The Structure of the RNA mp>5p>C Methyltransferase YebU from Escherichia coli Reveals a C-terminal RNA-recruiting PUA Domain

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• 作者：B. Martin Hallberg ; Ulrika B. Ericsson ; Kenneth A. Johnson ; Niels Mø ; ller Andersen ; Stephen Douthwaite ; P&#xe4 ; r Nordlund ; Albert E. Beuscher IV and Heidi Erlandsen
• 关键词：mp>5p>C RNA methyltransferase ; structure ; SAD phasing ; rRNA modification ; PUA domain
• 刊名：Journal of Molecular Biology
• 出版年：2006
• 期刊代码：102_00222836
• 类别：imm
• 出版时间：21 July 2006
• 卷：360
• 期：4
• 页码：774-787
• 文件大小：1448 K

摘要

Nucleotide methylations are the most common type of rRNA modification in bacteria, and are introduced post-transcriptionally by a wide variety of site-specific enzymes. Three 5-methylcytidine (mp>5p>C) bases are found in the rRNAs of Escherichia coli and one of these, at nucleotide 1407 in 16 S rRNA, is the modification product of the methyltransferase (MTase) YebU (also called RsmF). YebU requires S-adenosyl-l-methionine (SAM) and methylates C1407 within assembled 30 S subunits, but not in naked 16 S rRNA or within tight-couple 70 S ribosomes. Here, we describe the three-dimensional structure of YebU determined by X-ray crystallography, and we present a molecular model for how YebU specifically recognizes, binds and methylates its ribosomal substrate. The YebU protein has an N-terminal SAM-binding catalytic domain with structural similarity to the equivalent domains in several other mp>5p>C RNA MTases including RsmB and PH1374. The C-terminal one-third of YebU contains a domain similar to that in pseudouridine synthases and archaeosine-specific transglycosylases (PUA-domain), which was not predicted by sequence alignments. Furthermore, YebU is predicted to contain extended regions of positive electrostatic potential that differ from other RNA-MTase structures, suggesting that YebU interacts with its RNA target in a different manner. Docking of YebU onto the 30 S subunit indicates that the PUA and MTase domains make several contacts with 16 S rRNA as well as with the ribosomal protein S12. The ribosomal protein interactions would explain why the assembled 30 S subunit, and not naked 16 S rRNA, is the preferred substrate for YebU.