2FRX

Crystal structure of YebU, a m5C RNA methyltransferase from E.coli

2FRX の概要

• エントリーDOI: 10.2210/pdb2frx/pdb
• 分子名称: Hypothetical protein yebU (1 entity in total)
• 機能のキーワード: rossmann-type s-adenosylmethionine-dependent methyltransferase domain, c-terminal pua (pseudouridine synthases and archaeosine-specific transglycosylases) domain, transferase
• 由来する生物種: Escherichia coli
• 細胞内の位置: Cytoplasm : P76273
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 214633.80

構造登録者

Erlandsen, H.,Nordlund, P.,Hallberg, B.M.,Johnson, K.A.,Ericsson, U.B. (登録日: 2006-01-20, 公開日: 2006-08-29, 最終更新日: 2024-11-13)

主引用文献

Hallberg, B.M.,Ericsson, U.B.,Johnson, K.A.,Andersen, N.M.,Douthwaite, S.,Nordlund, P.,Beuscher IV, A.E.,Erlandsen, H.
The structure of the RNA m5C methyltransferase YebU from Escherichia coli reveals a C-terminal RNA-recruiting PUA domain
J.Mol.Biol., 360:774-787, 2006

PubMed 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.

PubMed: 16793063
DOI: 10.1016/j.jmb.2006.05.047

実験手法

X-RAY DIFFRACTION (2.9 Å)