Crystal structure of <i>Staphylococcus aureus</i> tyrosyl‐tRNA synthetase in complex with a class of potent and specific inhibitors

The 20 aminoacyl-tRNA synthetases catalyze the first step of protein synthesis and establish the rules of the genetic code through aminoacylation reactions. Biological fragments of two human enzymes, tyrosyl-tRNA synthetase (TyrRS) and tryptophanyl-tRNA synthetase, connect protein synthesis to cell-signaling pathways including angiogenesis. Alternative splicing or proteolysis produces these fragments. The proangiogenic N-terminal fragment mini-TyrRS has IL-8-like cytokine activity that, like other CXC cytokines, depends on a Glu-Leu-Arg motif. Point mutations in this motif abolish cytokine activity. The full-length native TyrRS lacks cytokine activity. No structure has been available for any mammalian tRNA synthetase that, in turn, might give insight into why mini-TyrRS and not TyrRS has cytokine activities. Here, the structure of human mini-TyrRS, which contains both the catalytic and the anticodon recognition domain, is reported to a resolution of 1.18 Å. The critical Glu-Leu-Arg motif is located on an internal ␣-helix of the catalytic domain, where the guanidino side chain of R is part of a hydrogen-bonding network tethering the anticodonrecognition domain back to the catalytic site. Whereas the catalytic domains of the human and bacterial enzymes superimpose, the spatial disposition of the anticodon recognition domain relative to the catalytic domain is unique in mini-TyrRS relative to the bacterial orthologs. This unique orientation of the anticodon-recognition domain can explain why the fragment mini-TyrRS, and not fulllength native TyrRS, is active in cytokine-signaling pathways.

Section: Resultsmentioning

confidence: 96%

mentioning

confidence: 99%

Crystal structure of a human aminoacyl-tRNA synthetase cytokine

Yang

Skene

McRee

et al. 2002

“…To date, a number of 3D structures of native TyrRS molecules have been determined (13)(14)(15)(16)(17)(18)(19), revealing the substrate recognition mechanisms of the natural enzymes. In the present study, we solved the structures of the 37V195C mutant E. coli TyrRS catalytic domain (19) complexed with 3-iodo-L-tyrosine and with the misrecognized ligand, L-tyrosine, at resolutions of 2.0 Å.…”

mentioning

confidence: 99%

Structural basis of nonnatural amino acid recognition by an engineered aminoacyl-tRNA synthetase for genetic code expansion

Kobayashi

Sakamoto

Takimura

et al. 2005

The genetic code in a eukaryotic system has been expanded by the engineering of Escherichia coli tyrosyl-tRNA synthetase (TyrRS) with the Y37V and Q195C mutations (37V195C), which specifically recognize 3-iodo- l -tyrosine rather than l -tyrosine. In the present study, we determined the 3-iodo- l -tyrosine- and l -tyrosine-bound structures of the 37V195C mutant of the E. coli TyrRS catalytic domain at 2.0-Å resolution. The γ-methyl group of Val-37 and the sulfur atom of Cys-195 make van der Waals contacts with the iodine atom of 3-iodo- l -tyrosine. The Val-37 and Cys-195 side chains are rigidly fixed by the neighboring residues forming the hydrophobic core of the TyrRS. The major roles of the two mutations are different for the 3-iodo- l -tyrosine-selective recognition in the first step of the aminoacylation reaction (the amino acid activation step): the Y37V mutation eliminates the fatal steric repulsion with the iodine atom, and the Q195C mutation reduces the l -tyrosine misrecognition. The structure of the 37V195C mutant TyrRS complexed with an l -tyrosyladenylate analogue was also solved, indicating that the 3-iodo- l -tyrosine and l -tyrosine side chains are similarly discriminated in the second step (the aminoacyl transfer step). These results demonstrate that the amino acid-binding pocket on the 37V195C mutant is optimized for specific 3-iodo- l -tyrosine recognition.

“…Except for the active site residues involved in amino acid binding, miniTyrRS in the complex has essentially the same conformation as in the unligand form (14). Superpositions of TrpRS and miniTyrRS structures from human and the published TyrRS (9,11,12) and TrpRS (10) structures from bacteria together enabled accurate alignment of over 90 sequences in their common core elements. Five examples of the 93 structure-based alignments, each with 173 residues that cover Ϸ50% of the total sequences, are shown in Fig.…”

Section: Structural Alignments and Active Site Identifications Enablementioning

confidence: 99%

Crystal structures that suggest late development of genetic code components for differentiating aromatic side chains

Yang

Otero

Skene

et al. 2003

107

Early forms of the genetic code likely generated ''statistical'' proteins, with similar side chains occupying the same sequence positions at different ratios. In this scenario, groups of related side chains were treated by aminoacyl-tRNA synthetases as a single molecular species until a discrimination mechanism developed that could separate them. The aromatic amino acids tryptophan, tyrosine, and phenylalanine likely constituted one of these groups. A crystal structure of human tryptophanyl-tRNA synthetase was solved at 2.1 Å with a tryptophanyl-adenylate bound at the active site. A cocrystal structure of an active fragment of human tyrosyltRNA synthetase with its cognate amino acid analog was also solved at 1.6 Å. The two structures enabled active site identifications and provided the information for structure-based sequence alignments of Ϸ45 orthologs of each enzyme. Two critical positions shared by all tyrosyl-tRNA synthetases and tryptophanyl-tRNA synthetases for amino acid discrimination were identified. The variations at these two positions and phylogenetic analyses based on the structural information suggest that, in contrast to many other amino acids, discrimination of tyrosine from tryptophan occurred late in the development of the genetic code.