Catalyzes the initial reaction in intramitochondrial fatty acid synthesis, by activating malonate and methylmalonate, but not acetate, into their respective CoA thioester. May have some preference toward very-long-chain substrates. ATP + CoA + tetracosanoate = AMP + diphosphate + tetracosanoyl-CoA ATP + CoA + malonate = AMP + diphosphate + malonyl-CoA Belongs to the ATP-dependent AMP-binding enzyme family.