Pepsin active site

Hydrolytic activity of pepsin is maximal at pH 2-3, the stomach pH, and aspartate is an essential component of the active site. Pepsin is inactive at pH 7. Which enzymatic reaction mechanisms is most likely of major importance in the action of pepsin ... 

Aspartic endopeptidase Aspartic acid (2 residues) in the active site Pepsin, cathepsin D, rennin (chymosin)... 

FIGURE 14.11 The pH activity profiles of four different enzymes. Trypsin, an intestinal protease, has a slightly alkaline pH optimnm, whereas pepsin, a gastric protease, acts in the acidic confines of the stomach and has a pH optimmn near 2. Papain, a protease found in papaya, is relatively insensitive to pHs between 4 and 8. Cholinesterase activity is pH-sensitive below pH 7 but not between pH 7 and 10. The cholinesterase pH activity profile suggests that an ionizable group with a pK near 6 is essential to its activity. Might it be a histidine residue within the active site ... 

Mammals, fungi, and higher plants produce a family of proteolytic enzymes known as aspartic proteases. These enzymes are active at acidic (or sometimes neutral) pH, and each possesses two aspartic acid residues at the active site. Aspartic proteases carry out a variety of functions (Table 16.3), including digestion pepsin and ehymosin), lysosomal protein degradation eathepsin D and E), and regulation of blood pressure renin is an aspartic protease involved in the production of an otensin, a hormone that stimulates smooth muscle contraction and reduces excretion of salts and fluid). The aspartic proteases display a variety of substrate specificities, but normally they are most active in the cleavage of peptide bonds between two hydrophobic amino acid residues. The preferred substrates of pepsin, for example, contain aromatic residues on both sides of the peptide bond to be cleaved. 

The HIV-l protease is a remarkable viral imitation of mammalian aspartic proteases It is a dimer of identical subunits that mimics the two-lobed monomeric structure of pepsin and other aspartic proteases. The HIV-l protease subunits are 99-residue polypeptides that are homologous with the individual domains of the monomeric proteases. Structures determined by X-ray diffraction studies reveal that the active site of HIV-l protease is formed at the interface of the homodimer and consists of two aspartate residues, designated Asp and Asp one contributed by each subunit (Figure 16.29). In the homodimer, the active site is covered by two identical flaps, one from each subunit, in contrast to the monomeric aspartic proteases, which possess only a single active-site flap. 

The proteases are secreted as inactive zymogens the active site of the enzyme is masked by a small region of its peptide chain, which is removed by hydrolysis of a specific peptide bond. Pepsinogen is activated to pepsin by gastric acid and by activated pepsin (autocatalysis). In the small intestine, trypsinogen, the precursor of trypsin, is activated by enteropeptidase, which is secreted by the duodenal epithelial cells trypsin can then activate chymotrypsinogen to chymotrypsin, proelas-tase to elastase, procarboxypeptidase to carboxypepti-dase, and proaminopeptidase to aminopeptidase. 

Pepsin consists of a single polypeptide chain of molecular weight 34 644 and 327 amino acid residues. Ser-68 is phosphorylated, but this phosphate may be removed without significantly altering the catalytic properties of the enzyme. As in other acid proteases, the active site is an extended area that can accommodate... 

The pepsin, activated by cleavage of a proenzyme, has two putative active site domains comprising hydrophobic-hydrophobic-Asp-Thr-Gly amino acids, is potentially glycosylated and has a free cysteine residue which may allow it to form dimers, as in the case of human and Plasmodium falciparum-derived aspartyl proteases (Longbottom et al., 1997). However,... 

Figure 2. A ribbon diagram of rhizopus pepsin (PDB code 5APR). The catalytically important Asp dyad (Asp218 and Asp35) side-chains are shown in stick diagrams. The P-hair pin flap that covers the active site cleft is located in the bottom of the diagram.

Recently, Noort et al developed a procedure that is based on straightforward isolation of adducted BuChE from plasma by means of affinity chromatography with a procainamide column, followed by pepsin digestion and LC/electrospray tandem MS analysis of a specific nonapeptide containing the phosphonylated active site serine-198 residue (5). This method surpasses the limitations of the fluoride-reactivation method, since it can also deal with dealkylated ( aged ) phosphonylated BuChE. The method allowed the positive analysis of several serum samples of Japanese victims of the terrorist attack in the Tokyo subway in 1995. Furthermore, the method could be applied for detection of ChE modifications induced by, e.g., diethyl paraoxon and pyridostigmine bromide, illustrating the broad scope of this approach. This new approach... 

Figure 1. Schematic representation of the relationships between proposed catalytic and inhibitory mechanisms. A. Postulated general acid-general base catalyzed mechanism for substrate hydrolysis by an aspartyl protease. The water molecule indicated is extensively hydrogen bonded to both aspartic acid residues plus other sites in the active site (see Reference 16 for details). Hydrogen bonds to water are omitted here. B. Kinetic events associated with the inhibition of pepsin by pepstatin. The pro-S hydroxyl group of statine displaces the enzyme immobilized water molecule shown in Figure lA. Variable aspartyl sequence numbers refer to penicillopepsin (pepsin, Rhizopus pepsin), respectively.

Figure 2. Stereo view of pepstatin bound in the R. chinensis pepsin active site. C-3 of statine carrying an OH group is indicated by the . Availability for hydrogen bonding is indicated by closeness of carboxyl groups of Asp-220 and Asp-32 to the statine hydroxyl and to each other.

In summary, the results with pepsin extend the renin data reported by Szelke and Boger and strongly support the postulate of Boger that statine is an analog of a dipeptide tetrahedral intermediate.(20) The C-3 hydroxyl group hydrogen bonds to Asp-213 (220) and Asp-33(35) and displaces a "bound" water molecule from the active site. The isobutyl side chain of statine corresponds to the PI substituent that binds to the SI subsite on the enzyme. The C-1 and C-2 atoms of statine serve to span... 

In order to establish that the addition process observed for in the active site of pepsin is analogous to that occurring with peptide substrates, the experiments were... 

These data unambiguously establish that a gem diol species is formed in the active site of pepsin when the ketone analogs 6 and 10 are added to the aspartyl protease as shown in Figure 6 and exclude the formation of a covalent intermediate. Our data strongly support the general acid-general base catalysis mechanism for aspartyl proteases that is illustrated schematically in Figure 1. 

This rather rigid poly-proline loop, together with the loop comprised of residues 241-250, lies on either side of the active site flap formed by residues 72-81. Hence, in the renins, the cleft is covered by the flaps from both lobes rather than from the N-lobe alone as in other pepsin-like aspartic proteinases. This gives renin a superficial similarity to the dimeric, retroviral proteinases where each subunit provides an equivalent flap that closes down on top of the inhibitor [44,45]. 

Pepsin is secreted as the inactive pepsinogen, which is activated by H+ ions at a pH below 5. Determination of its crystal structure revealed that in the proenzyme the N-terminal 44-residue peptide segment lies across the active site, blocking it.384 At low pH the salt bridges that stabilize the proenzyme are disrupted and the active site is opened up to substrates. 

Carboxybiotin. The structure of biotin suggested that bicarbonate might be incorporated reversibly into its position 2. However, this proved not to be true and it remained for F. Lynen and associates to obtain a clue from a "model reaction." They showed that purified P-methylcrotonyl-CoA carboxylase promoted the carboxylation of free biotin with bicarbonate (H14C03 ) and ATP. While the carboxylated biotin was labile, treatment with diazomethane (Eq. 14-6) gave a stable dimethyl ester of N-l -carboxybiotin.53 54 The covalently bound biotin at active sites of enzymes was also successfully labeled with 14C02 Treatment of the labeled enzymes with diazomethane followed by hydrolysis with trypsin and pepsin gave authentic N-l -carboxybiocytin. It was now clear that the cleavage of ATP is required to couple the C02 from HCOs to the biotin to form carboxybiotin. The enzyme must... 

---