9QRP

Thermus thermophilus seryl-tRNA synthetase bound to tRNA(ser)(GGA) and seryl-adenylate analogue.

This is a non-PDB format compatible entry.

Summary for 9QRP

• Entry DOI: 10.2210/pdb9qrp/pdb
• Descriptor: Serine--tRNA ligase, tRNA(Ser), GGA anticodon, 5'-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE, ... (6 entities in total)
• Functional Keywords: protein synthesis, aminoacyl-trna synthetase, trna, rna binding protein
• Biological source: Thermus thermophilus HB8; More
• Total number of polymer chains: 3
• Total formula weight: 128041.20

Authors

Cusack, S. (deposition date: 2025-04-04, release date: 2025-05-14)

Primary citation

Cusack, S.,Yaremchuk, A.,Tukalo, M.
The crystal structure of the ternary complex of T.thermophilus seryl-tRNA synthetase with tRNA(Ser) and a seryl-adenylate analogue reveals a conformational switch in the active site.
EMBO J, 15:2834-2842, 1996

PubMed Abstract: The low temperature crystal structure of the ternary complex of Thermus thermophilus seryl-tRNA synthetase with tRNA(Ser) (GGA) and a non-hydrolysable seryl-adenylate analogue has been refined at 2.7 angstrom resolution. The analogue is found in both active sites of the synthetase dimer but there is only one tRNA bound across the two subunits. The motif 2 loop of the active site into which the single tRNA enters interacts within the major groove of the acceptor stem. In particular, a novel ring-ring interaction between Phe262 on the extremity of this loop and the edges of bases U68 and C69 explains the conservation of pyrimidine bases at these positions in serine isoaccepting tRNAs. This active site takes on a significantly different ordered conformation from that observed in the other subunit, which lacks tRNA. Upon tRNA binding, a number of active site residues previously found interacting with the ATP or adenylate now switch to participate in tRNA recognition. These results shed further light on the structural dynamics of the overall aminoacylation reaction in class II synthetases by revealing a mechanism which may promote an ordered passage through the activation and transfer steps.

PubMed: 8654381

Experimental method

X-RAY DIFFRACTION (2.7 Å)