The lipoyl domain of the dihydrolipoyl acetyltransferase (E2) component of the pyruvate dehydrogenase multienzyme complex is recognized specifically by the lipoylating enzyme(s) in the cell and by the pyruvate dehydrogenase (E1) component in the parent complex. Highly conserved aspartic acid and alanine residues flank the lipoyl-lysine residue, on the N and C-terminal sides, respectively, in the sharp beta-turn in which the lipoyl-lysine residue is prominently displayed. A sub-gene encoding the lipoyl domain of the Bacillus stearothermophilus pyruvate dehydrogenase complex was subjected to mutagenesis in the vector M13mp18. Aspartic acid 41 was changed to glutamic acid (D41E), alanine (D41A) and lysine (D41K), and alanine 43 was changed to methionine (A43M), lysine (A43K) and glutamic acid (A43E). The double mutations D41KK42A and D41MA43M were also made. All mutant domains were capable of being lipoylated, apart from the D41KK42A domain where the lipoyl-lysine had been moved round the beta-turn by one position towards the N terminus. Neither the D41K nor the A43K mutants showed any doubly lipoylated domain and the single lipoyl group was found attached only to the correct lysine residue. Accurate positioning of the lipoyl-lysine in the beta-turn is thus an essential cue for lipoylation, but the conserved aspartic acid and alanine residues are not necessary for the domain to be recognized by the lipoylating enzyme(s). No biotinylation of the D41MA43M mutant domain was observed, although the sequence motif MKM is highly conserved as the biotinylation site in the structurally homologous biotinyl domain of biotin-containing enzymes. The mutations at the aspartic acid 41 position all lowered the rate of reductive acetylation of the lipoyl domain by the E1 component of the pyruvate dehydrogenase complex, as did the mutations A43E and A43K. The A43M mutant was reductively acetylated at the same rate as the wild-type domain. Thus, both the alanine and aspartic acid residues are important for recognition of the domain by E1, but there is no absolute dependence on retention of the sequence surrounding the lipoyl-lysine residue.