Serine protease structure

Kraut, J. Serine proteases structure and mechanism of catalysis. Anna. Rev. Biochem. 46 331-358, 1977. 

Kraut, J. (1977) Serine Proteases Structure and Mechanism of Catalysis Ann, Rev. Biochem 46 331-358... 

JF Bazan, RJ Fletterick. Viral cysteine proteases are homologous to the trypsin-like family of serine proteases structural and functional implications. Proc Natl Acad Sci (USA) 85 7872-7876, 1988. 

Kraut J (1977) Serine proteases Structure and mechanism of catalysis. Annu Rev Biochem 46 331... 

J. Kraut, Annu. Rev. Biochem., 46, 331 (1977). Serine Proteases Structure and Mechanism... 

Grtitter, M.G., et al. Crystal structure of the thrombin-hirudin complex a novel mode of serine protease inhibition. EMBO J. 9 2361-2365, 1990. 

James, M.N.G., et al. Structures of product and inhibitor complexes of Streptomyces griseus protease A at 1.8 A resolution. A model for serine protease catalysis. 

Smith, S.O., et al. Crystal versus solution structures of enzymes NMR spectroscopy of a crystalline serine protease. Science 244 961-964, 1989. 

Sprang, S., et al. The three-dimensional structure of Asn ° mutant of trypsin role of Asp ° in serine protease catalysis. Science 237 905-909, 1987. 

Figure 16.21 Structure of one subunit of the core protein of Slndbls virus. The protein has a similar fold to chymotrypsin and other serine proteases, comprising two Greek key motifs separated by an active site cleft. The C-terminus of the protein is bound in the catalytic site, making the coat protein inactive (Adapted from S. Lee et al., Structure 4 531-541, 1996.)...

Until recently, the catalytic role of Asp ° in trypsin and the other serine proteases had been surmised on the basis of its proximity to His in structures obtained from X-ray diffraction studies, but it had never been demonstrated with certainty in physical or chemical studies. As can be seen in Figure 16.17, Asp ° is buried at the active site and is normally inaccessible to chemical modifying reagents. In 1987, however, Charles Craik, William Rutter, and their colleagues used site-directed mutagenesis (see Chapter 13) to prepare a mutant trypsin with an asparagine in place of Asp °. This mutant trypsin possessed a hydrolytic activity with ester substrates only 1/10,000 that of native trypsin, demonstrating that Asp ° is indeed essential for catalysis and that its ability to immobilize and orient His is crucial to the function of the catalytic triad. 

X-ray crystallographic studies of serine protease complexes with transition-state analogs have shown how chymotrypsin stabilizes the tetrahedral oxyanion transition states (structures (c) and (g) in Figure 16.24) of the protease reaction. The amide nitrogens of Ser and Gly form an oxyanion hole in which the substrate carbonyl oxygen is hydrogen-bonded to the amide N-H groups. 

A beta barrel is a three-dimensional protein fold motif in which beta strands connected by loops form a barrellike structure. For example, this fold motif is found in many proteins of the immunoglobulin family and of the chymotrypsin family of serine proteases. 

The elucidation of the X-ray structure of chymotrypsin (Ref. 1) and in a later stage of subtilisin (Ref. 2) revealed an active site with three crucial groups (Fig. 7.1)-the active serine, a neighboring histidine, and a buried aspartic acid. These three residues are frequently called the catalytic triad, and are designated here as Aspc Hisc Serc (where c indicates a catalytic residue). The identification of the location of the active-site groups and intense biochemical studies led to several mechanistic proposals for the action of serine proteases (see, for example, Refs. 1 and 2). However, it appears that without some way of translating the structural information to reaction-potential surfaces it is hard to discriminate between different alternative mechanisms. Thus it is instructive to use the procedure introduced in previous chapters and to examine the feasibility of different... 

FIGURE 7.3. The force fields for the three resonance structures that describe mechanism a for the catalytic reaction of serine proteases. 

Acylation reaction, 171 Alanine, structure of, 110 Alcohol dehydrogenase, 205 Amide hydrolysis, see also Serine proteases Trypsin... 

SCF, see Self-consistent field treatment (SCF) Schroedinger equation, 2,4,74 Secular equations, 6,10, 52 solution by matrix diagonalization, 11 computer program for, 31-33 Self-consistent field treatment (SCF), of molecular orbitals, 28 Serine, structure of, 110 Serine proteases, 170-188. See also Subtilisin Trypsin enzyme family comparison of mechanisms for, 182-184, 183... 

Lin C, Lin K, Luong YP, Rao BG, Wei YY, Brennan DL, Fulghum JR, Hsiao HM, Ma S, Maxwell JP, Cottrell KM, Pemi RB, Gates CA, Kwong AD (2004) In vitro resistance studies of hepatitis C virus serine protease inhibitors, VX-950 and BILN 2061 structural analysis indicates different resistance mechanisms. J Biol Chem 279 17508-17514... 

Structural analysis of the rhinovirus and the hepatitis A virus 3C proteases (Allaire et al. 1994 Matthews et al. 1994) confirmed earlier predictions that the picomavirus 3C proteases are similar to chymotrypsin-Uke serine proteases in their fold. An important difference is that the serine nucleophile of serine proteases is replaced with a cysteine however, the 3C protease is stracturally distinct from the eukaryotic cysteine protease class of enzymes. 

Tong L, Qian C, Massariol MJ, Bonneau PR, Cordingley MG, Lagace L (1996) A new serine-protease fold revealed by the crystal structure of human cytomegalovirus protease. Nature 383 272-275... 

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