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M111825200v1
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Papers In Press, published online ahead of print January 4, 2002
J. Biol. Chem, 10.1074/jbc.M111825200
Submitted on December 12, 2001
Revised on January 4, 2002
Accepted on January 4, 2002

Characterization of the 23S rRNA m5U1939 Methyltransferase from Escherichia coli

Sanjay Agarwalla, James T. Kealey, Daniel V. Santi, and Robert M. Stroud

Biochemistry, University of California at San Francisco, San Francisco, CA 94143

Corresponding Author: stroud{at}msg.ucsf.edu

An E. coli open reading frame, ygcA, was identified as a putative 23S rRNA 5-methyluridine methyltransferase [Gustafsson et al., (1996) Nucleic Acids Res. 24, 3756-62]. We have cloned, expressed and purified the 50-kDa protein encoded by ygcA. The purified enzyme catalyzed the AdoMet-dependent methylation of 23S rRNA but did not act upon 16S rRNA or t-RNA. An HPLC based nucleoside analysis identified the reaction product as 5-methyluridine. The enzyme specifically methylated U1939 as determined by a nuclease protection assay and by methylation assays using site-specific mutants of 23S rRNA. A 40-nucleotide 23S rRNA fragment (nucleotide 1930-1969) also served as an efficient substrate for the enzyme. The apparent Km values for the 40-mer RNA oligonucleotide and AdoMet were 3 mu M and 26 mu M, respectively and the apparent kcat was about 0.06 s-1. The enzyme contains two equivalents of iron per monomer and has a sequence motif similar to a motif found in iron-sulfur proteins. We propose to name this gene rumA and accordingly the protein product as RumA for RNA uridine methyltransferase.


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