Plays a major role in biotin-dependent carboxylase biotinylation (PubMed:18156294). Catalyzes the addition of biotin to the biotin carboxyl carrier protein (BCCP) subunit of acetyl-CoA carboxylase (PubMed:9173880, PubMed:9874227, PubMed:18156294). Can also biotinylate methylcrotonyl-CoA carboxylase (PubMed:9874227, PubMed:18156294). Is responsible for most, if not all, biotin--protein ligase activity in Arabidopsis (PubMed:18156294). Is essential for plant viability and required for ovule development (PubMed:18156294). 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] Expressed in roots, leaves, stems, flowers, siliques and seeds. Embryonic lethality when homozygous due to aborted ovules that had not been fertilized. The alternative splicing of the 5'UTR of HCS1 mRNA controls the dual targeting of HCS1 protein through alternative use of distinct initiation codons. A small ORF (uORF24) located in the HCS1 mRNA 5'UTR is essential for the AUG choice. The presence of uORF24 favors the synthesis of a short protein form initiated at the second AUG, which consequently localizes in the cytosol. In the absence of uORF24, the translation initiation begins at the first AUG, allowing the production of a HCS1 protein headed by a transit peptide. Belongs to the biotin--protein ligase family.