Heteronuclear NMR studies of the interactions of 15N-labeled methionine-specific transfer RNAs with methionyl-tRNA transformylase

Abstract

In Escherichia coli the methionylated initiator methionyl-tRNA (tRNAfMet) is formylated on the aminoacyl moiety by the enzyme methionyl-tRNA transformylase. The methionylated elongator methionyl-tRNA (tRNAmMet) is not modified in this way. In order to gain structural information about this specific recognition, solution NMR studies were carried out. To be able to identify changes that were occurring in the tRNA molecule on interaction with the methionyl-tRNA transformylase, the imino protons involved in secondary and tertiary base pairing in the tRNAfMet and tRNAmMet molecules first had to be assigned to specific resonances in the NMR spectra. A combination of 2D NOESY, 2D HMQC, and 3D NOESY--HMQC spectra were used on uniformly 15N-labeled samples. After assignment of the base pairs of the tRNA, the two forms of tRNA were separately mixed with transformylase in a 1:1 molar ratio. The HMQC spectra of both the tRNAmMet and the tRNAfMet showed general broadening, but in the tRNAfMet HMQC spectra a decrease in the intensity of several resonances was also observed. These resonances had been assigned to the acceptor stem of the tRNA, confirming site-directed mutagenesis experiments that it is the acceptor stem of the tRNA which is important in conferring the specificity for the transformylase. The loss of intensity of the acceptor stem resonances suggests that this part of tRNAfMet melts upon binding to the enzyme.