Information on EC 2.1.1.190 - 23S rRNA (uracil1939-C5)-methyltransferase

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The enzyme appears in viruses and cellular organisms

EC NUMBER
COMMENTARY hide
2.1.1.190
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RECOMMENDED NAME
GeneOntology No.
23S rRNA (uracil1939-C5)-methyltransferase
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REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
S-adenosyl-L-methionine + uracil1939 in 23S rRNA = S-adenosyl-L-homocysteine + 5-methyluracil1939 in 23S rRNA
show the reaction diagram
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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].
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
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Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
evolution
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YefA is a COG2265 member. During evolution, COG2265 enzymes have undergone a series of changes in target specificity and YefA is closer to an archetypical m5U methyltransferase. A functional shift has occurred during the evolution of the Bacillus subtilis YefA and YfjO methyltransferases.To reflect its dual specificity, YefA is renamed RlmCD
malfunction
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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
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RlmD is the archetypical enzyme that is specific for m5U1939 in 23S rRNA
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
additional information
?
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NATURAL SUBSTRATES
NATURAL PRODUCTS
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
additional information
?
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
folate
dependent on
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
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pH 7.5, 37°C
0.003 - 0.034
uracil1939 in 23S rRNA
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.06
S-adenosyl-L-methionine
Escherichia coli
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pH 7.5, 37°C
0.006 - 0.18
uracil1939 in 23S rRNA
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7.5
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assay at
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
37
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assay at
PDB
SCOP
CATH
ORGANISM
UNIPROT
Escherichia coli (strain K12)
Escherichia coli (strain K12)
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
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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
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Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
(His)6-tag enzyme
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Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
expression of a intein-fusion protein with an C-terminal His-tag
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gene yefA, phylogenetic analysis, functional complementation of Bacillus subtilis knockout strain BG12826 yefA::pMutin2 and DELTAyefA::Cm deletion mutant, and of Escherichia coli enzyme-deficient BW 25113 DELTAtrmA/DELTArlmC/DELTArlmD strain
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ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
D265A
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the specific activity of the mutant enzyme is 830fold lower than that of the wild-type enzyme
D265E
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mutant enzyme has no activity
D363A
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mutation results in complete loss of activity
D363N
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the specific activity of the mutant enzyme is 2fold lower than that of the wild-type enzyme
E424Q
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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
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