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TitleStructural basis of a two-step tRNA recognition mechanism for plastid glycyl-tRNA synthetase.
Journal, issue, pagesNucleic Acids Res, Vol. 51, Issue 8, Page 4000-4011, Year 2023
Publish dateMay 8, 2023
AuthorsZhaoli Yu / Zihan Wu / Ye Li / Qiang Hao / Xiaofeng Cao / Gregor M Blaha / Jinzhong Lin / Guoliang Lu /
PubMed AbstractTwo types of glycyl-tRNA synthetase (GlyRS) are known, the α2 and the α2β2 GlyRSs. Both types of synthetase employ a class II catalytic domain to aminoacylate tRNAGly. In plastids and some ...Two types of glycyl-tRNA synthetase (GlyRS) are known, the α2 and the α2β2 GlyRSs. Both types of synthetase employ a class II catalytic domain to aminoacylate tRNAGly. In plastids and some bacteria, the α and β subunits are fused and are designated as (αβ)2 GlyRSs. While the tRNA recognition and aminoacylation mechanisms are well understood for α2 GlyRSs, little is known about the mechanisms for α2β2/(αβ)2 GlyRSs. Here we describe structures of the (αβ)2 GlyRS from Oryza sativa chloroplast by itself and in complex with cognate tRNAGly. The set of structures reveals that the U-shaped β half of the synthetase selects the tRNA in a two-step manner. In the first step, the synthetase engages the elbow and the anticodon base C35 of the tRNA. In the second step, the tRNA has rotated ∼9° toward the catalytic centre. The synthetase probes the tRNA for the presence of anticodon base C36 and discriminator base C73. This intricate mechanism enables the tRNA to access the active site of the synthetase from a direction opposite to that of most other class II synthetases.
External linksNucleic Acids Res / PubMed:36912079 / PubMed Central
MethodsEM (single particle)
Resolution3.59 - 4.5 Å
Structure data

33237

7xjy

EMDB-33237, PDB-7xjy:
Cryo-EM structure of Oryza sativa plastid glycyl-tRNA synthetase (apo form)
Method: EM (single particle) / Resolution: 3.6 Å

33238

7xjz

EMDB-33238, PDB-7xjz:
Cryo-EM strucrture of Oryza sativa plastid glycyl-tRNA synthetase in complex with tRNA (tRNA binding state)
Method: EM (single particle) / Resolution: 3.9 Å

33239

7xk0

EMDB-33239, PDB-7xk0:
Cryo-EM strucrture of Oryza sativa plastid glycyl-tRNA synthetase in complex with tRNA (tRNA locked state)
Method: EM (single particle) / Resolution: 3.59 Å

33240

7xk1

EMDB-33240, PDB-7xk1:
Cryo-EM structure of Oryza sativa plastid glycyl-tRNA synthetase in complex with two tRNAs (both in tRNA binding states)
Method: EM (single particle) / Resolution: 4.3 Å

34427

8h1c

EMDB-34427, PDB-8h1c:
Cryo-EM structure of Oryza sativa plastid glycyl-tRNA synthetase in complex with two tRNAs (one in tRNA binding state and the other in tRNA locked state)
Method: EM (single particle) / Resolution: 4.5 Å

Source
  • Oryza sativa subsp. japonica (Japanese rice)
  • oryza sativa japonica group (Japanese rice)
  • oryza sativa (Asian cultivated rice)
KeywordsLIGASE/RNA / GlyRS2 / Glycine-tRNA ligase / tRNA selection / GlyRS tRNA complex / chloroplasts / LIGASE / LIGASE-RNA complex

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