7YSE

Crystal structure of E. coli heterotetrameric GlyRS in complex with tRNA

Summary for 7YSE

• Entry DOI: 10.2210/pdb7yse/pdb
• Descriptor: Glycine--tRNA ligase alpha subunit, Glycine--tRNA ligase beta subunit, RNA (76-MER), ... (6 entities in total)
• Functional Keywords: aminoacyl-trna synthetase, hetertetramer, drug target, protein-trna complex, transferase, transferase-rna complex, transferase/rna
• Biological source: Escherichia coli K-12; More
• Total number of polymer chains: 6
• Total formula weight: 275554.86

Authors

Han, L.,Ju, Y.,Zhou, H. (deposition date: 2022-08-12, release date: 2023-02-01, Last modification date: 2023-11-29)

Primary citation

Han, L.,Luo, Z.,Ju, Y.,Chen, B.,Zou, T.,Wang, J.,Xu, J.,Gu, Q.,Yang, X.L.,Schimmel, P.,Zhou, H.
The binding mode of orphan glycyl-tRNA synthetase with tRNA supports the synthetase classification and reveals large domain movements.
Sci Adv, 9:eadf1027-eadf1027, 2023

PubMed Abstract: As a class of essential enzymes in protein translation, aminoacyl-transfer RNA (tRNA) synthetases (aaRSs) are organized into two classes of 10 enzymes each, based on two conserved active site architectures. The (αβ) glycyl-tRNA synthetase (GlyRS) in many bacteria is an orphan aaRS whose sequence and unprecedented X-shaped structure are distinct from those of all other aaRSs, including many other bacterial and all eukaryotic GlyRSs. Here, we report a cocrystal structure to elucidate how the orphan GlyRS kingdom specifically recognizes its substrate tRNA. This structure is sharply different from those of other aaRS-tRNA complexes but conforms to the clash-free, cross-class aaRS-tRNA docking found with conventional structures and reinforces the class-reconstruction paradigm. In addition, noteworthy, the X shape of orphan GlyRS is condensed with the largest known spatial rearrangement needed by aaRSs to capture tRNAs, which suggests potential nonactive site targets for aaRS-directed antibiotics, instead of less differentiated hard-to-drug active site locations.

PubMed: 36753552
DOI: 10.1126/sciadv.adf1027

Experimental method

X-RAY DIFFRACTION (2.907 Å)