Crystal structure of human selenocysteine tRNA

Abstract

Selenocysteine (Sec) is the 21st amino acid in translation. Sec tRNA (tRNASec) has an anticodon complementary to the UGA codon. We solved the crystal structure of human tRNASec. tRNASec has a 9-bp acceptor stem and a 4-bp T stem, in contrast with the 7-bp acceptor stem and the 5-bp T stem in the canonical tRNAs. The acceptor stem is kinked between the U6:U67 and G7:C66 base pairs, leading to a bent acceptor-T stem helix. tRNASec has a 6-bp D stem and a 4-nt D loop. The long D stem includes unique A14:U21 and G15:C20a pairs. The D-loop:T-loop interactions include the base pairs G18:U55 and U16:U59, and a unique base triple, U20:G19:C56. The extra arm comprises of a 6-bp stem and a 4-nt loop. Remarkably, the D stem and the extra arm do not form tertiary interactions in tRNASec. Instead, tRNASec has an open cavity, in place of the tertiary core of a canonical tRNA. The linker residues, A8 and U9, connecting the acceptor and D stems, are not involved in tertiary base pairing. Instead, U9 is stacked on the first base pair of the extra arm. These features might allow tRNASec to be the target of the Sec synthesis/incorporation machineries.

The Selenocysteine-specific Elongation Factor Contains a Novel and Multi-functional Domain

“…Itoh et al recently published the human tRNA Sec crystal structure and suggested a tRNA recognition model for eEFSec that differs from the canonical elongation factor eEF1A (27). The archaeal EFSec and human tRNA Sec docking model, based on the EF-Tu and Phe-tRNAPhe co-crystal, locates Domain IV in proximity to the variable arm of tRNA Sec .…”

“…Novel Allosteric Sec-tRNA Sec Interactions Found in Domain IV-Physical interactions of Domain IV with the Sec-tRNA Sec were proposed previously for SelB and eEFSec after examination from their respective crystal structures (27,33,34). Biochemical evidence to test this hypothesis was curtailed because of mutations in Domain IV of SelB rendering the protein insoluble and difficult to express and purify (35).…”

Selenoproteins: Molecular Pathways and Physiological Roles

“…Eukaryotic and archaeal tRNA [Ser]Sec have a 9/4 secondary structure, wherein the acceptor stem contains 9 bp and the T stem 4 bp (139,148,330). In contrast, bacterial tRNA [Ser]Sec has a 8/5 cloverleaf form, whereas all canonical tRNAs have 7/5 secondary structures (156,157). The structures of tRNA [Ser]Sec from Escherichia coli, Mathanococcus jannaschii, and Homo sapiens are shown in clover leaf models in FIGURE 2.…”

The Long D-stem of the Selenocysteine tRNA Provides Resilience at the Expense of Maximal Function

“…The absence of these interactions makes the tRNA Sec conformation more flexible compared with that of other cytosolic tRNAs. The existence of such flexibility has already been noticed when the available x-ray conformations of the tRNA Sec were compared with each other (5,8). The flexibility provided by the absence of standard tertiary interactions seems to be essential for the tRNA Sec function.…”