Lipoyl amidotransferase that catalyzes the transfer of lipoyl moieties from lipoyl-protein H of the glycine cleavage system (lipoyl- GCSH) to E2 subunits of the pyruvate dehydrogenase complex (PDCE2) (PubMed:29987032). Unable to catalyze the transfer of octanoyl from octanoyl-GCSH to PDCE2 (PubMed:29987032). In vitro, it is also able to catalyze the transfer of the lipoyl group from lipoyl-AMP to the specific lysine residue of lipoyl domains of lipoate-dependent enzymes but this reaction may not be physiologically relevant (Probable). . This is the function of LIPT1 (lipoyltransferase 1, Ensembl gene identifier ENSG00000144182).