2frx
From Proteopedia
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'''Crystal structure of YebU, a m5C RNA methyltransferase from E.coli''' | '''Crystal structure of YebU, a m5C RNA methyltransferase from E.coli''' | ||
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[[Category: Johnson, K A.]] | [[Category: Johnson, K A.]] | ||
[[Category: Nordlund, P.]] | [[Category: Nordlund, P.]] | ||
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Revision as of 01:14, 4 May 2008
Crystal structure of YebU, a m5C RNA methyltransferase from E.coli
Overview
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 Structure
2FRX is a Single protein structure of sequence from Escherichia coli. Full crystallographic information is available from OCA.
Reference
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 Page seeded by OCA on Sun May 4 04:14:28 2008
