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Information on EC 2.1.1.193 - 16S rRNA (uracil1498-N3)-methyltransferase and Organism(s) Escherichia coli and UniProt Accession P0AGL7

for references in articles please use BRENDA:EC2.1.1.193
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IUBMB Comments
The enzyme specifically methylates uracil1498 at N3 in 16S rRNA.
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This record set is specific for:
Escherichia coli
UNIPROT: P0AGL7
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The taxonomic range for the selected organisms is: Escherichia coli
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota, Archaea
Reaction Schemes
hide
S-adenosyl-L-methionine
+
uracil1498 in 16S rRNA
=
S-adenosyl-L-homocysteine
+
N3-methyluracil1498 in 16S rRNA
+
uracil1498 in 16S rRNA
=
+
N3-methyluracil1498 in 16S rRNA
Synonyms
rv2372c, duf558 protein, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
16S rRNA methyltransferase
-
DUF558 protein
-
m3U1498 specific methyltransferase
-
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
S-adenosyl-L-methionine + uracil1498 in 16S rRNA = S-adenosyl-L-homocysteine + N3-methyluracil1498 in 16S rRNA
show the reaction diagram
structure-function relationship and catalytic mechanism, overview
SYSTEMATIC NAME
IUBMB Comments
S-adenosyl-L-methionine:16S rRNA (uracil1498-N3)-methyltransferase
The enzyme specifically methylates uracil1498 at N3 in 16S 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 + uracil1498 in 16S rRNA
S-adenosyl-L-homocysteine + N3-methyluracil1498 in 16S 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 + uracil1498 in 16S rRNA
S-adenosyl-L-homocysteine + N3-methyluracil1498 in 16S rRNA
show the reaction diagram
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
S-adenosyl-L-methionine
one molecule bound per subunit of the enzyme homodimer
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
NH4+
most active in the presence of 100 mM NH4Cl at pH 7–9
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
EDTA
10 mM, complete inhibition
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
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
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0267
S-adenosyl-L-methionine
pH 7.0, 37°C
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
-
additional information
additional information
thermodynamics of S-adenosyl-L-methionine binding by RsmE, thermodynamic analysis, overview
-
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0007
S-adenosyl-L-methionine
pH 7.0, 37°C
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
-
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
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
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
29000
x * 29000, SDS-PAGE
50000
gel filtration
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
?
x * 29000, SDS-PAGE
dimer
forms dimers in solution
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
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
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
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
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Basturea, G.N.; Rudd, K.E.; Deutscher, M.P.
Identification and characterization of RsmE, the founding member of a new RNA base methyltransferase family
RNA
12
426-434
2006
Escherichia coli (P0AGL7), Escherichia coli
Manually annotated by BRENDA team
Basturea, G.N.; Deutscher, M.P.
Substrate specificity and properties of the Escherichia coli 16S rRNA methyltransferase, RsmE
RNA
13
1969-1976
2007
Escherichia coli (P0AGL7)
Manually annotated by BRENDA team
Zhang, H.; Wan, H.; Gao, Z.Q.; Wei, Y.; Wang, W.J.; Liu, G.F.; Shtykova, E.V.; Xu, J.H.; Dong, Y.H.
Insights into the catalytic mechanism of 16S rRNA methyltransferase RsmE (m3U1498) from crystal and solution structures
J. Mol. Biol.
423
576-589
2012
Escherichia coli (P0AGL7)
Manually annotated by BRENDA team