Hydrogen bonding thermolysin

Chemical reactivity and hydrogen bonding 320 Proton-transfer behaviour 321 Intramolecular hydrogen-bond catalysis 344 Enzyme catalysis and hydrogen bonding 354 Chymotrypsin 354 Thermolysin 355 Carboxypeptidase 355 Tyrosyl tRNA synthetase 356 Summary 366 Acknowledgements 367 References 367... 

In both carboxypeptidase A and thermolysin the active site Zn2+ is chelated by two imidazole groups and a glutamate side chain (Fig. 12-16). In carboxypeptidase A, Arg 145, Tyr 248, and perhaps Arg 127 form hydrogen bonds to the substrate. A water molecule is also bound to the Zn2+ ion. The presence of the positively charged side chain of Arg 145 and of a hydro-phobic pocket accounts for the preference of the enzyme for C-terminal amino acids with bulky, nonpolar side chains. The Zn2+ in thermolysin is also bound to two imidazole groups and that in D-alanyl-D-alanyl carboxypeptidase to three. 

M. D. Ballinger, I. D. Zipkin, and P. A. Bartlett, Differential binding energy a detailed evaluation of the influence of hydrogen-bonding and hydrophobic groups on the inhibition of thermolysin by phosphorus-containing inhibitors,... 

Soc., 113,297 (1991). Differential Binding Energy A Detailed Evaluation of the Influence of Hydrogen Bonding and Hydrophobic Groups on the Inhibition of Thermolysin by Phosphorus-Containing Inhibitors. 

The structure of thermolysin-inhibitor complexes has shown the presence of a deep PI specificity pocket and the details of hydrogen bonding between enzyme and inhibitor [28]. Side-chain atoms of the enzyme are involved in interaction with the inhibitor amides and the inhibitor conformation is such that the subsites PI and P2 both point into the enzyme core (Rg-9). 

Figure 10. Comparison of the details of inhibitor binding in the two families superposition of the catalytic centers of collagenase (Fig. 6) and thermolysin (Fig. 9). The catalytic zinc atom is shown as a cyan sphere, with the collagenase-in-hibitor complex in yellow and the thermolysin complex shown in magenta. Thin cylinders denote putative hydrogen bonds. The green sphere shows the location of a structural calcium atom observed in collagenase. For clarity, only the alpha-carbon atoms of the proteins are shown. The differences in the relative oreintation of the subsites are evident.

Nice isosteric variations were observed in a series of thermolysin inhibitors. For these isosteres the replacement of the phosphonamide (X = NH) function by a phos-phonate (X = O) or a phosphinate (X = CH2) fnnction demonstrated clearly that the maximal activity was associated with the phosphonamide which is able to establish a hydrogen bond with alanine 113 (Figure 15.6). 

An analysis of phosphonamidate and phosphonate transition-state analogs for the thermolysin reaction was reported (95, 96) and the data were interpreted to suggest that one hydrogen bond could contribute 4 kcal/mol binding to stabilize the formation of the tetrahedral transition state. A reevaluation was re-... 

A wide range of metal ions is present in metalloenzymes as cofactors. Copper zinc snperoxide dismntase is a metalloenzyme that nses copper and zinc to help catalyze the conversion of snperoxide anion to molecnlar oxygen and hydrogen peroxide. Thermolysin is a protease that nses a tightly bonnd zinc ion to activate a water atom, which then attacks a peptide bond. Aconitase is one of the enzymes of the citric acid cycle it contains several iron atoms bonnd in the form of iron-sulfur clusters, which participate directly in the isomerization of citrate to isocitrate. Other metal ions fonnd as cofactors in metalloenzymes include molybdenum (in nitrate rednctase), seleninm (in glutathione peroxidase), nickel (in urease), and vanadinm (in fungal chloroperoxidase). see also Catalysis and Catalysts Coenzymes Denaturation Enzymes Krebs Cycle. 

---