Enzyme activated chain segment

In the course of activation, chain segment 187-194 is rotated by 180°, bringing the catalytic amino acids to within 0.3 nm of the surface of the molecule. Substrate hydrolysis involves formation of an acyl-enzyme intermediate between the acid group of the peptide substrate and the hydroxyl of the Serjgs. The strongly nucleophilic character of this hydroxyl is due to the neighboring proton donor (or acceptor) His,. The effect is amplified by Asp Q (see Charge relay system). 

There are two multifimctional proteins in the pathway for de novo biosynthesis of pyrimidine nucleotides. A trifunctional protein, called dihydroorotate synthetase (or CAD, where the letters are the initials of the three enzymic activities), catalyzes reactions 1, 2, and 3 of the pathway (HCOj" — CAP — CA-asp — DHO in Fig. 14-17). The activities of carbamoyl phosphate synthetase, aspartate transcarbamoylase, and dihydroorotase are contained in discrete globular domains of a single polypeptide chain of 243 kDa, where they are covalently connected by segments of polypeptide which are susceptible to digestion by proteases such as trypsin. 

Figure 26.9 X-ray crystal structure of citrate synthase. Part (a) is a space-filling model and part (b) is a ribbon model, which emphasizes the a-helical segments of the protein chain and indicates that the enzyme is dimeric that is, it consists of two identical chains held together by hydrogen bonds and other intermolecular attractions. Part (cl is a close-up of the active site in which oxaloacetate and an unreactive acetyl CoA mimic are bound.

DNA polymerase I is a nonessential enzyme, since viable E. coli mutants lack it (pol A). This conclusion is complicated, however, since the enzyme catalyzes three separate chemical reactions. It polymerizes deoxyribonucleoside triphosphates, and it has two exonucleolytic activities, a 3 to 5 activity and a 5 to 3 activity. The pol A - mutants lack only the polymerization activity. Other mutants lacking both the polymerase and the 5 to 3 exonuclease activity are lethal. Thus the exonuclease function is the more important one. This fits with the role of this enzyme in removing damaged DNA segments (DNA repair) and in removing covalently attached RNA from DNA chains. We will later see that small RNAs serve as primers of DNA synthesis. 

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