PDBsum entry 3a4l

Transferase

PDB id: 3a4l

Contents

Protein chains

236 a.a.

Ligands

ANP ×2

EDO ×4

Metals

_MG ×2

IOD ×2

Waters ×301

References listed in PDB file

Key reference

Title

Structure of a tRNA-Dependent kinase essential for selenocysteine decoding.

Authors

Y.Araiso, R.L.Sherrer, R.Ishitani, J.M.Ho, D.Söll, O.Nureki.

Ref.

Proc Natl Acad Sci U S A, 2009, 106, 16215-16220. [DOI no: 10.1073/pnas.0908861106]

PubMed id

19805283

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).

Figure 1.
Overall structure of MjPSTK. (A) Ribbon representation of the crystal structure of the MjPSTK dimer, consisting of the N-terminal domain (residues 3–177, blue) and the C-terminal domain (188–231 and 237–252, orange). The AMPPNP molecule is shown as a ball-and-stick model. (B) Surface representations of PSTK (left), rotated 90° (right), consisting of the core region (residues 3–39, 52–117, and 126–177, blue), the A76-binding region (40–51, green) the lid region (118–125, yellow), and the C-terminal domain (188–231 and 237–252, orange), with the active site colored pink. The solvent-accessible surface was calculated with the program MSMS (26). The AMPPNP molecule is shown as a ball-and-stick model. The white and black arrows show the width and the depth, respectively, of the tRNA binding groove.

Figure 2.
The detailed structure of the N-terminal and C-terminal domains. (A) Ribbon representation of the crystal structure of the N-terminal domain. Each region is defined according to Fig. 1. (B) Ribbon representation of the crystal structure of the C-terminal domain, defined according to Fig. 1. The iodide ion is colored yellow. (C) The N-terminal domain of E. coli AdK in complex with ADP. (D) The N-terminal domain of E. coli GntK in complex with AMPPCP. The coloring scheme is the same as in (A).