ISSN:
1573-5001
Keywords:
Dynamic NMR refinement
;
MD with time-averaged restraints
;
TΨC-loop
;
RUMT
;
RNA/protein recognition
Source:
Springer Online Journal Archives 1860-2000
Topics:
Biology
,
Chemistry and Pharmacology
Notes:
Abstract tRNA (m5U54)-methyltransferase (RUMT) catalyzes the S-adenosylmethionine-dependentmethylation of uridine-54 in the TΨC-loop of all transfer RNAs in E. coli to form the 54-ribosylthymine residue. However, in all tRNA structures, residue 54 is completely buried andthe question arises as to how RUMT gains access to the methylation site. A 17-mer RNAhairpin consisting of nucleotides 49–65 of the TΨ-loop is a substrate for RUMT.Homonuclear NMR methods in conjunction with restrained molecular dynamics (MD)methods were used to determine the solution structure of the 17-mer T-arm fragment. Theloop of the hairpin exhibits enhanced flexibility which renders the conventional NMR averagestructure less useful compared to the more commonly found situation where a molecule existsin predominantly one major conformation. However, when resorting to softer refinementmethods such as MD with time-averaged restraints, the conflicting restraints in the loop canbe satisfied much better. The dynamic structure of the T-arm is represented as an ensembleof 10 time-clusters. In all of these, U54 is completely exposed. The flexibility of the TΨ-loop in solution in conjunction with extensive binding studies of RUMT with the TΨC-loop and tRNA suggest that the specificity of the RUMT/tRNA recognition is associated withtRNA tertiary structure elements. For the methylation, RUMT would simply have to breakthe tertiary interactions between the D- and T-loops, leading to a melting of the T-armstructure and making U54 available for methylation.
Type of Medium:
Electronic Resource
URL:
http://dx.doi.org/10.1023/A:1018618606857
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