2frx
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Crystal structure of YebU, a m5C RNA methyltransferase from E.coli
OverviewOverview
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.
About this StructureAbout this Structure
2FRX is a Single protein structure of sequence from Escherichia coli. Full crystallographic information is available from OCA.
ReferenceReference
The structure of the RNA m5C methyltransferase YebU from Escherichia coli reveals a C-terminal RNA-recruiting PUA domain., Hallberg BM, Ericsson UB, Johnson KA, Andersen NM, Douthwaite S, Nordlund P, Beuscher AE 4th, Erlandsen H, J Mol Biol. 2006 Jul 21;360(4):774-87. Epub 2006 Jun 6. PMID:16793063
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