Scissile peptide bond

The mechanism of catalysis by these enzymes has been extensively investigated (for review see ref. 10). Essentially, the active site serine via its side chain hydroxyl group performs a nucleophilic attack on the carbonyl carbon of the scissile peptide bond thus forming a tetrahedral intermediate. A histidine residue in the active site serves as a general base accepting the proton from the serine residue. The acyl enzyme thus formed is broken down via a nucleophilic attack of a water molecule to complete the hydrolysis of the peptide bond. 

The catalytic mechanism in this class is based upon similar chemical principles as the mechanism of the serine proteinases. A cysteine residue in the active site is activated by a histidine imidazolium side chain and carries out a nucleophilic attack on the carbonyl carbon of the scissile peptide bond with the complex going through an acyl intermediate transition state (28,29). Certain members of this class of enzymes have pH optima in the acidic range and... 

A catalytic mechanism (Figure 14) was proposed on the basis of kinetic, spectroscopic and crystallographic data . The substrate peptide binds to Zn2 with its N-terminal amino group and to Znj with the carbonyl oxygen of the scissile peptide bond. Additionally, the N-terminus interacts with Aspl79. Upon substrate binding, the bridging water... 

Carboxypeptidase A"" (CPA, EC 3.4.17.1) is a proteolytic enzyme that cleaves C-terminal amino acid residues with hydrophobic side chains selectively. Several X-ray structures are available" The active site of CPA consists of a hydrophobic pocket (primary substrate recognition site) that is primarily responsible for the substrate specificity, a guanidinium moiety of Argl45 that forms hydrogen bonds to the carboxylate of the substrate, and Glu270, whose carboxylate plays a critical role, functioning either as a nucleophile to attack the scissUe carboxamide carbonyl carbon of the substrate or as a base to activate the zinc-bound water molecule, which in turn attacks the scissile peptide bond ". However, semiempirical calculations had shown that the direct attack of... 

One enigmatic feature of renin is its extreme substrate specificity, its only known natural substrate being a single Leu-Val peptide bond of angiotensinogen. The minimal synthetic analog is the 6-13 octapeptide that encompasses the scissile peptide bond of angiotensinogen between residues 10 and 11 [5]. It has... 

All peptidases catalyze the general reaction depicted in Figure C2.2.2, the hydrolysis of a peptide bond. The different peptidases are unique with respect to their specificity that is, their ability to accommodate particular sets of amino acids in the vicinity of a potentially scissile peptide bond. Some peptidases have very broad specificities, such as papain, which has few limi-... 

Various peptide Michael acceptors have been described as a new class of inactivators for cysteine proteases. 5-7 The carbonyl group of the scissile peptide bond in the substrate is replaced by a nucleophile trapping moiety such as a vinylogous structure. An amino acid vinyl sulfone, l-(methylsulfonyl)-4-phenylbut-l-en-3-amine [H2NCH(Bzl)CH=CHS02Me] and a dipeptide derivative, Gly-HNCH(Bzl)CH=CHS02Me have both been prepared as inhibitors of cysteine proteases, leucine aminopeptidase and dipeptidyl peptidase I, respectively.1 5 A series of peptide vinyl sulfones has been synthesized as potent inhibitors for different cysteine proteases. 1A8 ... 

The cysteine proteases can be divided into three classes the papain-like, the caspases (and related enzymes), and the picorna viral cysteine proteases. The proposed catalytic mechanism for cysteine protease peptide cleavage is related to the serine protease mechanism but with a cysteine thiol acting as the nucleophile that attacks the scissile peptide bond carbonyl. 

While a few very potent non-peptide protease inhibitors (Pis) have been isolated from plants many plant protease inhibitor proteins (PIPs) have evolved to have protease interaction Kj values in the nanomolar and picomolar range. These extraordinary affinities derive from the matching of the PI protein amino sequence about the scissile peptide bond (Pl-Pl ) and evolution of adjacent sequences to fit and interact appropriately within the target protease active site [1, 120, 121]. The structure and function of the different classes of PI proteins from plants are succinctly but comprehensively reviewed below. 

Peptide Chloromethyl Ketones. Peptide chloromethyl ketone inhibitors have been studied extensively and a fairly detailed picture of the inhibition reaction (see Figure 3) has emerged from numerous chemical and crystallographic studies (30,31). The inhibitor resembles a serine protease substrate with the exception that the scissile peptide bond of the substrate is replaced with a chloromethyl ketone functional group in the inhibitor. The inhibitor binds to the serine protease in the extended substrate binding site and the reactive chloromethyl ketone functional group is placed then in the proper position to alkylate the active-site histidine residue. In addition, the serine OH reacts with the inhibitor carbonyl group to form a hemiketal. 

Fig. 3.S Putative catalytic mechanism of the novel active site in fl7. The reaction begins when the nucleophilic oxygen of Thr-1 donates its proton to its own a-amino group and attacks the carbonyl carbon of the substrate. The negatively charged tetrahedral intermediate is stabilized by hydrogen bonding. The acylation step is complete when the a-amino group of Thr donates a proton to the nitrogen of the scissile peptide bond. A covalent bond is formed between the substrate...

Enzymes, which hydrolyse the internal peptide bonds, are called as eiidopeptidases. Endopeptidases have side chain requirements for the residues flanking the scissile peptide bond. (Peptide bond to be cleaved). The important endopeptidases and their sources are listed below... 

Proteolytic enzymes, such as the serine proteases, are among the best characterized of all enzymes.They are important in digestive processes because they break down proteins. They each catalyze the same type of reaction, that is. the breaking of peptide bonds by hydrolysis. The crystal structures of several serine proteases have been determined, and the mechanism of hydrolysis is similar for each. The specificity of each enzyme is, however, different and is dictated by the nature of the side chains flanking the scissile peptide bond (the bond that is broken in catalytic mechanism. Chymotrypsin is one of the best characterized of these serine proteases. The preferred substrates of chymotrypsin have bulky aromatic side chains. The crystal structure determination of the active site of chymotrypsin, illustrated in Figure 18.12, has provided much of the information used to elucidate a plausible mechanism of action of the enzyme. In the first step of any catalyzed reaction, the enzyme and substrate form a complex, ES, the Michaelis complex. The hydrolysis of the peptide bond by chymotrypsin involves three amino acid residues,... 

Incorporation of the hydroxyethylene, dihydroxyethylene and other statine-like residues in place of the scissile peptide bond in substrate-based analogues, along with other amino acid or non-peptide changes at the N- and C-termini, led to more potent, selective and relatively small molecular weight inhibitors of renin. Examples of such compounds include Ro 42-5892 (117), ICl 219623 (118) and CGP38560 (119). Ro 42-5892 was... 

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