Comments on the recent crystal structure of TsaBDE complex of bacterial t6A biosynthesis system and its significance for understanding TC-AMP processing.

The N(6)-threonylcarbamoyl adenosine (t6A) modification at position 37 of a tRNA of the anticodon loop is universal and central to the translational fidelity of all known organisms. The ternary complex of TsaBDE is the central and essential workstation for t6A biosynthesis in bacteria. The recently published crystal structure of Thermotoga maritima (T.maritima) TsaBDE complex (Missoury et al., 2018) has ~15% incorrectly-placed, misplaced/mistraced, or missing residues. These structural errors have precipitated incorrect conclusions about the disordering of the active site and inferred action of the TsaE element. In this report, we rectify the published structural model of the T.maritima TsaBDE complex. In stark contrast, a corrected structural model of TsaBDE shows that both active sites of the TsaD element are fully occupied with threonylcarbamoyladenosine (TC-AMP), an unstable intermediate chemical moiety of the t6A biosynthesis pathway. This observation has profound implications for understanding the funneling of intermediates in the t6A pathway and also in helping to elucidate tRNA binding modes. Based on the structural details described in here we propose a unifying principle for binding the tRNA to the TsaD subunit of the complex which is universally required in all known t6A modification pathways.