Peptide hydrolysis, catalyzed carboxypeptidase

Fig. 31. Mechanistic proposal for peptide hydrolysis catalyzed by carboxypeptidase A (Christianson and Lipscomb, 1989). (a) The precatalytic Michaelis complex with substrate carbonyl hydrogen bonded to Arg-127 allows for nucleophilic attack by a water molecule promoted by zinc and assisted by Glu-270 (an outer-sphere C==O Zn interaction is not precluded), (b) Tbe stabilized tetrahedral intermediate collapses, with required proton donation by Glu-270 (Monzingo and Matthews, 1984) Glu-270 may play a bifunctional catalytic role (Schepartz and Breslow, 1987), which results in the product complex (c). [Reprinted with permission from Christianson, D. W., Lipscomb, W. N. (1989) Acc. Chem. Res. 22,62-69. Copyright 1989 American Chemical Society.]...

The COOH-terminal amino acid of a peptide or protein may be analyzed by either chemical or enzymatic methods. The chemical methods are similar to the procedures for NH2-terminal analysis. COOH-terminal amino acids are identified by hydrazinolysis or are reduced to amino alcohols by lithium borohydride. The modified amino acids are released by acid hydrolysis and identified by chromatography. Both of these chemical methods are difficult, and clear-cut results are not readily obtained. The method of choice is peptide hydrolysis catalyzed by carboxypeptidases A and B. These two enzymes catalyze the hydrolysis of amide bonds at the COOH-terminal end of a peptide (Equation E2.3), since carboxypeptidase action requires the presence of a free a-carboxyl group in the substrate. 

The combination of Lewis add and nucleophile activations in 12-14 requires four-membered ring transition states. Interestingly, the mechanism for carboxypeptidase A (CPA) catalyzed hydrolysis of peptides also appears to involve joint Lewis add and nucleophile activations that lead to the formation of a four-membered ring transition state. Christianson and Lipscomb [57] have determined the crystal structure (15) of a ketone bound to CPA. Surprisingly, the ketone is in its hydrated form with both oxygens of the gem-diol bound to the active-site zinc of CPA (Figure 6.12). 

Proteins are hydrolyzed very slowly with storage in water at neutral pH. However, addition of proteases can increase the rate of hydrolysis about 10 billion times over the spontaneous rate. The chymotrypsin mechanism depicted in Figure 2.53 is shared by trypsin and elastase. These three proteases are members of a family called the serine proteases (named after Ser 195), Carboxypeptidase Aand pepsin catalyze peptide hydrolysis by different mechanisms and are not part of this family. 

Figure 10, Phenyl acetate inhibition of carboxypeptidase A-catalyzed hydrolysis of peptide, Dns-(Gly)g-i.-Phe, 1 X and the ester, Dns-(Gly)3-L.-0Phe, 4 X iO M (57), Enzyme concentrations were 5 X iO" and 4 X IO" M for ester and peptide hydrolysis, respectively (48, 57). Assays were performed in the absence (dashed Une) and presence (solid line) of 1 X phenyl acetate, 0Ac, at 25°C and...

The primary structure of a protein is the sequence of its amino acids and the location of all its disulfide bridges. The N-terminal amino acid of a peptide or protein can be determined with Edman s reagent. The C-terminal amino acid can be identified with carboxypeptidase. Partial hydrolysis hydrolyzes only some of the peptide bonds. An exopeptidase catalyzes the hydrolysis of a peptide bond at the end of a peptide chain. An endopeptidase catalyzes the hydrolysis of a peptide bond that is not at the end of a peptide chain. 

Knowing how the protein chain is folded is a key ingredient m understanding the mechanism by which an enzyme catalyzes a reaction Take carboxypeptidase A for exam pie This enzyme catalyzes the hydrolysis of the peptide bond at the C terminus It is... 

FIGURE 27 19 Proposed mechanism of hydrolysis of a peptide catalyzed by carboxypeptidase A The peptide is bound at the active site by an ionic bond between its C terminal ammo acid and the positively charged side chain of arginine 145 Coordination of Zn to oxygen makes the carbon of the carbonyl group more positive and increases the rate of nucleophilic attack by water... 

Carboxypeptidases are zinc-containing enzymes that catalyze the hydrolysis of polypeptides at the C-terminal peptide bond. The bovine enzyme form A is a monomeric protein comprising 307 amino acid residues. The structure was determined in the laboratory of William Lipscomb, Harvard University, in 1970 and later refined to 1.5 A resolution. Biochemical and x-ray studies have shown that the zinc atom is essential for catalysis by binding to the carbonyl oxygen of the substrate. This binding weakens the C =0 bond by... 

There are two main classes of proteolytic digestive enzymes (proteases), with different specificities for the amino acids forming the peptide bond to be hydrolyzed. Endopeptidases hydrolyze peptide bonds between specific amino acids throughout the molecule. They are the first enzymes to act, yielding a larger number of smaller fragments, eg, pepsin in the gastric juice and trypsin, chymotrypsin, and elastase secreted into the small intestine by the pancreas. Exopeptidases catalyze the hydrolysis of peptide bonds, one at a time, fi"om the ends of polypeptides. Carboxypeptidases, secreted in the pancreatic juice, release amino acids from rhe free carboxyl terminal, and aminopeptidases, secreted by the intestinal mucosal cells, release amino acids from the amino terminal. Dipeptides, which are not substrates for exopeptidases, are hydrolyzed in the brush border of intestinal mucosal cells by dipeptidases. 

Procarboxypeptidase A is activated by the removal of a peptide of some 64 residues from the N-terminus by trypsin.153 This zymogen has significant catalytic activity. As well as catalyzing the hydrolysis of small esters and peptides, procarboxypeptidase removes the C-terminal leucine from lysozyme only seven times more slowly than does carboxypeptidase. Also, the zymogen hydrolyzes Bz-Gly-L-Phe with kcsA = 3 s-1 and KM = 2.7 mM, compared with values of 120 s 1 and 1.9 mM for the reaction of the enzyme.154 In contrast to the situation in chymotrypsinogen, the binding site clearly pre-exists in procarboxypeptidase, and the catalytic apparatus must be nearly complete. 

This enzyme [EC 3.4.16.4], also known as serine-type D-alanyl-D-alanine carboxypeptidase, catalyzes the hydrolysis of D-alanyl-D-alanine to yield two D-alanine. This enzyme comprises a group of membrane-bound, bacterial enzymes of the peptidase family Sll. They are distinct from the zinc D-alanyl-D-alanine carboxypeptidase [EC 3.4.17.14]. The enzyme also hydrolyzes the D-alanyl-D-alanine peptide bond in the polypeptide of the cell wall. In addition, the enzyme will also catalyze the transpeptidation of peptidyl-alanyl moieties that are A-acetyl-substituents of D-alanine. The protein is inhibited by j8-lactam antibiotics, which acylate the active-site seryl residue. 

This enzyme [EC 3.4.16.5] (also known as serine-type carboxypeptidase I, cathepsin A, carboxypeptidase Y, and lysosomal protective protein) is a member of the peptidase family SIO and catalyzes the hydrolysis of the peptide bond, with broad specificity, located at the C-terminus of a polypeptide. The pH optimum ranges from 4.5 to 6.0. The enzyme is irreversibly inhibited by diisopropyl fluorophosphate and is sensitive to thiolblocking reagents. 

An important difference between thermolysin and carboxypeptidase leads to the major uncertainty in the mechanism of carboxypeptidase. This difference is that the catalytic carboxylate of carboxypeptidase is far more sterically accessible. The crucial question is whether or not the carboxypeptidase-catalyzed hydrolysis of peptides proceeds via general-base catalysis, as in equation 16.26, or via nucleophilic catalysis, as in 16.27. Early kinetic work concentrated on establishing the participation of the various groups in catalysis. 

There are simple reagents that react selectively with the carboxyl terminus of a peptide, but they have not proved as generally useful for analysis of the C-terminal amino acids as has the enzyme carboxypeptidase A. This enzyme catalyzes the hydrolysis of the peptide bond connecting the amino acid with the terminal carboxyl groups to the rest of the peptide. Thus the amino acids at the carboxyl end will be removed one by one through the action of the enzyme. Provided that appropriate corrections are made for different rates of hydrolysis of peptide bonds for different amino acids at the carboxyl end of the peptide, the sequence of up to five or six amino acids in the peptide can be deduced from the order of their release by carboxypeptidase. Thus a sequence such as peptide-Ser-Leu-Tyr could be established by observing that carboxypeptidase releases amino acids from the peptide in the order Tyr, Leu, Ser ... 

Trypsin, chymotrypsin, and elastase—three members of the serine protease family—catalyze the hydrolysis of proteins at internal peptide bonds adjacent to different types of amino acids. Trypsin prefers lysine or arginine residues chymotrypsin, aromatic side chains and elastase, small, nonpolar residues. Carboxypeptidases A and B, which are not serine proteases, cut the peptide bond at the carboxyl-terminal end of the chain. Carboxypeptidase A preferentially removes aromatic residues carboxypeptidase B, basic residues. (Illustration copyright by Irving Geis. Reprinted by permission.)... 

A-4. The carboxypeptidase-catalyzed hydrolysis of a pentapeptide yielded phenylalanine (Phe). One cycle of an Edman degradation gave a derivative of leucine (Leu). Partial hydrolysis yielded the fragments Leu-Val-Gly and Gly-Ala among others. Deduce the structure of the peptide. 

In models for carboxypeptidase A we showed the intracomplex catalyzed hydrolysis of an ester by a metal ion and a carboxylate ion [106], which are the catalytic groups of carboxypeptidase A. Some mechanistic proposals for the action of carboxypeptidase involve an anhydride intermediate that then hydrolyzes to the product and the regenerated enzyme. Although we later found convincing evidence that the enzyme does not use the anhydride mechanism in cleaving peptides [96-99], it may well use such a mechanism with esters. In a mimic of part of this mechanism we showed [107], but see also Ref. 108, that we could achieve very rapid hydrolysis of an anhydride by bound Zn2+, which is the metal ion in the enzyme. In another model, a carboxylate ion and a phenolic hydroxyl group, which are in the enzyme active site, could cooperatively catalyze the cleavage of an amide by the anhydride mechanism [109]. 

Because only 40 to 60 amino acid residues can be determined by the Edman procedure, additional methods are needed for larger proteins. Determination of the C-terminal amino acid can be accomplished by treating the protein with carboxypeptidase. This enzyme selectively catalyzes the hydrolysis of the C-terminal amino acid. After the first amino acid has been removed, the enzyme begins to cleave the second amino acid, and so forth. By following the rates at which the amino acids appear, it is possible to determine the first few amino acids at the C-terminal end of the protein by employing this enzyme. However, because the enzyme hydrolyzes different peptide bonds at different rates, it is possible to identify only a few amino acids before the reaction mixture becomes too complex. 

Enzyme-catalyzed hydrolysis, exploiting the esterase activity of proteases such as trypsin and chymotrypsint ° l or carboxypeptidase has opened alternative routes to the deprotection of several peptide methyl, ethyl, and ferf-butyl esters. In fact, methyl, ethyl, and benzyl esters are successfully hydrolyzed from protected peptides using the alkaline protease from Bacillus subtilis or alcalase from Bacillus licheniformis which accepts... 

Stopped-flow fluorescence studies of ES complexes provided a direct comparison of the peptide binding aflBnities of the zinc and cadmium enzymes and, simultaneously, an explanation for the different roles of metals in peptide and ester hydrolysis (48). Cadmium carboxypeptidase binds the peptide Dns-(Gly)3-L-Phe as readily as does [(CPD)Zn] but catalyzes its hydrolysis at a rate that is reduced considerably (Figure 8). Initial rate studies of oligopeptides are in agreement with this observation. For all peptides examined, the catalytic rate constants of the cadmium enzyme are decreased markedly, but the association constants (1) (Km values) of the cadmium enzyme are identical to those of the zinc enzyme (48,51,57). However, in marked contrast, for all esters examined the catalytic rate constants of the cadmium enzyme are nearly the same as those of the zinc enzyme, but the association constants are decreased greatly. 

Table V. Carboxylic Acid Inhibitors of the Carboxypeptidase A-Catalyzed Hydrolysis of Esters and Peptides ...

---