Crystal structure of a eukaryote/archaeon-like prolyl-tRNA synthetase and its complex with tRNA(Pro)(CGG)

Prolyl-tRNA synthetase (ProRS) is a class IIa synthetase that, according to sequence analysis, occurs in different organisms with one of two quite dis tinct structural architectures: prokaryote-like and eukaryote/archaeon-like , The primary sequence of ProRS from the hypothermophilic eubacterium Therm us thermophilus (ProRSTT) shows that this enzyme is surprisingly eukaryote/ archaeon-like We describe its crystal structure at 2.43 (A) over circle res olution, which reveals a feature that is unique among class II synthetases. This is an additional zinc-containing domain after the expected class IIa anticodon-binding domain and whose C-terminal extremity, which ends in an a bsolutely conserved tyrosine, folds back into the active site. We also pres ent an improved structure of ProRSTT complexed with tRNA(PRO)(CGG) at 2.85 Angstrom resolution. This structure represents an initial docking state of the tRNA in which the anticodon stem-loop is engaged, particularly via the tRNA(PRO)-specific bases G35 and G36, but the 3' end does not enter the act ive site. Considerable structural changes in tRNA and/or synthetase, which are probably induced by small substrates, are required to achieve the confo rmation active for aminoacylation.