The 3C proteases of the encephalomyocarditis virus and the hepatitis A virus are both type III substrates for the mammalian ubiquitin-protein ligase E3␣. The conjugation of ubiquitin to these proteins requires internal ten-amino acid-long protein destruction signal sequences. To evaluate how these destruction signals modulate interactions that must occur between E3␣ and the 3C proteases, we have kinetically analyzed the formation of ubiquitin-3C protease conjugates in a reconstituted system of purified E1, HsUbc2b/E2 14Kb , and human E3␣. Our measurements show that the encephalomyocarditis virus 3C protease is ubiquitinated in this system with K m ؍ 42 ؎ 11 M and V max ؍ 0.051 ؎ 0.01 pmol/min whereas the parameters for the ubiquitination of the hepatitis A virus 3C protease are K m ؍ 20 ؎ 5 M and V max ؍ 0.018 ؎ 0.003 pmol/min. Mutations in the destruction signal sequences resulted in changes in the rate at which E3␣ conjugates ubiquitin to the altered 3C protease proteins. The K m and V max values for these reactions change proportionally in the same direction. These results suggest differences in rates of conjugation of ubiquitin to 3C proteases are primarily a k cat effect. Replacing specific encephalomyocarditis virus 3C protease lysine residues with arginine residues was found to increase, rather than decrease, the rate of ubiquitin conjugation, and the K m and V max values for these reactions are both higher than for the wild type protein. The ability of E3␣ to catalyze the conjugation of ubiquitin to both 3C proteases was found to be inhibited by lysylalanine and phenylalanylalanine, demonstrating that the same sites on E3␣ that bind destabilizing N-terminal amino acids in type I and II substrates also interact with the 3C proteases.The selection of proteins for destruction by the ubiquitin 26 S/proteasome pathway depends upon specific interactions that occur between the targeted substrates and enzymes involved in the formation of the ubiquitin-target protein conjugates. A hierarchical family of pathways, each composed of at least three enzymes, accomplishes the attachment of ubiquitin to proteins destined to be degraded (1-3). Common to all of these pathways is the ubiquitin-activating enzyme, E1, 1 which recruits free ubiquitin through the ATP-dependent formation of a thiolester bond between a cysteine in the E1 and the C-terminal glycine of the ubiquitin molecule. This ubiquitin is then transferred to one of several members of the E2 family of proteins that are referred to as ubiquitin carrier proteins or ubiquitin-conjugating enzymes. Finally, the ubiquitin is transferred from the E2 to the target substrate protein through the action of an ubiquitin-protein ligase, or E3. Although each E2 protein appears to function with several specific ubiquitinprotein ligases, each E3 can specifically interact with only a limited number of substrate proteins. Regardless of the E3 involved in the ubiquitination process, following the conjugation of the first ubiquitin molecule to a primary amine on the subst...