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Information on EC 2.1.1.190 - 23S rRNA (uracil1939-C5)-methyltransferase and Organism(s) Escherichia coli and UniProt Accession P55135

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IUBMB Comments
The enzyme specifically methylates uracil1939 at C5 in 23S rRNA . The enzyme contains an [4Fe-4S] cluster coordinated by four conserved cysteine residues .
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This record set is specific for:
Escherichia coli
UNIPROT: P55135
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The taxonomic range for the selected organisms is: Escherichia coli
The expected taxonomic range for this enzyme is: Bacteria, Archaea, Eukaryota
Reaction Schemes
hide
S-adenosyl-L-methionine
+
uracil1939 in 23S rRNA
=
S-adenosyl-L-homocysteine
+
5-methyluracil1939 in 23S rRNA
+
uracil1939 in 23S rRNA
=
+
5-methyluracil1939 in 23S rRNA
Synonyms
rlmfo, mcap0476, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
RNA uridine methyltransferase A
-
m5U methyltransferase
-
-
RNA m5U methyltransferase
-
-
RumA
-
formerly
SYSTEMATIC NAME
IUBMB Comments
S-adenosyl-L-methionine:23S rRNA (uracil1939-C5)-methyltransferase
The enzyme specifically methylates uracil1939 at C5 in 23S rRNA [1]. The enzyme contains an [4Fe-4S] cluster coordinated by four conserved cysteine residues [2].
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
S-adenosyl-L-methionine + uracil1939 in 23S rRNA
S-adenosyl-L-homocysteine + 5-methyluracil1939 in 23S rRNA
show the reaction diagram
S-adenosyl-L-methionine + uracil1939 in 23S rRNA
S-adenosyl-L-homocysteine + 5-methyluracil1939 in 23S rRNA
show the reaction diagram
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
S-adenosyl-L-methionine + uracil1939 in 23S rRNA
S-adenosyl-L-homocysteine + 5-methyluracil1939 in 23S rRNA
show the reaction diagram
-
-
-
-
?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
S-adenosyl-L-methionine
-
-
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.026
S-adenosyl-L-methionine
pH 7.5, 37°C
0.003 - 0.034
uracil1939 in 23S rRNA
-
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.06
S-adenosyl-L-methionine
pH 7.5, 37°C
0.006 - 0.18
uracil1939 in 23S rRNA
-
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
malfunction
strains lacking the RumA methylase are gradually out-competed by wild type strains in growth competition experiments, suggesting that the m5U methylation improves ribosome performance. Base substitutions at U1939 in 23S rRNA have little effect on growth or the fidelity of translation, but alter the sensitivity of the ribosomes to the antibiotics fusidic acid and capreomycin
physiological function
-
RlmD is the archetypical enzyme that is specific for m5U1939 in 23S rRNA
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
hanging drop vapor diffusion method, the crystal structure is determined at 1.95 A resolution using a single crystal of the selenomethionyl protein. The protein is organized into three structural domains. The N-terminal domain (residues 15–74) is the smallest domain and is composed of five beta strands. The central domain (residues 75–92 and 125–262) and the catalytic domain (residues 93–124 and 263–431) are juxtaposed, and a concave surface is formed at the interface between them
hanging drop vapor diffusion method, the structure of a ternary complex containing RumA, S-adenosylhomocysteine and a covalently bound 23S rRNA fragment(1932–1968) with 5-fluoro-uridine at position 1939 is determined by molecular replacement methods
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
D265A
the specific activity of the mutant enzyme is 830fold lower than that of the wild-type enzyme
D265E
mutant enzyme has no activity
D363A
mutation results in complete loss of activity
D363N
the specific activity of the mutant enzyme is 2fold lower than that of the wild-type enzyme
E424Q
the mutant enzyme displays a biphasic reaction profile with an initial burst phase followed by a slow second phase, mutation results in at least 350fold reduction in the rate of proton abstraction
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
(His)6-tag enzyme
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expression of a intein-fusion protein with an C-terminal His-tag
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Persaud, C.; Lu, Y.; Vila-Sanjurjo, A.; Campbell, J.L.; Finley, J.; O'Connor, M.
Mutagenesis of the modified bases, m(5)U1939 and psi2504, in Escherichia coli 23S rRNA
Biochem. Biophys. Res. Commun.
392
223-227
2010
Escherichia coli (P55135)
Manually annotated by BRENDA team
Lee, T.T.; Agarwalla, S.; Stroud, R.M.
A unique RNA fold in the RumA-RNA-cofactor ternary complex contributes to substrate selectivity and enzymatic function
Cell
120
599-611
2005
Escherichia coli (P55135)
Manually annotated by BRENDA team
Agarwalla, S.; Kealey, J.T.; Santi, D.V.; Stroud, R.M.
Characterization of the 23 S ribosomal RNA m5U1939 methyltransferase from Escherichia coli
J. Biol. Chem.
277
8835-8840
2002
Escherichia coli (P55135)
Manually annotated by BRENDA team
Agarwalla, S.; Stroud, R.M.; Gaffney, B.J.
Redox reactions of the iron-sulfur cluster in a ribosomal RNA methyltransferase, RumA: optical and EPR studies
J. Biol. Chem.
279
34123-34129
2004
Escherichia coli (P55135)
Manually annotated by BRENDA team
Madsen, C.T.; Mengel-Jorgensen, J.; Kirpekar, F.; Douthwaite, S.
Identifying the methyltransferases for m(5)U747 and m(5)U1939 in 23S rRNA using MALDI mass spectrometry
Nucleic Acids Res.
31
4738-4746
2003
Escherichia coli (P55135)
Manually annotated by BRENDA team
Lee, T.T.; Agarwalla, S.; Stroud, R.M.
Crystal structure of RumA, an iron-sulfur cluster containing E. coli ribosomal RNA 5-methyluridine methyltransferase
Structure
12
397-407
2004
Escherichia coli (P55135)
Manually annotated by BRENDA team
Auxilien, S.; Rasmussen, A.; Rose, S.; Brochier-Armanet, C.; Husson, C.; Fourmy, D.; Grosjean, H.; Douthwaite, S.
Specificity shifts in the rRNA and tRNA nucleotide targets of archaeal and bacterial m5U methyltransferases
RNA
17
45-53
2011
Escherichia coli
Manually annotated by BRENDA team