title: The structure of the RNA m5C methyltransferase YebU from Escherichia coli reveals a C-terminal RNA-recruiting PUA domain.
abstract: 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 (m(5)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 m(5)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.
authors.affiliation: Department of Medical Biochemistry and Biophysics, Karolinska Institute, 17177 Stockholm, Sweden.
authors.forename: B Martin
authors.initials: BM
authors.lastname: Hallberg
authors.forename: Ulrika B
authors.initials: UB
authors.lastname: Ericsson
authors.forename: Kenneth A
authors.initials: KA
authors.lastname: Johnson
authors.forename: Niels Møller
authors.initials: NM
authors.lastname: Andersen
authors.forename: Stephen
authors.initials: S
authors.lastname: Douthwaite
authors.forename: Pär
authors.initials: P
authors.lastname: Nordlund
authors.forename: Albert E
authors.initials: AE
authors.lastname: Beuscher
authors.forename: Heidi
authors.initials: H
authors.lastname: Erlandsen
mesh_terms: D000595:Amino Acid Sequence; D001665:Binding Sites; D017124:Conserved Sequence; D004926:Escherichia coli / Q000201:enzymology*; D008780:Methyltransferases / Q000737:chemistry*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011485:Protein Binding; D017510:Protein Folding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D012335:RNA, Ribosomal / Q000378:metabolism*; D016415:Sequence Alignment; D013379:Substrate Specificity; D013499:Surface Properties
chemical_list: D012335:RNA, Ribosomal; D008780:Methyltransferases; C072271:m(5)C rRNA methyltransferase