site and is normally inaccessible to chemical modifying reagents. In 1987, however, Charles Craik, William Rutter, and their colleagues used site-directed mutagenesis (see Chapter 13) to prepare a mutant trypsin with an asparagine in place of Asp °. This mutant trypsin possessed a hydrolytic activity with ester substrates only 1/10,000 that of native trypsin, demonstrating that Asp ° is indeed essential for catalysis and that its ability to immobilize and orient His is crucial to the function of the catalytic triad. 

The elucidation of the X-ray structure of chymotrypsin (Ref. 1) and in a later stage of subtilisin (Ref. 2) revealed an active site with three crucial groups (Fig. 7.1)-the active serine, a neighboring histidine, and a buried aspartic acid. These three residues are frequently called the catalytic triad, and are designated here as Aspc Hisc Serc (where c indicates a catalytic residue). The identification of the location of the active-site groups and intense biochemical studies led to several mechanistic proposals for the action of serine proteases (see, for example, Refs. 1 and 2). However, it appears that without some way of translating the structural information to reaction-potential surfaces it is hard to discriminate between different alternative mechanisms. Thus it is instructive to use the procedure introduced in previous chapters and to examine the feasibility of different... 

Catalysis, specific acid, 163 Catalytic triad, 171,173 Cavity radius, of solute, 48-49 Charge-relay mechanism, see Serine proteases, charge-relay mechanism Charging processes, in solutions, 82, 83 Chemical bonding, 1,14 Chemical bonds, see also Valence bond model... 

Fig. 3 A ribbon diagram of the HCV NS3/4A protease ICU1 (Yao et al, 1999). The serine protease domain is shown in cyan with the catalytic triad highlighted in yellow, and the helicase domain is...

NS3 is a 631 amino acid protein, and its first 180 amino acids encode a serine protease of the chymotrypsin family (Figure 2.2A). It has a typical chymotrypsin-family fold consisting of two jS-barrels, with catalytic triad residues at the interface. His-57 and Asp-81 are contributed by the N-terminal jS-barrel and Ser-139 from the C-terminal jS-barrel. NS3 and closely related viral proteases are significantly smaller than other members of the chymotrypsin family, and many of the loops normally found between adjacent jS-strands in trypsin proteases are truncated in NS3 [31]. Probably... 

The outstanding inclusion ability and the carboxylic functions of host I raised the idea of co-erystallizing it with imidazole (Im) which, due to its versatile nature 114), is one of the frequently used components in enzyme active sites, generally presented by histidine. Formally, a system made of imidazole and an acid component may mimic two essential components of the so-called catalytic triad of the serine protease family of enzymes the acid function of Aspl02 and the imidazole nucleus of His57 115) (trypsin sequence numbering). The third (albeit essential) component of the triad corresponding to the alcohol function of Seri 95 was not considered in this attempt. This family of enzymes is of prime importance in metabolitic processes. 

L. Brady, A. M. Brzozowski, Z. S. Derewenda, E. Dodson, G. Dodson, S. Tolley, J. P. Turkenburg, L. Christiansen, B. Huge-Jensen, L. Norskov, L. Thim, U. Menge, A Serine Protease Triad Forms the Catalytical Centre of a Triacylglycerol Lipase , Nature 1990, 343,161-110. 

Structure of the human cytomegalovirus protease catalytic domain reveals a novel serine protease fold and catalytic triad, Cdl 1996, 86, 835-843. 

A sutfonylating agent (abbreviated PMSE) that irreversibly inhibits many serine esterases and serine proteases . Target enzymes usually react with PMSE and related alkylating agents through the activated imidazole group of a histidyl residue that is part of the catalytic triad. 

Carter, P., Abrahmsen, L. and Wells, J.A. (1991) Probing the mechanism and improving the rate of substrate-assisted catalysis in subtihsin BPN. Biochemistry, 30, 6142-6148. Carter, P. and Wells, J.A. (1988) Dissecting the catalytic triad of a serine protease. 

Among cysteine proteases of bacteria is a papainlike enzyme from Clostridium histolyticum with a specificity similar to that of trypsin 338 Tire anaerobic Porphyromonas gingivalis, which is implicated in perio-dental disease, produces both arginine- and lysine-specific cysteine proteases designated gingipains.339 3393 Some virally encoded cysteine proteases, including one from the polio virus, have trypsin-like sequences with the serine of the catalytic triad replaced by cysteine.340 341 A human adenovirus protease also has a Cys His Glu triad but a totally different protein fold.342... 

All of these esterases appear to act by mechanisms closely related to those of proteases. Acetylcholinesterase contains an active site serine that reacts with organophosphorus compounds (Box 12-E) and is part of an Asp-His-Ser catalytic triad which lies in a deep "gorge" as well as an oxyanion hole.637 A surprise is the absence of an essential carboxylate group that might bind the positively charged trimethylammonium... 

Below the active site of aspartate aminotransferase, as shown in Fig. 14-6, is a cluster of three buried histidine side chains in close contact with each other. The imidazole of H143 is hydrogen bonded to the D222 carboxylate, the same carboxylate that forms an ion pair with the coenzyme. This system looks somewhat like the catalytic triad of the serine proteases in reverse. As with the serine proteases, the proton-labeled Hb in Fig. 14-6 can be "seen" by NMR spectroscopy (Fig. 3-30). So can the proton Ha on the PLP ring. These protons... 

Catalytic dyad 620 Catalytic subunits 348 Catalytic triad 134, 611-614, 619, 635 of serine proteases 611—614 Cataracts 169 Catechol 838 Catecholamine(s) 553 Catechol O-methyltransferase (COMT) 591 Cathepsin(s) 619,621 G 610... 

Mammalian PCs, just like kexin, cleave their substrates carboxy-terminal of paired basic residues and they share a conserved catalytic domain resembling that of bacterial subtilisins. The catalytically important residues Asp, His, and Ser are arranged in the catalytic triad in a way that is typical for subtilisins but distinct from the arrangement found within the (chymo)trypsin clan of serine proteases. The subtilisins and (chymo)trypsins have thus served as a prime example of convergent evolution [140,141],... 

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