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Information on EC 2.1.1.178 - 16S rRNA (cytosine1407-C5)-methyltransferase
for references in articles please use BRENDA:EC2.1.1.178
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EC Tree 2 Transferases
2.1 Transferring one-carbon groups
2.1.1 Methyltransferases
2.1.1.178 16S rRNA (cytosine1407-C5)-methyltransferase
IUBMB Comments
The enzyme specifically methylates cytosine1407 at C5 in 16S rRNA.
The enzyme appears in viruses and cellular organisms
Reaction Schemes
show+
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cytosine1407 in 16S rRNA
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5-methylcytosine1407 in 16S rRNA
Synonyms
16S rRNA methyltransferase, housekeeping methyltransferase RsmF, RNA m5C methyltransferase YebU, RsmF, RsmF housekeeping methyltransferase, YebU, more
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
16S rRNA methyltransferase
housekeeping methyltransferase RsmF
RsmF
RsmF housekeeping methyltransferase
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
S-adenosyl-L-methionine + cytosine1407 in 16S rRNA = S-adenosyl-L-homocysteine + 5-methylcytosine1407 in 16S rRNA
S-adenosyl-L-methionine + cytosine1407 in 16S rRNA = S-adenosyl-L-homocysteine + 5-methylcytosine1407 in 16S rRNA
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S-adenosyl-L-methionine + cytosine1407 in 16S rRNA = S-adenosyl-L-homocysteine + 5-methylcytosine1407 in 16S rRNA
the YebU structure is used to propose the most likely mechanism for its substrate specificity and recognition
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SYSTEMATIC NAME
IUBMB Comments
S-adenosyl-L-methionine:16S rRNA (cytosine1407-C5)-methyltransferase
The enzyme specifically methylates cytosine1407 at C5 in 16S rRNA.
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SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
LITERATURE
COMMENTARY
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
S-adenosyl-L-methionine + cytosine1400 in 16S rRNA
S-adenosyl-L-homocysteine + 5-methylcytosine1400 in 16S rRNA
S-adenosyl-L-methionine + cytosine1404 in 16S rRNA
S-adenosyl-L-homocysteine + 5-methylcytosine1404 in 16S rRNA
S-adenosyl-L-methionine + cytosine1407 in 16S rRNA
S-adenosyl-L-homocysteine + 5-methylcytosine1407 in 16S rRNA
additional information
?
-
Substrates: substrate recognition mechanism, overview
Products: -
Products: -
?
S-adenosyl-L-methionine + cytosine1400 in 16S rRNA
S-adenosyl-L-homocysteine + 5-methylcytosine1400 in 16S rRNA
Substrates: -
Products: -
Products: -
?
S-adenosyl-L-methionine + cytosine1400 in 16S rRNA
S-adenosyl-L-homocysteine + 5-methylcytosine1400 in 16S rRNA
Substrates: RsmF completely methylates C1400 when either 16S rRNA or 30S subunits are used as a substrate
Products: -
Products: -
?
S-adenosyl-L-methionine + cytosine1400 in 16S rRNA
S-adenosyl-L-homocysteine + 5-methylcytosine1400 in 16S rRNA
Thermus thermophilus HB8 / ATCC 27634 / DSM 579
Substrates: -
Products: -
Products: -
?
S-adenosyl-L-methionine + cytosine1404 in 16S rRNA
S-adenosyl-L-homocysteine + 5-methylcytosine1404 in 16S rRNA
Substrates: -
Products: -
Products: -
?
S-adenosyl-L-methionine + cytosine1404 in 16S rRNA
S-adenosyl-L-homocysteine + 5-methylcytosine1404 in 16S rRNA
Substrates: RsmF methylates C1404 to about 35% with 16S rRNA and completely with 30S subunits
Products: -
Products: -
?
S-adenosyl-L-methionine + cytosine1404 in 16S rRNA
S-adenosyl-L-homocysteine + 5-methylcytosine1404 in 16S rRNA
Thermus thermophilus HB8 / ATCC 27634 / DSM 579
Substrates: -
Products: -
Products: -
?
S-adenosyl-L-methionine + cytosine1404 in 16S rRNA
S-adenosyl-L-homocysteine + 5-methylcytosine1404 in 16S rRNA
Thermus thermophilus HB8 / ATCC 27634 / DSM 579
Substrates: RsmF methylates C1404 to about 35% with 16S rRNA and completely with 30S subunits
Products: -
Products: -
?
S-adenosyl-L-methionine + cytosine1407 in 16S rRNA
S-adenosyl-L-homocysteine + 5-methylcytosine1407 in 16S rRNA
Substrates: nucleotide C1407 is located at a functionally active region of the 30 S subunit interface close to the P site. YebU-directed methylation of this nucleotide seems to be conserved in bacteria
Products: -
Products: -
?
S-adenosyl-L-methionine + cytosine1407 in 16S rRNA
S-adenosyl-L-homocysteine + 5-methylcytosine1407 in 16S rRNA
Substrates: purified recombinant YebU protein retains its specificity for C1407 in vitro, and methylates 30 S subunits (but not naked 16 S rRNA or 70 S ribosomes) isolated from yebU knockout strains
Products: -
Products: -
?
S-adenosyl-L-methionine + cytosine1407 in 16S rRNA
S-adenosyl-L-homocysteine + 5-methylcytosine1407 in 16S rRNA
Substrates: -
Products: -
Products: -
?
S-adenosyl-L-methionine + cytosine1407 in 16S rRNA
S-adenosyl-L-homocysteine + 5-methylcytosine1407 in 16S rRNA
-
Substrates: nucleotide C1407 forms part of the aminoglycoside binding pocket of the 16S rRNA
Products: -
Products: -
?
S-adenosyl-L-methionine + cytosine1407 in 16S rRNA
S-adenosyl-L-homocysteine + 5-methylcytosine1407 in 16S rRNA
-
Substrates: -
Products: -
Products: -
?
S-adenosyl-L-methionine + cytosine1407 in 16S rRNA
S-adenosyl-L-homocysteine + 5-methylcytosine1407 in 16S rRNA
-
Substrates: nucleotide C1407 forms part of the aminoglycoside binding pocket of the 16S rRNA
Products: -
Products: -
?
S-adenosyl-L-methionine + cytosine1407 in 16S rRNA
S-adenosyl-L-homocysteine + 5-methylcytosine1407 in 16S rRNA
-
Substrates: -
Products: -
Products: -
?
S-adenosyl-L-methionine + cytosine1407 in 16S rRNA
S-adenosyl-L-homocysteine + 5-methylcytosine1407 in 16S rRNA
-
Substrates: -
Products: -
Products: -
?
S-adenosyl-L-methionine + cytosine1407 in 16S rRNA
S-adenosyl-L-homocysteine + 5-methylcytosine1407 in 16S rRNA
Substrates: -
Products: -
Products: -
?
S-adenosyl-L-methionine + cytosine1407 in 16S rRNA
S-adenosyl-L-homocysteine + 5-methylcytosine1407 in 16S rRNA
Substrates: RsmF produces only trace amounts of methylation of C1407 with 16S rRNA and about 75% with 30S subunits
Products: -
Products: -
?
S-adenosyl-L-methionine + cytosine1407 in 16S rRNA
S-adenosyl-L-homocysteine + 5-methylcytosine1407 in 16S rRNA
Thermus thermophilus HB8 / ATCC 27634 / DSM 579
Substrates: -
Products: -
Products: -
?
S-adenosyl-L-methionine + cytosine1407 in 16S rRNA
S-adenosyl-L-homocysteine + 5-methylcytosine1407 in 16S rRNA
Thermus thermophilus HB8 / ATCC 27634 / DSM 579
Substrates: RsmF produces only trace amounts of methylation of C1407 with 16S rRNA and about 75% with 30S subunits
Products: -
Products: -
?
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NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
LITERATURE
COMMENTARY
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
S-adenosyl-L-methionine + cytosine1400 in 16S rRNA
S-adenosyl-L-homocysteine + 5-methylcytosine1400 in 16S rRNA
S-adenosyl-L-methionine + cytosine1404 in 16S rRNA
S-adenosyl-L-homocysteine + 5-methylcytosine1404 in 16S rRNA
S-adenosyl-L-methionine + cytosine1407 in 16S rRNA
S-adenosyl-L-homocysteine + 5-methylcytosine1407 in 16S rRNA
S-adenosyl-L-methionine + cytosine1400 in 16S rRNA
S-adenosyl-L-homocysteine + 5-methylcytosine1400 in 16S rRNA
Substrates: -
Products: -
Products: -
?
S-adenosyl-L-methionine + cytosine1400 in 16S rRNA
S-adenosyl-L-homocysteine + 5-methylcytosine1400 in 16S rRNA
Thermus thermophilus HB8 / ATCC 27634 / DSM 579
Substrates: -
Products: -
Products: -
?
S-adenosyl-L-methionine + cytosine1404 in 16S rRNA
S-adenosyl-L-homocysteine + 5-methylcytosine1404 in 16S rRNA
Substrates: -
Products: -
Products: -
?
S-adenosyl-L-methionine + cytosine1404 in 16S rRNA
S-adenosyl-L-homocysteine + 5-methylcytosine1404 in 16S rRNA
Thermus thermophilus HB8 / ATCC 27634 / DSM 579
Substrates: -
Products: -
Products: -
?
S-adenosyl-L-methionine + cytosine1407 in 16S rRNA
S-adenosyl-L-homocysteine + 5-methylcytosine1407 in 16S rRNA
Substrates: nucleotide C1407 is located at a functionally active region of the 30 S subunit interface close to the P site. YebU-directed methylation of this nucleotide seems to be conserved in bacteria
Products: -
Products: -
?
S-adenosyl-L-methionine + cytosine1407 in 16S rRNA
S-adenosyl-L-homocysteine + 5-methylcytosine1407 in 16S rRNA
-
Substrates: nucleotide C1407 forms part of the aminoglycoside binding pocket of the 16S rRNA
Products: -
Products: -
?
S-adenosyl-L-methionine + cytosine1407 in 16S rRNA
S-adenosyl-L-homocysteine + 5-methylcytosine1407 in 16S rRNA
-
Substrates: -
Products: -
Products: -
?
S-adenosyl-L-methionine + cytosine1407 in 16S rRNA
S-adenosyl-L-homocysteine + 5-methylcytosine1407 in 16S rRNA
-
Substrates: nucleotide C1407 forms part of the aminoglycoside binding pocket of the 16S rRNA
Products: -
Products: -
?
S-adenosyl-L-methionine + cytosine1407 in 16S rRNA
S-adenosyl-L-homocysteine + 5-methylcytosine1407 in 16S rRNA
-
Substrates: -
Products: -
Products: -
?
S-adenosyl-L-methionine + cytosine1407 in 16S rRNA
S-adenosyl-L-homocysteine + 5-methylcytosine1407 in 16S rRNA
-
Substrates: -
Products: -
Products: -
?
S-adenosyl-L-methionine + cytosine1407 in 16S rRNA
S-adenosyl-L-homocysteine + 5-methylcytosine1407 in 16S rRNA
Substrates: -
Products: -
Products: -
?
S-adenosyl-L-methionine + cytosine1407 in 16S rRNA
S-adenosyl-L-homocysteine + 5-methylcytosine1407 in 16S rRNA
Thermus thermophilus HB8 / ATCC 27634 / DSM 579
Substrates: -
Products: -
Products: -
?
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
introduction of a recombinant version of the Sgm methyltransferase gene from Micromonospora zionensis into an Escherichia coli strain that has a full complement of housekeeping methyltransferases. Analyses of the 16S rRNA shows that the m5C1407-specific housekeeping methyltransferase RsmF (YebU) is outcompeted by Sgm as the resistance methyltransferase gains access to its own m7G1405 target on the 30S ribosomal subunit. A single amino acid change in Sgm, which lowers the level of conferred resistance, reduces the ability of Sgm to interfere with RsmF methylation on the 30S subunit
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additional information
-
RmtC, EC 2.1.1.179, in the presence of aminoglycosides impedes methylation at the N5 position of nucleotide C1407 when the N7 position of G1405 is methylated, MALDI mass spectrometry product analysis, mechanism, overview
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
Highest Expressing Human Cell Lines
Cell Line LinksPlease wait a moment until the data is sorted. This message will disappear when the data is sorted.
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
malfunction
metabolism
physiological function
malfunction
inactivation of the yebU gene leads to loss of methylation at C1407 in 16S rRNA. yebU knockout strains display slower growth and reduced fitness in competition with wild-type cells (at 37°C and 42°C)
malfunction
-
DELTArsmF null mutant bacteria have a decreased susceptibility to aminoglycosides, including 4,6- and 4,5-deoxystreptamine aminoglycosides
malfunction
-
DELTArsmF null mutant bacteria have a decreased susceptibility to aminoglycosides, including 4,6- and 4,5-deoxystreptamine aminoglycosides
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metabolism
two methyltransferases, RsmB and RsmF, are responsible for all four 5-methylcytidine modifications in 16S rRNA of Thermus thermophilus, overview. RsmB produces m5C967, while RsmF methylates C1400, C1404, and C1407 in a 30S subunit substrate, but only C1400 and C1404 when naked 16S rRNA is the substrate. C1400 and C1404 are sufficiently buried in the mature ribosome structure so require extensive unfolding of the rRNA to be accessible to RsmF
metabolism
Thermus thermophilus HB8 / ATCC 27634 / DSM 579
-
two methyltransferases, RsmB and RsmF, are responsible for all four 5-methylcytidine modifications in 16S rRNA of Thermus thermophilus, overview. RsmB produces m5C967, while RsmF methylates C1400, C1404, and C1407 in a 30S subunit substrate, but only C1400 and C1404 when naked 16S rRNA is the substrate. C1400 and C1404 are sufficiently buried in the mature ribosome structure so require extensive unfolding of the rRNA to be accessible to RsmF
-
physiological function
-
the housekeeping methylation at C1407 is involved in intrinsic aminoglycoside susceptibility in Escherichia coli
physiological function
-
the housekeeping methylation at C1407 is involved in intrinsic aminoglycoside susceptibility in Escherichia coli
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Show AA Sequence and Transmembrane Helices (1741 entries)
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Please use the AA Sequence and Transmembrane Helices Search for a specific query.
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
additional information
comparison of Thermus thermophilus RsmB and RsmF protein sequences, secondary and tertiary structure, differences in substrate binding, overview
additional information
Thermus thermophilus HB8 / ATCC 27634 / DSM 579
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comparison of Thermus thermophilus RsmB and RsmF protein sequences, secondary and tertiary structure, differences in substrate binding, overview
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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
YebU crystals are grown at room temperature by the hanging-drop, vapour-diffusion method, Crystal structure solved at 2.9 A resolution. The enzyme has an N-terminal catalytic domain that binds S-adenosylmethionine. The C-terminal domain has structural similarity to PUA domains of pseudouridine synthases and archaeosine-specific transglycosylases. The YebU structure is used to propose the most likely mechanism for its substrate specificity and recognition
RsmF in a complex with cofactor S-adenosyl-methionine, three crystal structures, X-ray diffrcation structure determination and analysis at 1.3 A resolution
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
additional information
-
construction of a series of in-frame knockout and knock-in mutants of Escherichia coli, corresponding to the genotypes rsmF+, DELTArsmF, rsmF+ rmtC+, and DELTArsmF rmtC+, mutant strain growth kinetics, overview
additional information
-
construction of a series of in-frame knockout and knock-in mutants of Escherichia coli, corresponding to the genotypes rsmF+, DELTArsmF, rsmF+ rmtC+, and DELTArsmF rmtC+, mutant strain growth kinetics, overview
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additional information
construction of a null mutant strain in which TTHA1387 is inactivated by homologous recombination and insertion of a heat stable kanamycin-resistance gene
additional information
Thermus thermophilus HB8 / ATCC 27634 / DSM 579
-
construction of a null mutant strain in which TTHA1387 is inactivated by homologous recombination and insertion of a heat stable kanamycin-resistance gene
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TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
60 - 70
no difference in the relative growth proportions of the wild-type and rsmF mutant at 70°C. However, at 60°C, the rsmF null mutant constitutes only around 5% of the population, and at 80°C the rsmF null mutant is unable to grow at all
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PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
the Escherichia coli YebU gene is cloned into the PT73.3HisGW vector.25 The resulting construct encodes a polypeptide with the YebU gene and both N- and C-terminal hexa-histidine tails
the yebU gene is cloned as a partial and as a fulllength sequence with the respective purposes of creating a knockout strain and expressing recombinant YebU protein. Full-length YebU protein with a C-terminal histidine-tag is expressed in Escherichia coli
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Andersen, N.M.; Douthwaite, S.
YebU is a m5C methyltransferase specific for 16 S rRNA nucleotide 1407
J. Mol. Biol.
359
777-786
2006
Escherichia coli (P76273)
brenda
Hallberg, B.M.; Ericsson, U.B.; Johnson, K.A.; Andersen, N.M.; Douthwaite, S.; Nordlund, P.; Beuscher, A.E. 4th; 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
Escherichia coli (P76273), Escherichia coli
brenda
Cubrilo, S.; Babic, F.; Douthwaite, S.; Maravic Vlahovicek, G.
The aminoglycoside resistance methyltransferase Sgm impedes RsmF methylation at an adjacent rRNA nucleotide in the ribosomal A site
RNA
15
1492-1497
2009
Escherichia coli (P76273)
brenda
Gutierrez, B.; Escudero, J.A.; San Millan, A.; Hidalgo, L.; Carrilero, L.; Ovejero, C.M.; Santos-Lopez, A.; Thomas-Lopez, D.; Gonzalez-Zorn, B.
Fitness cost and interference of Arm/Rmt aminoglycoside resistance with the RsmF housekeeping methyltransferases
Antimicrob. Agents Chemother.
56
2335-2341
2012
Escherichia coli, Escherichia coli BW25113
brenda
Demirci, H.; Larsen, L.H.; Hansen, T.; Rasmussen, A.; Cadambi, A.; Gregory, S.T.; Kirpekar, F.; Jogl, G.
Multi-site-specific 16S rRNA methyltransferase RsmF from Thermus thermophilus
RNA
16
1584-1596
2010
Thermus thermophilus (Q5SJI2), Thermus thermophilus HB8 / ATCC 27634 / DSM 579 (Q5SJI2)
brenda
Lioy, V.S.; Goussard, S.; Guerineau, V.; Yoon, E.J.; Courvalin, P.; Galimand, M.; Grillot-Courvalin, C.
Aminoglycoside resistance 16S rRNA methyltransferases block endogenous methylation, affect translation efficiency and fitness of the host
RNA
20
382-391
2014
Escherichia coli, Escherichia coli MM294
brenda
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