3A4L

Crystal structure of archaeal O-phosphoseryl-tRNA(Sec) kinase

Summary for 3A4L

• Entry DOI: 10.2210/pdb3a4l/pdb
• Related: 3A4M 3A4N
• Descriptor: L-seryl-tRNA(Sec) kinase, PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER, MAGNESIUM ION, ... (6 entities in total)
• Functional Keywords: p-loop motif, walker a motif, atp binding motif, atp-binding, kinase, nucleotide-binding, transferase
• Biological source: Methanocaldococcus jannaschii (Methanococcus jannaschii)
• Total number of polymer chains: 2
• Total formula weight: 63581.36

Authors

Araiso, Y.,Ishitani, R.,Soll, D.,Nureki, O. (deposition date: 2009-07-10, release date: 2009-10-20, Last modification date: 2024-03-13)

Primary citation

Araiso, Y.,Sherrer, R.L.,Ishitani, R.,Ho, J.M.L.,Soll, D.,Nureki, O.
Structure of a tRNA-dependent kinase essential for selenocysteine decoding
Proc.Natl.Acad.Sci.USA, 106:16215-16220, 2009

PubMed Abstract: Compared to bacteria, archaea and eukaryotes employ an additional enzyme for the biosynthesis of selenocysteine (Sec), the 21(st) natural amino acid (aa). An essential RNA-dependent kinase, O-phosphoseryl-tRNA(Sec) kinase (PSTK), converts seryl-tRNA(Sec) to O-phosphoseryl-tRNA(Sec), the immediate precursor of selenocysteinyl-tRNA(Sec). The sequence of Methanocaldococcus jannaschii PSTK (MjPSTK) suggests an N-terminal kinase domain (177 aa) followed by a presumed tRNA binding region (75 aa). The structures of MjPSTK complexed with ADP and AMPPNP revealed that this enzyme belongs to the P-loop kinase class, and that the kinase domain is closely related to gluconate kinase and adenylate kinase. ATP is bound by the P-loop domain (residues 11-18). Formed by antiparallel dimerization of two PSTK monomers, the enzyme structure shows a deep groove with positive electrostatic potential. Located in this groove is the enzyme's active site, which biochemical and genetic data suggest is composed of Asp-41, Arg-44, Glu-55, Tyr-82, Tyr-83, Met-86, and Met-132. Based on structural comparison with Escherichia coli adenylate kinase a docking model was generated that assigns these amino acids to the recognition of the terminal A76-Ser moieties of Ser-tRNA(Sec). The geometry and electrostatic environment of the groove in MjPSTK are perfectly complementary to the unusually long acceptor helix of tRNA(Sec).

PubMed: 19805283
DOI: 10.1073/pnas.0908861106

Experimental method

X-RAY DIFFRACTION (1.8 Å)