Elastase binding pocket

FIGURE 16.19 The substrate-binding pockets of trypsin, chymotrypsin, and elastase. 

Figure 1.18 Comparison of the binding pockets in (a) chymotrypsin, with IV-formyl-L-tryptophan bound, and (b) elastase, with IV-formyl-L-alanine bound. The binding pocket in trypsin is very similar to that in chymotrypsin, except that residue 189 is an aspartate to bind positively charged side chains. Note the hydrogen bonds between the substrate and the backbone of the enzyme.

Figure 4. The effect of length of hydrocarbon side chains of alkyl isocyanates on their interactions with three related proteolytic enzymes. Schematics of proposed interactions of alkyl isocyanates with the binding pockets of trypsin, chymotrypsin, and elastase (22).

The binding pockets in trypsin, chymotrypsin, and elastase. The negatively charged aspartate is shown in red, and the relatively nonpolar amino acids are shown in green. The structures of the binding pockets explain why trypsin binds long, positively charged amino acids chymotrypsin binds flat, nonpolar amino acids and elastase binds only small amino acids. 

The serine endopeptidases include the chymotrypsin family (EC 3.4.21.1), trypsin (EC 3.4.21.4), elastase (EC 3.4.21.37), thrombin (EC 3.4.21.5), subtilisin (EC 3.4.21.62) and a-lytic proteases (EC 3.4.21.12). The enzymes are all endopeptidases. The substrate specificities of the individual members of this group are often quite different, which is attributed to different structures of the binding pockets. 

The different specificities of the proteolytic enzymes are due to specificity pockets at the binding site (Fig. 15-8). These pockets on the surface of the enzyme accommodate the side-chain of the amino acid residue located on the carbonyl side of the scissile bond of the substrate. In trypsin, a serine residue present in chymotrypsin is replaced by an aspartate residue. This allows the binding of cationic arginine and lysine residues instead of bulky aromatic side chains. In elastase, two glycine residues of chymotrypsin are replaced by valine and threonine. Their bulky side chains block the specificity pocket so that elastase hydrolyzes peptide bonds adjacent to smaller, uncharged side chains. 

In the recent studies, the enzyme shows that the overall polypeptide fold of chymotrypsin-like serine protease possesses essential SI specificity determinants characteristic of elastase using the multiple isomorphous replacement (MIR) method and refined to 2.3 A resolution Fig. (5). Structure-based inhibitor modeling demonstrated that EFEa s SI specificity pocket is preferable for elastase-specific small hydrophobic PI residues, while its accommodation of long and/or bulky PI residues is also feasible if enhanced binding of the substrate and induced fit of the SI pocket are achieved [Fig. (6) shows the active sites of serine protease]. EFEa is thereby endowed with relatively broad substrate specificity, including the dual fibrinolysis. This structure is the first report of an earthworm fibrinolytic enzyme component, a serine protease originated from annelid worm [17]. 

The pancreatic trypsin inhibitor binds to trypsin, chymotrypsin, plasmin, and kallikrein, but does not inhibit elastase and subtilisin. Model-building studies of the inhibitor chymotrypsin complex show that the enzyme and Inhibitor have highly complementary structures. If Lys-15 (in a non-protonated form) is placed in the spedficity pocket with the C and NH of Lys-15 in similar positions to those of tryptophan in the formyl-L-tryptophan-chymotrypsin complex, the residues on the AT-terminal side of lysine then form an antiparallel jS-structure with the enzyme similar to that proposed for y-chymostrypsin (1). There appear to be a number of favourable hydro-... 

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