Literature summary for 2.1.1.266 extracted from

Punekar, A.; Liljeruhm, J.; Shepherd, T.; Forster, A.; Selmer, M.
Structural and functional insights into the molecular mechanism of rRNA m6A methyltransferase RlmJ (2013), Nucleic Acids Res., 41, 9537-9548.

Search for more literature for 2.1.1.266

Cloned(Commentary)

Cloned (Comment)	Organism
gene rlmJ, sequence comparisons, recombinant expression of wild-type and mutant enzymes	Escherichia coli

Crystallization (Commentary)

Crystallization (Comment)	Organism
purified recombinant enzyme in apoform, in complex with the cofactor S-adenosyl-L-methionine, or with product S-adenosyl-L-homocysteine plus substrate analogue AMP, X-ray diffraction structure determination and analysis at 1.85-2.0 A resolution, enzyme apostructure analysis using PDB ID 2OO3, rigid-body refinement of the RlmJAPO structure against the RlmJSAM data	Escherichia coli

Protein Variants

Protein Variants	Comment	Organism
D164A	site-directed mutagenesis	Escherichia coli
H6D	site-directed mutagenesis	Escherichia coli
K18A	site-directed mutagenesis	Escherichia coli
K18R	site-directed mutagenesis	Escherichia coli
Y4A	site-directed mutagenesis	Escherichia coli
Y4F	site-directed mutagenesis	Escherichia coli

Natural Substrates/ Products (Substrates)

Natural Substrates	Organism	Comment (Nat. Sub.)	Natural Products	Comment (Nat. Pro.)	Rev.	Reac.
S-adenosyl-L-methionine + adenine2030 in 23S rRNA	Escherichia coli	-	S-adenosyl-L-homocysteine + N6-methyladenine2030 in 23S rRNA	-	?

Organism

Organism	UniProt	Comment	Textmining
Escherichia coli	P37634	MG1655, gene rlmJ	-

Purification (Commentary)

Purification (Comment)	Organism
recombinant wild-type and mutant enzymes	Escherichia coli

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.	Reac.
S-adenosyl-L-methionine + adenine2030 in 23S rRNA	-	Escherichia coli	S-adenosyl-L-homocysteine + N6-methyladenine2030 in 23S rRNA	-	?
S-adenosyl-L-methionine + adenine2030 in 23S rRNA	In vitro transcription of 23S rRNA substrate from the wild-type BW25113 strain. RlmJ methylates in vitro transcribed 23S rRNA, as well as a minimal substrate corresponding to helix 72, demonstrating independence of modifications and tertiary interactions in the RNA substrate. RlmJ displays specificity for adenosine, substrate binding site structure, overview. Location of A2030 in Escherichia coli 23S rRNA, overview	Escherichia coli	S-adenosyl-L-homocysteine + N6-methyladenine2030 in 23S rRNA	-	?

Synonyms

Synonyms	Comment	Organism
ribosomal RNA large subunit methyltransferase J	UniProt	Escherichia coli
rlmJ	-	Escherichia coli
rRNA m6A methyltransferase	-	Escherichia coli

Cofactor

Cofactor	Comment	Organism	Structure
S-adenosyl-L-methionine	dependent on, cofactor binding site structure determined with bound S-adenosyl-L-homocysteine and AMP, overview	Escherichia coli

General Information

General Information	Comment	Organism
evolution	the active site of RlmJ with motif IV sequence 164DPPY167 is more similar to DNA m6A MTases than to RNA m6 2A MTases, and structural comparison suggests that RlmJ binds its substrate base similarly to DNA MTases T4Dam and M.TaqI	Escherichia coli
malfunction	knockout of rlmJ does not affect the growth rate, but lowers the competitive fitness at long-term growth in stationary phase and provides a small growth advantage under anaerobic conditions	Escherichia coli
additional information	enzyme RlmJ displays a variant of the Rossmann-like methyltransferase fold with an inserted helical subdomain. Binding of cofactor and substrate induces a large shift of the N-terminal motif X tail to make it cover the cofactor binding site and trigger active-site changes in motifs IV and VIII, substrate binding site structure, overview. Critical roles of enzyme residues Y4, H6, K18 and D164 in methyl transfer, the enzyme requires only H72 of the RNA substrate for activity, overview. Enzyme apostructure analysis using PDB ID 2OO3, rigid-body refinement of the RlmJAPO structure against the RlmJSAM data. Structural model of a catalytic complex, overview	Escherichia coli
physiological function	RlmJ catalyzes the m6A2030 methylation of 23S rRNA during ribosome biogenesis in Escherichia coli	Escherichia coli

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Release 2023.1 (January 2023)