4WQ4

E. coli YgjD(E12A)-YeaZ heterodimer in complex with ATP

Summary for 4WQ4

• Entry DOI: 10.2210/pdb4wq4/pdb
• Descriptor: tRNA N6-adenosine threonylcarbamoyltransferase, tRNA threonylcarbamoyladenosine biosynthesis protein TsaB, FE (III) ION, ... (8 entities in total)
• Functional Keywords: heterodimer, ygjd-yeaz, glu12ala, t6a, transferase
• Biological source: Escherichia coli; More
• Cellular location: Cytoplasm : P05852 P76256
• Total number of polymer chains: 4
• Total formula weight: 127258.15

Authors

Zhang, W.,Collinet, B. (deposition date: 2014-10-21, release date: 2015-01-28, Last modification date: 2024-11-06)

Primary citation

Zhang, W.,Collinet, B.,Perrochia, L.,Durand, D.,van Tilbeurgh, H.
The ATP-mediated formation of the YgjD-YeaZ-YjeE complex is required for the biosynthesis of tRNA t6A in Escherichia coli.
Nucleic Acids Res., 43:1804-1817, 2015

PubMed Abstract: 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.

PubMed: 25578970
DOI: 10.1093/nar/gku1397

Experimental method

X-RAY DIFFRACTION (2.33 Å)