Pseudouridine synthetase Pus1 of Saccharomyces cerevisiae: Kinetic characterisation, tRNA structural requirement and real-time analysis of its complex with tRNA

Pseudouridine synthetase Pus1 from Saccharomyces cerevisiae is a multisite- specific enzyme that catalyses the formation of pseudouridine residues at d ifferent positions in several tRNA transcripts. Recombinant Pus1, tagged wi th six histidine residues at its N terminus was expressed in Escherichia co li and purified. Transcripts of yeast tRNA(Val) and intronless yeast tRNA(I le) were used as substrates to measure pseudouridine formation at position 27. The catalytic parameters K-m and k(cat) for tRNA(Val) and tRNA were 420 (+/-100) nM and 0.4(+/-0.1) min(-1), 740(+/-100) nM and 0.5(+/-0.1) min(-1) , respectively. Pus1 possesses a general affinity for tRNA, irrespective of whether they are substrates. Its equilibrium dissociation constant ranges from 15 nM for the substrate yeast tRNA(Val) and non-substrate yeast intron less tRNA(Phe), to 150 nM for the substrate yeast intronless tRNA(Ile). The difference in the affinity for the different tRNA species is not reflected in the specific activity of the enzyme, indicating that the binding of Pus 1 to tRNA is not the kinetically limiting step. The importance of tertiary base-pairs was investigated with several variants of yeast tRNAs. Although dispensable for activity, both the presence of a D-stem-loop and the presen ce of a G26.A44 base-pair, near the target uridine U27, are important eleme nts for Pus1 tRNA high affinity recognition. The presence of a G26.A44 base -pair in tRNA increases its association constant rate with Pus1 (k(a)) by a factor of approximately 100, resulting in a decrease of the overall equili brium dissociation constant (K-d). The dissociation rate (k(d)) is the same , independent of the presence of a G26.A44 base-pair in the tRNA. A model d escribing the interaction of Pus1 with tRNA is proposed. (C) 1999 Academic Press.