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J. Biol. Chem., Vol. 283, Issue 39, 26548-26556, September 26, 2008

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Crystal Structure of the Thermus thermophilus 16 S rRNA Methyltransferase RsmC in Complex with Cofactor and Substrate Guanosine^*

From the Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912

Post-transcriptional modification is a ubiquitous feature of ribosomal RNA in all kingdoms of life. Modified nucleotides are generally clustered in functionally important regions of the ribosome, but the functional contribution to protein synthesis is not well understood. Here we describe high resolution crystal structures for the N²-guanine methyltransferase RsmC that modifies residue G1207 in 16 S rRNA near the decoding site of the 30 S ribosomal subunit. RsmC is a class I S-adenosyl-L-methionine-dependent methyltransferase composed of two methyltransferase domains. However, only one S-adenosyl-L-methionine molecule and one substrate molecule, guanosine, bind in the ternary complex. The N-terminal domain does not bind any cofactor. Two structures with bound S-adenosyl-L-methionine and S-adenosyl-L-homocysteine confirm that the cofactor binding mode is highly similar to other class I methyltransferases. Secondary structure elements of the N-terminal domain contribute to cofactor-binding interactions and restrict access to the cofactor-binding site. The orientation of guanosine in the active site reveals that G1207 has to disengage from its Watson-Crick base pairing interaction with C1051 in the 16 S rRNA and flip out into the active site prior to its modification. Inspection of the 30 S crystal structure indicates that access to G1207 by RsmC is incompatible with the native subunit structure, consistent with previous suggestions that this enzyme recognizes a subunit assembly intermediate.

Received for publication, May 26, 2008 , and in revised form, July 22, 2008.

The atomic coordinates and structure factors (codes 3DMF, 3DMG, and 3DMH) have been deposited in the Protein Data Bank, Research Collaboratory for Structural Bioinformatics, Rutgers University, New Brunswick, NJ (http://www.rcsb.org/).

^* This work was supported, in whole or in part, by National Institutes of Health Grant GM19756 (to A. E. D.). This work was also supported by Brown University (to G. J.). The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

The on-line version of this article (available at http://www.jbc.org) contains supplemental Figs. 1 and 2.

¹ To whom correspondence should be addressed: Dept. of Molecular Biology, Cell Biology and Biochemistry, Brown University, Box G-E129, Providence, RI 02912. Tel.: 401-863-6123; Fax: 401-863-6114; E-mail: Gerwald_Jogl{at}brown.edu.

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