A three-dimensional structure model of the complex of glutamyl-tRNA synthetase and its cognate tRNA

Post-translational control of tetrapyrrole biosynthesis in plants, algae, and cyanobacteria

The tetrapyrrole biosynthetic pathway provides the vital cofactors and pigments for photoautotrophic growth (chlorophyll), several essential redox reactions in electron transport chains (haem), N- and S-assimilation (sirohaem), and photomorphogenic processes (phytochromobilin). While the biochemistry of the pathway is well understood and almost all genes encoding enzymes of tetrapyrrole biosynthesis have been identified in plants, the post-translational control and organization of the pathway remains to be clarified. Post-translational mechanisms controlling metabolic activities are of particular interest since tetrapyrrole biosynthesis needs adaptation to environmental challenges. This review surveys post-translational mechanisms that have been reported to modulate metabolic activities and organization of the tetrapyrrole biosynthesis pathway.

Exit strategies for charged tRNA from GluRS

For several class I aminoacyl-tRNA synthetases (aaRSs), the rate-determining step in aminoacylation is the dissociation of charged tRNA from the enzyme. In this study, the following factors affecting the release of the charged tRNA from aaRSs are computationally explored: the protonation states of amino acids and substrates present in the active site, and the presence and the absence of AMP and elongation factor Tu. Through molecular modeling, internal pK(a) calculations, and molecular dynamics simulations, distinct, mechanistically relevant post-transfer states with charged tRNA bound to glutamyl-tRNA synthetase from Thermus thermophilus (Glu-tRNA(Glu)) are considered. The behavior of these nonequilibrium states is characterized as a function of time using dynamical network analysis, local energetics, and changes in free energies to estimate transitions that occur during the release of the tRNA. The hundreds of nanoseconds of simulation time reveal system characteristics that are consistent with recent experimental studies. Energetic and network results support the previously proposed mechanism in which the transfer of amino acid to tRNA is accompanied by the protonation of AMP to H-AMP. Subsequent migration of proton to water reduces the stability of the complex and loosens the interface both in the presence and in the absence of AMP. The subsequent undocking of AMP or tRNA then proceeds along thermodynamically competitive pathways. Release of the tRNA acceptor stem is further accelerated by the deprotonation of the alpha-ammonium group on the charging amino acid. The proposed general base is Glu41, a residue binding the alpha-ammonium group that is conserved in both structure and sequence across nearly all class I aaRSs. This universal handle is predicted through pK(a) calculations to be part of a proton relay system for destabilizing the bound charging amino acid following aminoacylation. Addition of elongation factor Tu to the aaRS.tRNA complex stimulates the dissociation of the tRNA core and the tRNA acceptor stem.

Evidence for unfolding of the single-stranded GCCA 3'-End of a tRNA on its aminoacyl-tRNA synthetase from a stacked helical to a foldback conformation

The conformation of a tRNA in its initial contact with its cognate aminoacyl-tRNA synthetase was investigated with the Escherichia coli glutamyl-tRNA synthetase-tRNA(Glu) complex. Covalent complexes between the periodate-oxidized tRNA(Glu) and its synthetase were obtained. These complexes are specific since none were formed with any other oxidized E. coli tRNA. The three major residues cross-linked to the 3'-terminal adenosine of oxidized tRNA(Glu) are Lys115, Arg209, and Arg48. Modeling of the tRNA(Glu)-glutamyl-tRNA synthetase based on the known crystal structures of Thermus thermophilus GluRS and of the E. coli tRNA(Gln)-glutaminyl-tRNA synthetase complex shows that these three residues are located in the pocket that binds the acceptor stem, and that Lys115, located in a 26 residue loop closed by coordination to a zinc atom in the tRNA acceptor stem-binding domain, is the first contact point of the 3'-terminal adenosine of tRNA(Glu). In our model, we assume that the 3'-terminal GCCA single-stranded segment of tRNA(Glu) is helical and extends the stacking of the acceptor stem. This assumption is supported by the fact that the 3' CCA sequence of tRNA(Glu) is not readily circularized in the presence of T4 RNA ligase under conditions where several other tRNAs are circularized. The two other cross-linked sites are interpreted as the contact sites of the 3'-terminal ribose on the enzyme during the unfolding and movement of the 3'-terminal GCCA segment to position the acceptor ribose in the catalytic site for aminoacylation.

The anticodon-binding domain of tyrosyl-tRNA synthetase: state of folding and origin of the crystallographic disorder

The C-terminal domain (residues 320-419) of tyrosyl-tRNA synthetase (TyrRS) from Bacillus stearothermophilus is disordered in the crystal structure. Its function consists of binding the anticodon of tRNA(Tyr). We undertook to characterize its conformational state. A hybrid between the C-terminal fragment and a His-tag sequence was constructed and purified in large amounts. Analyses by mass spectrometry and analytical ultracentrifugation showed that the C-terminal fragment, thus purified, was not degraded and that it neither dimerized nor aggregated. Its far- and near-UV circular dichroism spectra revealed a high content in secondary structures and an asymmetrical environment of its aromatic residues. Each spectrum could be reconstructed by the difference between the corresponding spectra for the full-length TyrRS and for its N-terminal fragment. The Stokes radius of the C-terminal fragment, measured by size exclusion chromatography, indicated a condensed globular state. The fluorescence of ANS (a small hydrophobic probe) showed that the surface of the C-terminal fragment was more hydrophilic than that of a molten globule. These results on the C-terminal fragment and our previous observations that it can undergo cooperative transitions, demonstrated the following points: it is not in a disordered or molten globular state, it has a defined and stable three-dimensional structure, its structures are similar in its isolated and integrated forms, and the apparent disorder in the crystals of the full-length synthetase must be due to the flexibility of the polypeptide segment that links the N- and C-terminal domains. Thus, TyrRS has not evolved strong noncovalent interactions between its catalytic and anticodon-binding domains, contrary to the other synthetases.

The identity determinants required for the discrimination between tRNAGlu and tRNAAsp by glutamyl-tRNA synthetase from Escherichia coli

We previously elucidated the major determinant set for Escherichia coli tRNAGlu identity (U34, U35, C36, A37, G1*C72, U2*A71, U11*A24, U13*G22**Alpha46, and Delta47) and showed that the set is sufficient to switch the identity of tRNAGln to Glu [Sekine, S., Nureki, O., Sakamoto, K., Niimi, T., Tateno, M., Go, M., Kohno, T., Brisson, A., Lapointe, J. & Yokoyama, S. (1996) J. Mol. Biol. 256, 685-700]. In the present study, we attempted to switch the identity of tRNAAsp, which has a sequence similar to that of tRNAGlu, and consequently possesses many nucleotide residues corresponding to the Glu identity determinants (U35, C36, A37, G1*C72, and U11*A24). A simple transplantation of the rest of the major determinants (U34, U2*A71, U13*G22**Alpha46, and Delta47) to the framework of tRNAAsp did not result in a sufficient switch of the tRNAAsp identity to Glu. To confer an optimal glutamate accepting activity to tRNAAsp, two other elements, C4*G69 in the middle of the acceptor stem and C12*G23**C9 in the augmented D helix, were required. Consistently, the two base pairs, C4*G69 and C12*G23, in tRNAGlu had been shown to exist in the interface with glutamyl-tRNA synthetase (GluRS) by phosphate-group footprinting. We also found the two elements in the framework of tRNAGln, and determined that their contributions successfully changed the identity of tRNAGln to Glu in the previous study. By the identity-determinant set (C4*G69 and C12*G23**C9 in addition to U34, U35, C36, A37, G1*C72, U2*A71, U11*A24, U13*G22**Alpha46, and Delta47) the activity of GluRS was optimized and efficient discrimination from the noncognate tRNAs was achieved.

Role of zinc in tRNA-acceptor stem binding by glutamyl-tRNA synthetase from E.coli: a molecular modeling study

A model of the N-terminal half of glutamyl-tRNA synthetase from E. coli was constructed on the basis of similarity in sequence and function of Glutaminyl- and Glutamyl-tRNA synthetases. The glutaminyl-tRNA synthetase does not contain any zinc atom, but glutamyl-tRNA synthetase from E. coli contains one atom of zinc. The specific role of zinc is not yet known. In this article, molecular modeling is employed to show that the zinc atom is well outside the contact region of the acceptor stem of tRNA. The placement of a zinc atom at a significant distance from the tRNA acceptor stem indicates that the role of zinc is likely to be indirect and structural.