Protein folding mechanisms homologous proteins

Cirilli et al.11171 cloned the gene of diaminopimelate epimerase from Haemophilus influenzae, and purified and crystallized the enzyme. The enzyme is monomeric and has a unique protein fold, in which the amino terminal and carboxyl terminal halves of the molecule fold into structurally homologous and superimposable domains (Fig. 17-13). Cys 73 of the amino terminal domain is found in the disulfide linkage, at the domain interface, with Cys 217 of the carboxy terminal domain 117. Thus, it is most conceivable that these two cysteine residues stay in reduced form in the active enzyme and function as the acid and base in the mechanism. Koo and Blanchard 118 explored a number of kinetic and isotope approaches to clarify the mechanism of the enzyme. However, which of the two cysteine residues is responsible for proton abstraction from the two enantiomeric Ca-H bonds is not yet known. 

Hen egg white lysozyme is a small protein of Mr 14 500 and 129 amino acid residues. This enzyme was introduced in Chapter 1, where it was pointed out that examination of the crystal structure of the enzyme stimulated most of the solution studies. Hen egg white lysozyme has the distinction of being the first enzyme to have had its structure solved by x-ray crystallography.207 It is an atypical member of the hexosaminidase class of glycosyl transfer enzymes. It catalyzes the hydrolysis of substrates with retention of stereochemistry. T4 lysozyme was for many years thought to have the same fold and mechanism of lysozyme, despite there being no sequence homology. But it has now been found that the T4 enzyme has inversion of configuration and so operates by a different mechanism.208,209 A mechanism proposed for the enzymatic reaction was based on the structure of the... 

Cys residues in eAspAT. Only Cys-191 is conserved among mammalian and K coli AspAT. The other four Cys residues in K coli do not have any homology with the mammalian enzymes, except for Cys-82, which is found in pig c Asp AT (Table 5.4). They mutated all five Cys residues individually and in combinations, and found that all Cys mutants showed the proper function and stability.65 Thus, it is unlikely that any of the five Cys residues are involved in the folding process. There are several Cys residues found in mAspAT. Among them, Cys-166 is the only thiol group exposed in the spatial structure of the protein. Giannattasio et al.6 have proposed a hypothesis that Cys-166 in mAspAT may be involved in the import mechanism of this isozyme which must be transported into mitochondria. 

Figure4.1 Protein tyrosine phosphatase IB (2hnq (a)) and CDC25B (lcwt (b)) employ the same catalytic mechanism for hydrolysis of phosphorylated substrates but share no sequence homology and exhibit very different folds. The similarity of their binding sites can, however, be detected on the level of the interaction properties exposed to a ligand.

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