Binding Properties of Split tRNA to the C-terminal Domain of Methionyl-tRNA Synthetase of Nanoarchaeum equitans

• Published in: Journal of molecular evolution Vol. 84; no. 5-6; pp. 267 - 278
• Main Authors: Suzuki, Hidemichi, Kaneko, Akihiro, Yamamoto, Taro, Nambo, Mahoko, Hirasawa, Ito, Umehara, Takuya, Yoshida, Hisashi, Park, Sam-Yong, Tamura, Koji
• Format: Journal Article
• Language: English
• Published: New York Springer US 01-06-2017; Springer Nature B.V
• Subjects: Amino Acid Sequence; Amino acids; Animal Genetics and Genomics; Binding Sites; Biomedical and Life Sciences; Cell Biology; Chemical synthesis; Crystal structure; Dimerization; Evolutionary Biology; Homology; Life Sciences; Methionine-tRNA Ligase - metabolism; Microbiology; Nanoarchaeota - genetics; Nanoarchaeota - metabolism; Oligonucleotides; Original Article; Plant Genetics and Genomics; Plant Sciences; Protein Domains; Protein Structure, Tertiary; Proteins; Quartz; Quartz crystal microbalance; Ribonucleic acid; RNA; RNA - metabolism; RNA, Transfer - metabolism; tRNA; tRNA-binding protein; Binding; Quartz crystal microbalance; tRNA; Methionyl-tRNA synthetase; Crystal structure; Nanoarchaeum equitans
• ISSN: 0022-2844; 1432-1432
• DOI: 10.1007/s00239-017-9796-6

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.