Serine proteases, calcium binding

Figure 4.6 Hydrogen bonding in functional nests (a) oxyanion hole in serine protease binding the substrate tetrahedral intermediate, (b) P-loop showing the p-phosphate (middle phosphate residue) of GTP bound to a compound nest, (c) Ca2+ binding in calmodulin. The calcium is bound to three carboxylate oxygen atoms which are in turn bound to bound to a five-amide compound nest (d) the cysteine-bound Fe2 unit in spinach ferredoxin.

The subtilisins are a large family of serine proteases that have been extensively studied because of their importance in the detergent industry. The retain a common conserved fold and identical active site residues (Fig. 10). Two conserved calcium-binding sites are present in all subtilisins, and additional sites may be present in subtilisins from different organisms (Siezen and Leunissen, 1997). 

A protein S, the cofactor of activated protein C, has four EGF-like modules in tandem. The stracture of N-terminal EGF modules is very similar to that of non-calcium-binding modules. Calcium binding only results in a limited local conformational change. The N-terminal loop is better defined and moves toward the major /3-sheet. The N-terminal non-catalytic Gla and EGF-like domains provide coagulation serine proteases with different calcium affinities for certain biological membranes, and also mediate protein-protein interactions. ... 

The TRADD or FADD domains bind to adapter proteins in the cytosol and together they form of a death inducing signaling complex (DISC). This complex recruits caspase-8, one of a family of calcium ion-activated serine proteases (caspases) which cleave polypeptides on the C-terminal side of their aspartate residues. DISC activates caspase-8 to activate a Bcl-2 activator, BID (Fig. 13.1 Oa). The resultant tBid fragment activates effector Bcl-2 proteins on the endoplasmic reticular membrane and mitochondrial outer membrane. 

The Gla-containing proteins of the blood coagulation system are all modular with the Gla-domain N terminal. Factors VII, IX, and X and protein C form a group with the same domain structure. The Gla domain is followed by two EGF-like domains, of which the first one also binds calcium (see Section IV.C), and a serine protease domain, also with a calcium-binding site (see Section IV.D). Prothrombin and protein S have somewhat different domain structures (145, 146). In prothrombin the Gla domain is followed by a hexapeptide with a disulfide loop, two kringle domains, and the C-terminal serine protease domain. In protein S the Gla domain is followed by the thrombin-sensitive loop, four EGF-like domains, and the C-terminal domain that is homologous to plasma steroid hormone-binding proteins. 

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