3ADB

Crystal structure of O-phosphoseryl-tRNA kinase complexed with selenocysteine tRNA and AMPPNP (crystal type 1)

Summary for 3ADB

• Entry DOI: 10.2210/pdb3adb/pdb
• Related: 3ADC 3ADD
• Descriptor: L-seryl-tRNA(Sec) kinase, selenocysteine tRNA, PHOSPHATE ION, ... (6 entities in total)
• Functional Keywords: protein-rna complex, trna, atp-binding, kinase, nucleotide-binding, transferase, transferase-rna complex, transferase/rna
• Biological source: Methanocaldococcus jannaschii (Methanococcus jannaschii); More
• Total number of polymer chains: 4
• Total formula weight: 122448.07

Authors

Itoh, Y.,Chiba, S.,Sekine, S.,Yokoyama, S. (deposition date: 2010-01-18, release date: 2010-07-28, Last modification date: 2024-10-09)

Primary citation

Chiba, S.,Itoh, Y.,Sekine, S.,Yokoyama, S.
Structural Basis for the Major Role of O-Phosphoseryl-tRNA Kinase in the UGA-Specific Encoding of Selenocysteine
Mol.Cell, 39:410-420, 2010

PubMed Abstract: The 21(st) amino acid, selenocysteine (Sec), is assigned to the codon UGA and is biosynthesized on the selenocysteine-specific tRNA (tRNA(Sec)) with the corresponding anticodon. In archaea/eukarya, tRNA(Sec) is ligated with serine by seryl-tRNA synthetase (SerRS), the seryl moiety is phosphorylated by O-phosphoseryl-tRNA kinase (PSTK), and the phosphate group is replaced with selenol by Sep-tRNA:Sec-tRNA synthase. PSTK selectively phosphorylates seryl-tRNA(Sec), while SerRS serylates both tRNA(Ser) and tRNA(Sec). In this study, we determined the crystal structures of the archaeal tRNA(Sec).PSTK complex. PSTK consists of two independent linker-connected domains, the N-terminal catalytic domain (NTD) and the C-terminal domain (CTD). The D-arm.CTD binding occurs independently of and much more strongly than the acceptor-arm.NTD binding. PSTK thereby distinguishes the characteristic D arm with the maximal stem and the minimal loop of tRNA(Sec) from the canonical D arm of tRNA(Ser), without interacting with the anticodon. This mechanism is essential for the UGA-specific encoding of selenocysteine.

PubMed: 20705242
DOI: 10.1016/j.molcel.2010.07.018

Experimental method

X-RAY DIFFRACTION (2.8 Å)