8IE2

Crystal structure of Lactiplantibacillus plantarum GlyRS

Summary for 8IE2

• Entry DOI: 10.2210/pdb8ie2/pdb
• Descriptor: Glycine--tRNA ligase alpha subunit, Glycine--tRNA ligase beta subunit (2 entities in total)
• Functional Keywords: aminoacyl-trna synthetase, transferase, ligase
• Biological source: Lactiplantibacillus plantarum WCFS1; More
• Total number of polymer chains: 8
• Total formula weight: 453450.42

Authors

Yamashita, S.,Tomita, K. (deposition date: 2023-02-15, release date: 2023-06-07, Last modification date: 2023-09-13)

Primary citation

Nagato, Y.,Yamashita, S.,Ohashi, A.,Furukawa, H.,Takai, K.,Tomita, K.,Tomikawa, C.
Mechanism of tRNA recognition by heterotetrameric glycyl-tRNA synthetase from lactic acid bacteria.
J.Biochem., 174:291-303, 2023

PubMed Abstract: Glycyl-tRNA synthetases (GlyRSs) have different oligomeric structures depending on the organisms. While a dimeric α2 GlyRS species is present in archaea, eukaryotes and some eubacteria, a heterotetrameric α2β2 GlyRS species is found in most eubacteria. Here, we present the crystal structure of heterotetrameric α2β2 GlyRS, consisting of the full-length α and β subunits, from Lactobacillus plantarum (LpGlyRS), gram-positive lactic bacteria. The α2β2LpGlyRS adopts the same X-shaped structure as the recently reported Escherichia coli α2β2 GlyRS. A tRNA docking model onto LpGlyRS suggests that the α and β subunits of LpGlyRS together recognize the L-shaped tRNA structure. The α and β subunits of LpGlyRS together interact with the 3'-end and the acceptor region of tRNAGly, and the C-terminal domain of the β subunit interacts with the anticodon region of tRNAGly. The biochemical analysis using tRNA variants showed that in addition to the previously defined determinants G1C72 and C2G71 base pairs, C35, C36 and U73 in eubacterial tRNAGly, the identification of bases at positions 4 and 69 in tRNAGly is required for efficient glycylation by LpGlyRS. In this case, the combination of a purine base at Position 4 and a pyrimidine base at Position 69 in tRNAGly is preferred.

PubMed: 37261968
DOI: 10.1093/jb/mvad043

Experimental method

X-RAY DIFFRACTION (3.6 Å)