E. coli YgjD(E12A)-YeaZ heterodimer in complex with ATP
Classification:
TRANSFERASE
Technique:
X-Ray Diffraction
Resolution:
2.33
R value free:
0.253
R value observed:
0.205
R value work:
0.202
Abstract of the PDB Structure's related Publication:
The essential and universal N(6)-threonylcarbamoyladenosine (t(6)A) modification at position 37 of ANN-decoding tRNAs plays a pivotal role in translational fidelity through enhancement of the cognate codon recognition and stabilization of the codon-anticodon interaction. In Escherichia coli, the YgjD (TsaD), YeaZ (TsaB), YjeE (TsaE) and YrdC (TsaC) proteins are necessary and sufficient for the in vitro biosynthesis of t(6)A, using tRNA, ATP, L-threonine and bicarbonate as substrates. YrdC synthesizes the short-lived L-threonylcarbamoyladenylate (TCA), and YgjD, YeaZ and YjeE cooperate to transfer the L-threonylcarbamoyl-moiety from TCA onto adenosine at position 37 of substrate tRNA. We determined the crystal structure of the heterodimer YgjD-YeaZ at 2.3 Å, revealing the presence of an unexpected molecule of ADP bound at an atypical site situated at the YgjD-YeaZ interface. We further showed that the ATPase activity of YjeE is strongly activated by the YgjD-YeaZ heterodimer. We established by binding experiments and SAXS data analysis that YgjD-YeaZ and YjeE form a compact ternary complex only in presence of ATP. The formation of the ternary YgjD-YeaZ-YjeE complex is required for the in vitro biosynthesis of t(6)A but not its ATPase activity.
TsaD, the ortholog of eukaryal/archaeal Kae1, is a weak ATPase (produces ADP) and binds A37-containing tRNA. TsaD forms an essential interaction network with TsaB (YeaZ, a paralog of TsaD) and TsaE (YjeE) proteins. Together with TsaC (multiprotein complex), ATP, threonine and bicarbonate as cofactors, they catalyze the in vitro formation of t6A (threonyl-carbamoylation) at position 37 of bacterial tRNA decoding ANN codons (ile, Met, Thr, Lys, Asn, Ser and Arg).