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Nucleic Acids Research Advance Access published online on June 18, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm411
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© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Structural Biology

Functional specialization of domains tandemly duplicated within 16S rRNA methyltransferase RsmC

S. Sunita1, Elzbieta Purta2,3, Malgorzata Durawa2, Karolina L. Tkaczuk2,4, J. Swaathi1, Janusz M. Bujnicki2 and J. Sivaraman1,*

1Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, 2Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, 3Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106 Warsaw and 4Institute of Technical Biochemistry, Technical University of Lodz, B. Stefanowskiego 4/10, 90-924 Lodz, Poland

*To whom correspondence should be addressed. Tel: +65 65161163; Fax: +65 67792486; Email: dbsjayar{at}nus.edu.sg

Received February 14, 2007. Revised May 3, 2007. Accepted May 5, 2007.

RNA methyltransferases (MTases) are important players in the biogenesis and regulation of the ribosome, the cellular machine for protein synthesis. RsmC is a MTase that catalyzes the transfer of a methyl group from S-adenosyl-L-methionine (SAM) to G1207 of 16S rRNA. Mutations of G1207 have dominant lethal phenotypes in Escherichia coli, underscoring the significance of this modified nucleotide for ribosome function. Here we report the crystal structure of E. coli RsmC refined to 2.1 Å resolution, which reveals two homologous domains tandemly duplicated within a single polypeptide. We characterized the function of the individual domains and identified key residues involved in binding of rRNA and SAM, and in catalysis. We also discovered that one of the domains is important for the folding of the other. Domain duplication and subfunctionalization by complementary degeneration of redundant functions (in particular substrate binding versus catalysis) has been reported for many enzymes, including those involved in RNA metabolism. Thus, RsmC can be regarded as a model system for functional streamlining of domains accompanied by the development of dependencies concerning folding and stability.


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