Modomics - A Database of RNA Modifications

Full name:	Ribosomal RNA small subunit methyltransferase F
Synonym:	YebU, JW5301
GI:	3915994
Orf:	b1835
COG:	COG0144
UniProt:	P76273
Structures:	\| 2FRX \|
Complex:
Enzyme type:	methyltransferase
Position of modification - modification:	s:1407(1407) - m5C

Comments:

RsmF methylates C1407 in the stem of helix 44 near the 3’-end of 16S rRNA within assembled 30S subunits (it does not work on naked 16S rRNA or within tight-couple 70S ribosome). The ribosomal protein S12 is specially important. The enzyme has an N-terminal SAM-binding catalytic domain with structural similarity to the equivalent domains in several other m5C RNA MTases (including RsmB). However, E. coli RsmF has also a C-terminal PUA-domain similar to that in pseudouridine synthases (Pus) and archaeosine-specific transglycosylases (Tgt). It also contains extended regions of positive electrostatic potential that differ from other RNA MTase structures. Methylation of C1407 by RsmF is impeded by Sgm methyltransferase that catalyzes the formation of m7G on its adjacent G1405 target on the 30S ribosomal subunit. Thus resistance to certain aminoglycosides depends on the interplay of two different methyltransferases: RsmF and Sgm. RsmF is conserved in bacteria.

Protein sequence:

MAQHTVYFPDAFLTQMREAMPSTLSFDDFLAACQRPLRRSIRVNTLKISVADFLQLTAPYGWTLTPIPWCEEGFWIERDNEDALPLGSTAEHLSGLFYIQ
EASSMLPVAALFADGNAPQRVMDVAAAPGSKTTQISARMNNEGAILANEFSASRVKVLHANISRCGISNVALTHFDGRVFGAAVPEMFDAILLDAPCSGE
GVVRKDPDALKNWSPESNQEIAATQRELIDSAFHALRPGGTLVYSTCTLNQEENEAVCLWLKETYPDAVEFLPLGDLFPGANKALTEEGFLHVFPQIYDC
EGFFVARLRKTQAIPALPAPKYKVGNFPFSPVKDREAGQIRQAATGVGLNWDENLRLWQRDKELWLFPVGIEALIGKVRFSRLGIKLAETHNKGYRWQHE
AVIALASPDNMNAFELTPQEAEEWYRGRDVYPQAAPVADDVLVTFQHQPIGLAKRIGSRLKNSYPRELVRDGKLFTGNA

Enzymatic activities:

Reaction	Substrate	Type	Position
C:m5C	rRNA (r)	SSU/16S/prokaryotic cytosol	1407

Publications:

Title	Authors	Journal	Details	PubMed Id	DOI
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	[details]	16793063	-
YebU is a m5C methyltransferase specific for 16 S rRNA nucleotide 1407.	Andersen NM, Douthwaite S	J Mol Biol	[details]	16678201	-
The aminoglycoside resistance methyltransferase Sgm impedes RsmF methylation at an adjacent rRNA nucleotide in the ribosomal A site.	Cubrilo S, Babic F, Douthwaite S, Maravic Vlahovicek G	RNA	[details]	19509304	-