Serine proteinase family

Studies of proteinase activities comprise some of the most important current research efforts in the field of theoretical enzyme mechanisms. Results from crystallography and kinetics in the 70 s and 80 s paved the way for such theoretical studies, mainly of the serine proteinase family. Such studies are extending nowadays, as more structures of proteinases are solved with high resolution and more detailed kinetic studies are conducted. But, while earlier structural results were available for the native structures alone, recent crystallographic evidence is available for complexes with peptide analogs, with intermediate analogs and with mutant enzymes. When these structural studies are coupled with results of kinetic research, a large database is formed for the theoretician to consider as a basis for construction, simulation and analysis by computer models. 

Comparative studies on homologous proteins show a high conservation of the structural fold and constellation of amino acid side chains at the active site. The best example is that of the serine proteinase family of trypsin, chymotrypsin, elastase and protease A from Streptomyces griseus (see, for example, reference 97) (Fig. 10). 

The serine proteinases all have the same substrate, namely, polypeptide chains of proteins. However, different members of the family preferentially cleave polypeptide chains at sites adjacent to different amino acid residues. The structural basis for this preference lies in the side chains that line the substrate specificity pocket in the different enzymes. 

Lesk, A. M., and Fordham, W. D., 1996. Conservation and variability in the structures of serine proteinases of die chymotrypsin family. Journal of Molecular Biology 258 501—537. 

Proteinase-activated recqrtors (PARs) are a unique family of G-protein-coupled receptors (GPCRs) that are activated in response to serine proteinases. There are four PAR family members PAR-1 through to PAR-4. PAR-1 and PAR-3 respond to thrombin, PAR-2 responds to trypsin, whilst PAR-4 is sensitive to both thrombin- and trypsin-related proteinases. 

A tethered ligand is the new N-terminal formed following serine proteinase-mediated cleavage of the original N-terminal of a PAR family member, which is responsible for activation of the receptor. 

Based on their sequence homology, disulfide connectivity, and cysteine location within the sequence and chemistry of the reactive site. Pis can be assigned to distinct families, as classified by Laskowski and Kato. Kunitz-type, Bowman—Birk-type, Potato type I and type II, and squash inhibitors are members of these families shown in Table 3. For inhibitors not falling into these classifications more families have been proposed. Pis can also be classified by their target/mode of action. Plants have been found to express Pis that target serine proteinases, cysteine proteinases, aspartic proteinases, and metallo-proteinases. Serine and cysteine protease inhibitors are the best-studied PIs. ... 

Brazzein is another small sweet-tasting protein whose solution structure has been recently solved by NMR. Brazzein tastes 2000 times sweeter than sucrose on a weight basis and is exceptionally thermostable. As indicated by NMR, the structure of this 54 residue, single-chain polypeptide does not change between 32 and 82 °C and retains its sweetness after incubation at 98 °C for two hours.Brazzein contains one a-helix and three strands of antiparallel jd-sheet stabilized by four intramolecular disulphide bonds. It has been proposed that the disulphide bonds could be responsible for the thermostability of brazzein by forming a compact structure at the tertiary level.The structure of brazzein does not resemble that of the other two sweet proteins with known structures, monellin and thaumatin, whereas sequence alignment and structural prediction indicate that brazzein shares the fold of a newly identified family of serine proteinase inhibitors. 

Glutamyl endopeptidase [EC 3.4.21.19] (also known as staphylococcal serine proteinase, V8 proteinase, protease V8, and endoproteinase Glu-C), a member of the peptidase family S2B, catalyzes the hydrolysis of Asp-Xaa and Glu-Xaa peptide bonds. In appropriate buffers, the specificity of the bond cleavage is restricted to Glu-Xaa. Peptide bonds involving bulky side chains of hydrophobic aminoacyl residues are hydrolyzed at a lower rate. 

This enzyme [EC 3.4.21.53], also known as endopepti-dase La, ATP-dependent serine proteinase, and ATP-dependent protease La, catalyzes the hydrolysis of peptide bonds in large proteins (for example, globin, casein, and denaturated serum albumin) in the presence of ATP (which is hydrolyzed to ADP and orthophosphate). Vanadate ion inhibits both reactions. A similar enzyme occurs in animal mitochondria. Protease La belongs to the peptidase family S16. 

Members of both structural families of serine proteinases, the trypsinlike and the subtilisin-like, have been found to bind Ca " (references in Tables 1 and II). The role of Ca " in all of these proteolytic enzymes appears to be one of stabilization of structure and/or maintenance of... 

Siezen, R. J.,de Vos, W. M.,Leunisen, J. A. Dijkstra,B. W. (1991). Homology modelling and protein engineering strategy of subtilases, the family of subtilisin-like serine proteinases. Protein Engineering, 4, 719-37. 

AE Gorbalenya, VM Blinov, AP Donchenko. Poliovirus-encoded proteinase 3C a possible evolutionary link between cellular serine and cysteine proteinase families. FEBS Lett 194 253-257, 1986. 

In subtilisin, a representative of the second family of serine proteinases, the relative dispositions of Asp and His are in some contrast to those described above (Fig. 5C). The plane of the carboxyl group of the catalytic Asp is now rotated with respect to the imidazole in a direction opposite to the one observed in RmL and trypsin 081 (which accepts an H-bond from N81 of the catalytic His) is now stabilized by an additional H-bond donated by the main-chain amide of Thr-33. 

The earliest observation that implied evolutionary links between all lipases was that of the consensus pentapeptide G-X-S-X-G, subsequently shown to contain the nucleophilic serine. The apparent similarity of this sequence to that found around the active serine in the chy-motrypsin and subtilisin families of serine proteinases prompted a number of authors to infer an evolutionary relationship between the three families. Further evidence in support of such a link came from secondary structure prediction studies indicating that the nucleophilic serine in a lipase is most likely within a /3 turn, structurally reminiscent of proteinases (Reddy et ai, 1986). In fact, one of the commonly used phrases found in introductions to many papers dealing directly or indirectly with lipases refers to the consensus G-X-S-X-G pentapeptide found in the active site of all serine proteinases and esterases. We now know that the implication that homology and/or structural similarities exist between the enzymes belonging to these diverse groups is incorrect. The matter has been dealt with in the literature (Derewenda and Derewenda, 1991 Liao et ai, 1992), but it seems appropriate to review some of the conclusions. 

We are now returning to the recurring issue of possible evolutionary links between lipases and serine proteinases. We already know that detailed comparisons ruled out any homology between the two families of... 

In cysteine proteinases (CP), activity depends upon a cysteine thiol group. Papain, actinidin, and a few lysosomal cathepsins are the best known members of this family. They hydrolyze peptides and esters in a generally similar fashion to serine proteinases. Two residues are directly involved in the catalytic process, Cys and His, with apparent pKa values of 4.2 and 8.6, respectively. This is the reverse of their normal pKa order, with His being more acidic than Cys. A bell-shaped relation of activity vs. pH for papain is spread out, with maximal activity around pH=6.5 and about half of the activity is retained near 4.5 and 8.5, dropping fast below and above these values. Thus, the active species has a zwitterion state, with a cysteine anion (thiolate) and a histidine cation. CP were discussed in a few reviews (Baker and Drenth, 1987 Fersht, 1985 Polgar and Halasz, 1982)... 

Encron rizolipasc. endogenous pyrogen > interleukin-1. ENDOPEPTIDASE INHIBITORS act at one or other of the endopeptidase enzymes that cleave the C-terminal residue from oligopeptides or proteins (thus are stricdy proteinases). They can be divided into classes on the basis of their functional characteristics. These classes are dealt with separately in terms of their alternate names, notable substrates and inhibitors. They often act along with ectopeptidases - the carboxypeptidases and amino-peptidases. Endopeptidase inhibitors contain members of the metalloproteinase and serine protease families. Some are important neuropeptidases - concerned with degradation of... 

CHAPTER 36, FIGURE 7 A group of structurally similar protein inhibitors of the serine proteinases known as SERPINS (SERine Proteinase INhibitors). The structure shown is human antithrombin. The reference SERPIN, a j-proteinase inhibitor or a. -antitrypsin contains -30% a helix (9 helices) and 40% sheet (5 3 sheets). Other members of the SERPIN family contain both additional helices and p sheets. The reactive center loop of antithrombin, residues 378-396, contains the reactive site residues Arg and Ser . Upon reaction with the target proteinase or after cleavage by the target proteinase (a reaction that inactivates the inhibitor without inactivating the proteinase), the reactive center loop folds between the S3 and S5 sheets. 

Human leukocyte elastase inhibitors. HLE belongs to the chymotrypsin family of serine proteinases the enzyme consists of a single polypeptide chain of 218 amino acid residues and four disulfide bridges. HLE has been proposed to be a primary mediator of many pulmonary disorders such as em-... 

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