1WYD

Crystal Structure of Aspartyl-tRNA synthetase from Sulfolobus tokodaii

Summary for 1WYD

• Entry DOI: 10.2210/pdb1wyd/pdb
• Descriptor: hypothetical aspartyl-tRNA synthetase, CHLORIDE ION, SULFATE ION, ... (5 entities in total)
• Functional Keywords: aspartyl-trna synthetase, archaea, sulfolobus tokodaii, ligase
• Biological source: Sulfolobus tokodaii
• Cellular location: Cytoplasm: Q976I3
• Total number of polymer chains: 2
• Total formula weight: 99027.37

Authors

Maeda, Y.,Hossain, M.T.,Ubukata, S.,Suzuki, K.,Sekiguchi, T.,Takenaka, A. (deposition date: 2005-02-12, release date: 2006-07-04, Last modification date: 2024-03-13)

Primary citation

Sato, Y.,Maeda, Y.,Shimizu, S.,Hossain, M.T.,Ubukata, S.,Suzuki, K.,Sekiguchi, T.,Takenaka, A.
Structure of the nondiscriminating aspartyl-tRNA synthetase from the crenarchaeon Sulfolobus tokodaii strain 7 reveals the recognition mechanism for two different tRNA anticodons
ACTA CRYSTALLOGR.,SECT.D, 63:1042-1047, 2007

PubMed Abstract: In protein synthesis, 20 types of aminoacyl-tRNA synthetase (aaRS) are generally required in order to distinguish between the 20 types of amino acid so that each achieves strict recognition of the cognate amino acid and the cognate tRNA. In the crenarchaeon Sulfolobus tokodaii strain 7 (St), however, asparaginyl-tRNA synthetase (AsnRS) is missing. It is believed that AspRS instead produces Asp-tRNA(Asn) in addition to Asp-tRNA(Asp). In order to reveal the recognition mechanism for the two anticodons, GUC for aspartate and GUU for asparagine, the crystal structure of St-AspRS (nondiscriminating type) has been determined at 2.3 A resolution as the first example of the nondiscriminating type of AspRS from crenarchaea. A structural comparison with structures of discriminating AspRSs indicates that the structures are similar to each other overall and that the catalytic domain is highly conserved as expected. In the N-terminal domain, however, the binding site for the third anticodon nucleotide is modified to accept two pyrimidine bases, C and U, but not purine bases. The C base can bind to form a hydrogen bond to the surrounding main-chain amide group in the discriminating AspRS, while in the nondiscriminating AspRS the corresponding amino-acid residue is replaced by proline, which has no amide H atom for hydrogen-bond formation, thus allowing the U base to be accommodated in this site. In addition, the residues that cover the base plane are missing in the nondiscriminating AspRS. These amino-acid changes make it possible for both C and U to be accepted by the nondiscriminating AspRS. It is speculated that this type of nondiscriminating AspRS has been introduced into Thermus thermophilus through horizontal gene transfer.

PubMed: 17881821
DOI: 10.1107/S0907444907038292

Experimental method

X-RAY DIFFRACTION (2.3 Å)