5Z5E

Crystal structure of the Glycyl-tRNA synthetase (GlyRS) in Nanoarchaeum equitans

Summary for 5Z5E

• Entry DOI: 10.2210/pdb5z5e/pdb
• Descriptor: NEQ417, SULFATE ION, GLYCEROL, ... (4 entities in total)
• Functional Keywords: ligase
• Biological source: Nanoarchaeum equitans (strain Kin4-M)
• Total number of polymer chains: 2
• Total formula weight: 126931.08

Authors

Noguchi, H.,Park, S.Y.,Tamura, K. (deposition date: 2018-01-18, release date: 2019-01-30, Last modification date: 2023-11-22)

Primary citation

Fujisawa, A.,Toki, R.,Miyake, H.,Shoji, T.,Doi, H.,Hayashi, H.,Hanabusa, R.,Mutsuro-Aoki, H.,Umehara, T.,Ando, T.,Noguchi, H.,Voet, A.,Park, S.Y.,Tamura, K.
Glycyl-tRNA synthetase from Nanoarchaeum equitans: The first crystal structure of archaeal GlyRS and analysis of its tRNA glycylation.
Biochem.Biophys.Res.Commun., 511:228-233, 2019

PubMed Abstract: This study reports the X-ray crystallographic structure of the glycyl-tRNA synthetase (GlyRS) of Nanoarchaeum equitans - a hyperthermophilic archaeal species. This is the first archaeal GlyRS crystal structure elucidated. The GlyRS comprises an N-terminal catalytic domain and a C-terminal anticodon-binding domain with a long β-sheet inserted between these domains. An unmodified transcript of the wild-type N. equitans tRNA was successfully glycylated using GlyRS. Substitution of the discriminator base A73 of tRNA with any other nucleotide caused a significant decrease in glycylation activity. Mutational analysis of the second base-pair C2G71 of the acceptor stem of tRNA elucidated the importance of the base-pair, especially G71, as an identity element for recognition by GlyRS. Glycylation assays using tRNA G71 substitution mutants and a GlyRS mutant where Arg223 is mutated to alanine strengthen the possibility that the carbonyl oxygen at position 6 of G71 would hydrogen-bond with the guanidine nitrogen of Arg223 in N. equitans GlyRS.

PubMed: 30771900
DOI: 10.1016/j.bbrc.2019.01.142

Experimental method

X-RAY DIFFRACTION (2.098 Å)