Biotin--protein ligase catalyzing the biotinylation of the 4 biotin-dependent carboxylases acetyl-CoA-carboxylase, pyruvate carboxylase, propionyl-CoA carboxylase, and methylcrotonyl-CoA carboxylase. apo-[methylmalonyl-CoA:pyruvate carboxytransferase] + ATP + biotin = AMP + diphosphate + H(+) + holo-[methylmalonyl-CoA:pyruvate carboxytransferase] apo-[propionyl-CoA:carbon-dioxide ligase (ADP-forming)] + ATP + biotin = AMP + diphosphate + H(+) + holo-[propionyl-CoA:carbon-dioxide ligase (ADP-forming)] apo-[3-methylcrotonoyl-CoA:carbon-dioxide ligase (ADP-forming)] + ATP + biotin = AMP + diphosphate + H(+) + holo-[3-methylcrotonoyl-CoA:carbon-dioxide ligase (ADP-forming)] ATP + biotin + L-lysyl-[protein] = AMP + diphosphate + H(+) + N(6)-biotinyl-L-lysyl-[protein] Monomer. Belongs to the biotin--protein ligase family.