A succession of substrate induced conformational changes ensures the aminoacid specificity of Thermus thermophilus prolyl-tRNA synthetase: Comparison with histidyl-tRNA synthetase

We describe the recognition by Thermus thermophilus prolyl-tRNA synthetase (ProRSTT) of proline, ATP and prolyl-adenylate and the sequential conformat ional changes occurring when the substrates bind and the activated intermed iate is formed. Proline and ATP binding cause respectively conformational c hanges in the proline binding loop and motif 2 loop. However formation of t he activated intermediate is necessary for the final conformational orderin g of a ten residue peptide ("ordering loop") close to the active site which would appear to be essential for functional tRNA 3' end binding. These ind uced fit conformational changes ensure that the enzyme is highly specific f or proline activation and aminoacylation. We also present new structures of apo and AMP bound histidyl-tRNA synthetase (HisRS) from T. thermophilus wh ich we compare to our previous structures of the histidine and histidyl-ade nylate bound enzyme. Qualitatively, similar results to those observed with T. thermophilus prolyl-tRNA synthetase are found. However histidine binding is sufficient to induce the co-operative ordering of the topologically equ ivalent histidine binding loop and ordering loop. These two examples contra st with most other class II aminoacyl-tRNA synthetases whose pocket for the cognate amino acid side-chain is largely preformed. T. thermophilus prolyl -tRNA synthetase appears to be the second class II aminoacyl-tRNA synthetas e, after HisRS, to use a positively charged amino acid instead of a divalen t cation to catalyse the amino acid activation reaction. (C) 2001 Academic Press.