5H34

Crystal structure of the C-terminal domain of methionyl-tRNA synthetase (MetRS-C) in Nanoarchaeum equitans

Summary for 5H34

• Entry DOI: 10.2210/pdb5h34/pdb
• Descriptor: Methionine-tRNA ligase (2 entities in total)
• Functional Keywords: trna, methionyl-trna synthetase, nanoarchaeum equitans, ligase
• Biological source: Nanoarchaeum equitans
• Cellular location: Cytoplasm : Q74MZ1
• Total number of polymer chains: 2
• Total formula weight: 30141.07

Authors

Suzuki, H.,Kaneko, A.,Yamamoto, T.,Nambo, M.,Umehara, T.,Yoshida, H.,Park, S.Y.,Tamura, K. (deposition date: 2016-10-20, release date: 2017-06-21, Last modification date: 2024-03-20)

Primary citation

Suzuki, H.,Kaneko, A.,Yamamoto, T.,Nambo, M.,Hirasawa, I.,Umehara, T.,Yoshida, H.,Park, S.Y.,Tamura, K.
Binding Properties of Split tRNA to the C-terminal Domain of Methionyl-tRNA Synthetase of Nanoarchaeum equitans.
J. Mol. Evol., 84:267-278, 2017

PubMed Abstract: The C-terminal domain of methionyl-tRNA synthetase (MetRS-C) from Nanoarchaeum equitans is homologous to a tRNA-binding protein consisting of 111 amino acids (Trbp111) from Aquifex aeolicus. The crystal structure of MetRS-C showed that it existed as a homodimer, and that each monomer possessed an oligonucleotide/oligosaccharide-binding fold (OB-fold). Analysis using a quartz crystal microbalance indicated that MetRS-C freshly isolated from N. equitans was bound to tRNA. However, binding of the split 3'-half tRNA species was stronger than that of the 5'-half species. The T-loop and the 3'-end regions of the split 3'-half tRNA were found to be responsible for the binding. The minimum structure for binding to MetRS-C might be a minihelix-like stem-loop with single-stranded 3'-terminus. After successive duplications of such a small hairpin structure with the assistance of a Trbp-like structure, the interaction of the T-loop region of the 3'-half with a Trbp-like structure could have been evolutionarily replaced by RNA-RNA interactions, along with many combinational tertiary interactions, to form the modern tRNA structure.

PubMed: 28589220
DOI: 10.1007/s00239-017-9796-6

Experimental method

X-RAY DIFFRACTION (1.748 Å)