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Enzyme Nomenclature
Information on EC 2.1.1.193 - 16S rRNA (uracil1498-N3)-methyltransferase
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The enzyme appears in viruses and cellular organisms
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EC NUMBER 
COMMENTARY 
2.1.1.193
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RECOMMENDED NAME
GeneOntology No.
16S rRNA (uracil1498-N3)-methyltransferase
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
S-adenosyl-L-methionine + uracil1498 in 16S rRNA = S-adenosyl-L-homocysteine + N3-methyluracil1498 in 16S rRNA
S-adenosyl-L-methionine + uracil1498 in 16S rRNA = S-adenosyl-L-homocysteine + N3-methyluracil1498 in 16S rRNA
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S-adenosyl-L-methionine + uracil1498 in 16S rRNA = S-adenosyl-L-homocysteine + N3-methyluracil1498 in 16S rRNA
structure-function relationship and catalytic mechanism, overview
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SYSTEMATIC NAME
IUBMB Comments
S-adenosyl-L-methionine:16S rRNA (uracil1498-N3)-methyltransferase
The enzyme specifically methylates uracil1498 at N3 in 16S rRNA.
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
evolution
RsmE is the founding member of a RNA methyltransferase family responsible for N3-methylation of U1498 in 16S ribosomal RNA. It is well conserved across bacteria and plants and may play an 30 important role in ribosomal intersubunit communication
malfunction
a yggJ deletion strain lacks the methyl group at U1498 as well as the specific methyltransferase activity. The deletion strain is unaffected in exponential growth in rich or minimal media at multiple temperatures, but it is defective when grown in competition with isogenic wild-type cells
physiological function
RsmE is responsible for methylation of U1498 in 16S ribosomal RNA in Escherichia coli
additional information
RsmE forms a flexible dimeric conformation that is essential for substrate binding. RsmE-S-adenosyl-L-methionine-uridylic acid complex modeling and substrate binding structure, overview. The MTase domain of one subunit in dimeric RsmE is responsible for binding of one S-adenosyl-L-methionine molecule and catalytic process while the PUA-like domain in the other subunit is mainly responsible for recognition of one substrate molecule, the ribosomal RNA fragment and ribosomal protein complex. The methylation process is required by collaboration of both subunits, and dimerization is functionally critical for catalysis. Molecular replacement of crystal structure, PDB ID 1VHY
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SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
S-adenosyl-L-methionine + uracil1498 in 16S rRNA
S-adenosyl-L-homocysteine + N3-methyluracil1498 in 16S rRNA
S-adenosyl-L-methionine + uracil1498 in 16S rRNA
S-adenosyl-L-homocysteine + N3-methyluracil1498 in 16S rRNA
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-
?
S-adenosyl-L-methionine + uracil1498 in 16S rRNA
S-adenosyl-L-homocysteine + N3-methyluracil1498 in 16S rRNA
activity is dependent on a fully assembled 30 S ribosome subunit
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-
?
S-adenosyl-L-methionine + uracil1498 in 16S rRNA
S-adenosyl-L-homocysteine + N3-methyluracil1498 in 16S rRNA
small ribosome subunits obtained from an RsmE deletion strain can be methylated by purified RsmE, neither 70S ribosomes nor 50S subunits are active. 16S rRNA obtained from the mutant strain, synthetic 16S rRNA, and 3' minor domain RNA are all very poor or inactive as substrates. 30S particles partially depleted of proteins by treatment with high concentrations of LiCl or in vitro reconstituted intermediate particles also show little or no methyl acceptor activity. RsmE requires a highly structured ribonucleoprotein particle as a substrate for methylation
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S-adenosyl-L-methionine + uracil1498 in 16S rRNA
S-adenosyl-L-homocysteine + N3-methyluracil1498 in 16S rRNA
the enzyme is highly specific for U1498 in 16S rRNA. The purified enzyme is able to incorporate methyl groups from S-adenosyl-L-methionine into 30S particles purified from the mutant strain but not into 30S particles purified from wild type. Approximately one methyl group could be incorporated per mutant 30S subunit at high levels of enzyme
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S-adenosyl-L-methionine + uracil1498 in 16S rRNA
S-adenosyl-L-homocysteine + N3-methyluracil1498 in 16S rRNA
RsmE requires a highly structured ribonucleoprotein particle (a fully assembled 30S ribosome subunit) as a substrate for methylation, and this methylation occurs late during 30S ribosome assembly
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?
S-adenosyl-L-methionine + uracil1498 in 16S rRNA
S-adenosyl-L-homocysteine + N3-methyluracil1498 in 16S rRNA
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?
S-adenosyl-L-methionine + uracil1498 in 16S rRNA
S-adenosyl-L-homocysteine + N3-methyluracil1498 in 16S rRNA
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?
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NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
S-adenosyl-L-methionine + uracil1498 in 16S rRNA
S-adenosyl-L-homocysteine + N3-methyluracil1498 in 16S rRNA
S-adenosyl-L-methionine + uracil1498 in 16S rRNA
S-adenosyl-L-homocysteine + N3-methyluracil1498 in 16S rRNA
P0AGL7
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-
-
?
S-adenosyl-L-methionine + uracil1498 in 16S rRNA
S-adenosyl-L-homocysteine + N3-methyluracil1498 in 16S rRNA
P0AGL7
activity is dependent on a fully assembled 30 S ribosome subunit
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-
?
S-adenosyl-L-methionine + uracil1498 in 16S rRNA
S-adenosyl-L-homocysteine + N3-methyluracil1498 in 16S rRNA
P0AGL7
RsmE requires a highly structured ribonucleoprotein particle (a fully assembled 30S ribosome subunit) as a substrate for methylation, and this methylation occurs late during 30S ribosome assembly
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?
S-adenosyl-L-methionine + uracil1498 in 16S rRNA
S-adenosyl-L-homocysteine + N3-methyluracil1498 in 16S rRNA
P9WGX1
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?
S-adenosyl-L-methionine + uracil1498 in 16S rRNA
S-adenosyl-L-homocysteine + N3-methyluracil1498 in 16S rRNA
Q9I694
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?
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
S-adenosyl-L-methionine
one molecule bound per subunit of the enzyme homodimer
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Mg2+
Mg2+
most active in the presence of 1015 mM Mg2+ at pH 79. At 30 mM Mg2+ optimal activity is reduced by 60%. In the presence of spermidine, Mg2+ is not required for activity. Activity could be restored up to 60% of that with Mg2+ by addition of spermidine at 30 mM
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INHIBITORS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
spermidine
in the presence of spermidine, Mg2+ is not required for activity. Activity could be restored up to 60% of that with Mg2+ by addition of spermidine at 30 mM
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.002
uracil1498 in 16S rRNA
pH 7.0, 37°C, the Km-value for 16S rRNA is measured as a Km for the physiological substrate, 30S ribosomal subunit
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additional information
additional information
thermodynamics of S-adenosyl-L-methionine binding by RsmE, thermodynamic analysis, overview
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.0013
uracil1498 in 16S rRNA
pH 7.0, 37°C, the Km-value for 16S rRNA is measured as a Km for the physiological substrate, 30S ribosomal subunit
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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PDB
SCOP
CATH
ORGANISM
UNIPROT
Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)
Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)
Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)
Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)
Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
Neisseria gonorrhoeae (strain ATCC 700825 / FA 1090)
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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SUBUNITS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
dimer
homodimer
the crystal structure in monomer shows that RsmE consists of two distinct but structurally related domains: the pseudouridine synthases and archaeosine-specific transglycosylasess-like RNA recognition and binding domain, PUA, and the conserved MTase domain with a deep trefoil knot
additional information
the methylation process is required by collaboration of both subunits, and dimerization is functionally critical for catalysis. Molecular replacement of crystal structure, PDB ID 1VHY. Structural comparisons of N-terminal and C-terminal domains of RsmE with related proteins, overview
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Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
sitting drop vapor diffusion method at room temperature, 0.15 M potassium thiocyanate and 24% w/v PEG monomethyl ether 2000, 3-4 days, crystal soaking in S-adenosyl-L-methionine solution or cocrystallization of enzyme and cofactor are not successful, X-ray diffraction structure determination and analysis at 2.25 A resolution, molecular replacement
sitting drop vapor diffusion method, using 100 mM Tris-HCl pH 8.0, 1.5 M potassium acetate, at 24°C
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Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
Ni-NTA column chromatography and Mono S column chromatography
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Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
cloned as a N-terminal His-tag fusion protein, which allows easy purification, purified recombinant YggJ specifically methylates m3U1498 in vitro
expressed in Escherichia coli BL21 (DE3) and RsmE-deleted Escherichia coli KL16 cells
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ENGINEERING
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
additional information
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the deletion of critical residues at the C-terminus of Rv2372c leads to an inability of the protein to form stable dimers and to abolition of the methyltransferase activity
additional information
the deletion of critical residues at the C-terminus of Rv2372c leads to an inability of the protein to form stable dimers and to abolition of the methyltransferase activity
Show AA Sequence (20509 entries)
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LINKS TO OTHER DATABASES (specific for EC-Number 2.1.1.193)
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