We have recently reported an in vitro-evolved precursor tRNA (pre-tRNA) that is able to catalyze aminoacylation on its own 3′-hydroxyl group. This catalytic pre-tRNA is susceptible to RNase P RNA, generating the 5′-leader ribozyme and mature tRNA. The 5′-leader ribozyme is also capable of aminoacylating the tRNA in trans, thus acting as an aminoacyl-tRNA synthetase-like ribozyme (ARS-like ribozyme). Here we report its structural characterization that reveals the essential catalytic core. The ribozyme consists of three stem-loops connected by two junction regions. The chemical probing analyses show that a U-rich region (U59–U62 in J2a/3 and U67–U68 in L3) of the ribozyme is responsible for the recognition of the phenylalanine substrate. Moreover, a GGU-motif (G70–U72) of the ribozyme, adjacent to the U-rich region, forms base pairs with the tRNA 3′ terminus. Our demonstration shows that simple RNA motifs can recognize both the amino acid and tRNA simultaneously, thus aminoacylating the 3′ terminus of tRNA in trans.