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Literature summary for 2.1.1.186 extracted from

  • Punekar, A.S.; Shepherd, T.R.; Liljeruhm, J.; Forster, A.C.; Selmer, M.
    Crystal structure of RlmM, the 2O-ribose methyltransferase for C2498 of Escherichia coli 23S rRNA (2012), Nucleic Acids Res., 40, 10507-10520.
    View publication on PubMedView publication on EuropePMC

Cloned(Commentary)

Cloned (Comment) Organism
gene rlmM, expression of His-tagged RlmM in Escherichia coli strain BL21(DE3) Escherichia coli

Crystallization (Commentary)

Crystallization (Comment) Organism
purified recombinant His-tagged RlmM free or in complex with S-adenosyl-L-methionine, sitting drop vapor diffusion method, 0.0015 ml 10 mg/ml protein solution os mixed with 0.0015 ml of reservoir solution containing 0.3 M ammonium tartrate, pH 7.0, and 20% PEG 3350, 20°C, 1 week, two crystal forms, X-ray diffraction structure determination and analysis at 1.9 A and 2.6 A resolution, respectively, molecular replacement Escherichia coli

Metals/Ions

Metals/Ions Comment Organism Structure
Mg2+ required Escherichia coli

Natural Substrates/ Products (Substrates)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
S-adenosyl-L-methionine + cytidine2498 in 23S rRNA Escherichia coli RlmM is active on 23S rRNA from an RlmM knockout strain but not on mature 50S subunits from the same strain S-adenosyl-L-homocysteine + 2'-O-methylcytidine2498 in 23S rRNA
-
?
S-adenosyl-L-methionine + cytidine2498 in 23S rRNA Escherichia coli BW25113 RlmM is active on 23S rRNA from an RlmM knockout strain but not on mature 50S subunits from the same strain S-adenosyl-L-homocysteine + 2'-O-methylcytidine2498 in 23S rRNA
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?

Organism

Organism UniProt Comment Textmining
Escherichia coli P0ADR6 gene rlmM
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Escherichia coli BW25113 P0ADR6 gene rlmM
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Purification (Commentary)

Purification (Comment) Organism
recombinant His-tagged RlmM from Escherichia coli strain BL21(DE3) by nickel affinity chromatography, gel filtration, and ultrafiltration Escherichia coli

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
S-adenosyl-L-methionine + cytidine2498 in 23S rRNA RlmM is active on 23S rRNA from an RlmM knockout strain but not on mature 50S subunits from the same strain Escherichia coli S-adenosyl-L-homocysteine + 2'-O-methylcytidine2498 in 23S rRNA
-
?
S-adenosyl-L-methionine + cytidine2498 in 23S rRNA 23S rRNA substrate structure, overview. The S-adenosyl-L-methionine-binding site is open and shallow, suggesting that RNA substrate binding may be required to form a conformation needed for catalysis. RlmM uses one side of the two domains and the inter-domain linker to recognize its RNA substrate Escherichia coli S-adenosyl-L-homocysteine + 2'-O-methylcytidine2498 in 23S rRNA
-
?
S-adenosyl-L-methionine + cytidine2498 in 23S rRNA RlmM is active on 23S rRNA from an RlmM knockout strain but not on mature 50S subunits from the same strain Escherichia coli BW25113 S-adenosyl-L-homocysteine + 2'-O-methylcytidine2498 in 23S rRNA
-
?
S-adenosyl-L-methionine + cytidine2498 in 23S rRNA 23S rRNA substrate structure, overview. The S-adenosyl-L-methionine-binding site is open and shallow, suggesting that RNA substrate binding may be required to form a conformation needed for catalysis. RlmM uses one side of the two domains and the inter-domain linker to recognize its RNA substrate Escherichia coli BW25113 S-adenosyl-L-homocysteine + 2'-O-methylcytidine2498 in 23S rRNA
-
?

Subunits

Subunits Comment Organism
More RlmM consists of an N-terminal THUMP domain and a C-terminal catalytic Rossmann-like fold MTase domain in a distinct arrangement, detailed structure analysis, overview Escherichia coli

Synonyms

Synonyms Comment Organism
2O-ribose methyltransferase
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Escherichia coli
RlmM
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Escherichia coli
ygdE
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Escherichia coli

Temperature Optimum [°C]

Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
37
-
assay at Escherichia coli

Temperature Stability [°C]

Temperature Stability Minimum [°C] Temperature Stability Maximum [°C] Comment Organism
additional information
-
Na2SO4 gives the highest thermal stability to RlmM Escherichia coli

pH Optimum

pH Optimum Minimum pH Optimum Maximum Comment Organism
7.6
-
assay at Escherichia coli

Cofactor

Cofactor Comment Organism Structure
S-adenosyl-L-methionine the S-adenosyl-L-methionine-binding site is open and shallow Escherichia coli

General Information

General Information Comment Organism
evolution the catalytic domain of RlmM is closely related to YiiB, TlyA and fibrillarins, with the second K of the catalytic tetrad KDKE shifted by two residues at the C-terminal end of a beta strand compared with most 2'O MTases Escherichia coli
physiological function RlmM catalyzes the S-adenosyl methionine-dependent 20O methylation of C2498 in 23S ribosomal RNA of Escherichia coli Escherichia coli