Hydrolases peptide hydrolase

Peptidases are enzymes that catalyse the hydrolysis of peptide bonds - the bonds between amino acids that are found in peptides and proteins. The terms protease , proteinase and proteolytic enzyme are synonymous, but strictly speaking can only be applied to peptidases that hydrolase bonds in proteins. Because there are many peptidases that act only on peptides, the term peptidase is recommended. Peptidases are included in subclass 3.4 of enzyme nomenclature [1,5]. 

Proteases (proteinases, peptidases, or proteolytic enzymes) are enzymes that break peptide bonds between amino acids of proteins. The process is called peptide cleavage, a common mechanism of activation or inactivation of enzymes. They use a molecule of water for this, and are thus classified as hydrolases. 

Figure 6.10 Generic mechanism for a zinc hydrolase acting on a peptide bond.

EE Sterchi, JF Woodley. Peptide hydrolases of the human small intestinal mucosa Distribution of activities between brush border membranes and cytosol. Clin Chim... 

C Shoaf, RM Berko, WD Heizer. Isolation and characterization of four peptide hydrolases from the brush border of rat intestinal mucosa. Biochem Biophys Acta 445 649-719, 1976. 

Holmquist, M. (2000) Alpha/beta-hydrolase fold enzymes structures, functions and mechanisms. Current Protein Peptide Science, 1, 209-235. 

The retrieval mechanism for the M6P receptor resembles the one previously described for the H/KDEL receptor [53]. Optimal binding of M6P receptor to M6P occurs at pH 6.5-6.7, the pH found in the TGN. When transport vesicles arrive at late endosomes, the pH is lowered by the action of H+ pumps. The affinity of the M6P receptor for its ligands is reduced at acid pHs, resulting in M6P receptor releasing the M6P in the late endosome. As a result, transport of lysosomal hydrolases occurs unidirectionally. Once the M6P receptor releases M6P-bearing hydrolases, the receptor can be returned to the TGN for reuse. Transport of the M6P receptor to either TGN or late endosome relies on signal peptides on the cytoplasmic tail region of the M6P receptor. 

See Section IV.1 for alternative methods of chiral resolution. Partial chemical hydrolysis of proteins and peptides with hot 6 M HC1, followed by enzymatic hydrolysis with pronase, leucine aminopeptidase and peptidyl D-amino acid hydrolase, avoids racemiza-tion of the amino acids281. The problems arising from optical rotation measurements of chiral purity were reviewed. Important considerations are the nonideal dependence of optical rotation on concentration and the effect of chiral impurities282. 

The role of the serine residue in hydrolysis was further examined using pseudo-substrates, e.g. p-nitrophenylacetate—substrates which were only very slowly utilized by the enzyme. The p-nitrophenyl group was slowly released and the acyl group became attached to the same serine in hydrolases which had been detected by DIPF (Kilby and Youatt, 1954). Mechanisms for peptide and ester hydrolysis were therefore proposed in which the acyl group became transiently and covalently bound to serines in catalytic sites (see Hartley et al. 1969). 

The NC-IUBMB has introduced a number of changes in the terminology following the proposals made by Barrett, Rawlings and co-workers [7] [8]. The term peptidase should now be used as a synonym for peptide hydrolase and includes all enzymes that hydrolyze peptide bonds. Previously the term peptidases was restricted to exopeptidases . The terms peptidase and protease are now synonymous. For consistency with this nomenclature, the term proteinases has been replaced by endopeptidases . To complete this note on terminology, we remind the reader that the terms cysteine endopeptidases and aspartic endopeptidases were previously called thiol proteinases and acid or carboxyl proteinases , respectively [9],... 

Peptide hydrolases (peptidases or proteases, i.e., enzymes hydrolyzing peptide bonds in peptides and proteins, see Chapt. 2) have received particular attention among hydrolases. As already described in Chapt. 2, peptidases are divided into exopeptidases (EC 3.4.11 -19), which cleave one or a few amino acids from the N- or C-terminus, and endopeptidas-es (proteinases, EC 3.4.21-99), which act internally in polypeptide chains [2], The presentation of enzymatic mechanisms of hydrolysis in the following sections will begin with peptidases and continue with other hydrolases such as esterases. 

Fig. 3.3. Major steps in the hydrolase-catalyzed hydrolysis of peptide bonds, taking chymo-trypsin, a serine hydrolase, as the example. Asp102, His57, and Ser195 represent the catalytic triad the NH groups of Ser195 and Gly193 form the oxyanion hole . Steps a-c acylation Steps d-f deacylation. A possible mechanism for peptide bond synthesis by peptidases is represented by the reverse sequence Steps f-a.

Fig. 3.6. Stereoelectronic control of the cleavage of the tetrahedral intermediate during hydrolysis of a peptide bond by a serine hydrolase. The thin lines represent the reactive groups of the enzyme (serine, imidazole ring of histidine) the thick lines represent the tetrahedral intermediate of the transition state. The full circles are O-atoms open circles are N-atoms. The dotted lines represent H-bonds the thick double arrow indicates an unfavorable dipole-dipole interaction [21]. A (R)-configured N-center B (S)-configured N-center.

The results showed a 59% confirmation rate (41% false positive rate), giving 4296 confirmed actives. Of the compounds initially selected with >40% inhibition, 69% confirmed at >40% inhibition. This can be broken down further into compounds that feU into enriched clusters and those that did not, with confirmation rates of 73 and 68% respectively. In this case, there was only a modest increase in the confirmation rate for compounds selected from enriched clusters. This might be attributed to the fact that the enrichment within the active clusters was only about 50% greater than the background hit rate (21 versus 14.7%) in contrast to the peptide hydrolase case where the enrichment was 2.6-fold higher. 

The confirmed actives selected from each of the three example projects shown are at varying stages of progression through the secondary assay process. The peptide hydrolase example is the most advanced and so has the most information available. The throughput limit for secondary assays in that case was just 500 molecules, and... 

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