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Information on EC 2.1.1.266 - 23S rRNA (adenine2030-N6)-methyltransferase
for references in articles please use BRENDA:EC2.1.1.266
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EC Tree 2 Transferases
2.1 Transferring one-carbon groups
2.1.1 Methyltransferases
2.1.1.266 23S rRNA (adenine2030-N6)-methyltransferase
IUBMB Comments
The recombinant RlmJ protein is most active in methylating deproteinized 23S ribosomal subunit, and does not methylate the completely assembled 50S subunits .
The enzyme appears in viruses and cellular organisms
Reaction Schemes
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adenine2030 in 23S rRNA
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N6-methyladenine2030 in 23S rRNA
Synonyms
ribosomal rna large subunit methyltransferase j, more
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
rlmJ
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
S-adenosyl-L-methionine + adenine2030 in 23S rRNA = S-adenosyl-L-homocysteine + N6-methyladenine2030 in 23S rRNA
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SYSTEMATIC NAME
IUBMB Comments
S-adenosyl-L-methionine:23S rRNA (adenine2030-N6)-methyltransferase
The recombinant RlmJ protein is most active in methylating deproteinized 23S ribosomal subunit, and does not methylate the completely assembled 50S subunits [1].
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SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
LITERATURE
COMMENTARY
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
S-adenosyl-L-methionine + adenine2030 in 23S rRNA
S-adenosyl-L-homocysteine + N6-methyladenine2030 in 23S rRNA
S-adenosyl-L-methionine + adenine2030 in 23S rRNA
S-adenosyl-L-homocysteine + N6-methyladenine2030 in 23S rRNA
Substrates: nascent 23S rRNA is the natural substrate for YhiR
Products: -
Products: -
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S-adenosyl-L-methionine + adenine2030 in 23S rRNA
S-adenosyl-L-homocysteine + N6-methyladenine2030 in 23S rRNA
Substrates: adenine-N6 methyltransferase, encoded by gene yhiR, is specific for modification of A2030 of 23S ribosomal RNA. YhiR by itself, without any additional proteins, is able to modify 23S rRNA
Products: mass spectrometric product identification, overview
Products: mass spectrometric product identification, overview
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S-adenosyl-L-methionine + adenine2030 in 23S rRNA
S-adenosyl-L-homocysteine + N6-methyladenine2030 in 23S rRNA
Substrates: -
Products: -
Products: -
?
S-adenosyl-L-methionine + adenine2030 in 23S rRNA
S-adenosyl-L-homocysteine + N6-methyladenine2030 in 23S rRNA
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Substrates: -
Products: -
Products: -
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S-adenosyl-L-methionine + adenine2030 in 23S rRNA
S-adenosyl-L-homocysteine + N6-methyladenine2030 in 23S rRNA
Substrates: enzyme RlmJ uses the cofactor S-adenosyl-L-methionine to methylate the exocyclic nitrogen N6 of nucleotide A2030 in 23S rRNA during ribosome assembly in Escherichia coli
Products: -
Products: -
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S-adenosyl-L-methionine + adenine2030 in 23S rRNA
S-adenosyl-L-homocysteine + N6-methyladenine2030 in 23S rRNA
Substrates: 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
Products: -
Products: -
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additional information
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Substrates: enzyme activity with in vitro modified potential YhiR substrates prepared from the enzyme-deficient DELTAyhiR strain: methylation of the 50S subunits, NH4Cl/ethanol split particles, LiCl split particles, and deproteinized 23S rRNA, overview
Products: -
Products: -
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additional information
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Substrates: enzyme activity with in vitro modified potential YhiR substrates prepared from the enzyme-deficient DELTAyhiR strain: methylation of the 50S subunits, NH4Cl/ethanol split particles, LiCl split particles, and deproteinized 23S rRNA, overview
Products: -
Products: -
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NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
LITERATURE
COMMENTARY
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
S-adenosyl-L-methionine + adenine2030 in 23S rRNA
S-adenosyl-L-homocysteine + N6-methyladenine2030 in 23S rRNA
S-adenosyl-L-methionine + adenine2030 in 23S rRNA
S-adenosyl-L-homocysteine + N6-methyladenine2030 in 23S rRNA
Substrates: nascent 23S rRNA is the natural substrate for YhiR
Products: -
Products: -
?
S-adenosyl-L-methionine + adenine2030 in 23S rRNA
S-adenosyl-L-homocysteine + N6-methyladenine2030 in 23S rRNA
Substrates: -
Products: -
Products: -
?
S-adenosyl-L-methionine + adenine2030 in 23S rRNA
S-adenosyl-L-homocysteine + N6-methyladenine2030 in 23S rRNA
-
Substrates: -
Products: -
Products: -
?
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
S-adenosyl-L-methionine
dependent on, cofactor binding site structure determined with bound S-adenosyl-L-homocysteine and AMP, overview
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ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
-
YhiR by itself, without any additional proteins, is able to modify 23S rRNA
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additional information
YhiR by itself, without any additional proteins, is able to modify 23S rRNA
-
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
Highest Expressing Human Cell Lines
Cell Line LinksPlease wait a moment until the data is sorted. This message will disappear when the data is sorted.
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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
malfunction
physiological function
additional information
malfunction
the phenotype of yhiR knockout gene is very mild under various growth conditions and at the stationary phase, except for a small growth advantage at anaerobic conditions. A very small subset of genes is affected by yhiR inactivation, while the majority of the proteome remains independent of the A2030 modification. Lack of modification at the 23S rRNA nucleotide: A2030 does not cause the accumulation of assembly intermediates. Phenotype of the yhiR gene knockout, overview
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
physiological function
the yhiR gene of Escherichia coli is solely responsible for the N6-methylation of A2030 of the 23S rRNA. Nucleotide m6A2030, buried inside the large ribosomal subunit close to the peptidyltransferase center, forms a strong stacked contact with the U571 residue of the 23S rRNA, thus connecting structural elements of domains II and V located at half-23S rRNA length distance in the primary structure. Modification of the 23S rRNA nucleotide A2030 occurs early in the 50S subunit assembly
physiological function
RlmJ catalyzes the m6A2030 methylation of 23S rRNA during ribosome biogenesis in Escherichia coli
additional information
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the yhiR gene should be renamed to rlmJ according to the rRNA methyltransferase nomenclature
additional information
the yhiR gene should be renamed to rlmJ according to the rRNA methyltransferase nomenclature
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
additional information
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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
Show AA Sequence and Transmembrane Helices (6285 entries)
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PDB
SCOP
CATH
UNIPROT
ORGANISM
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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
purified recombinant C-terminally His6-tagged enzyme, sitting drop vapour diffusion method, mixing of 0.0015 ml of protein solution with an equal amount of reservoir solution containing 0.2 M sodium sulfate decahydrate, 0.1 M Tris-HCl pH 8.5, 30% w/v PEG 4000, and equilibration against 0.08 ml of reservoir solution, 8 days, 20°C, X-ray diffraction strucure determination and analysis at 1.8 A resolution
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
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
additional information
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strain JW3466 lacks the yhiR gene on the chromosome, i.e. strain DELTAyhiR, phenotype of the yhiR gene knockout, overview
additional information
strain JW3466 lacks the yhiR gene on the chromosome, i.e. strain DELTAyhiR, phenotype of the yhiR gene knockout, overview
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PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant C-terminally His6-tagged enzyme from Escherichia coli strain BL21(DE3) by nickel affinity chromatography, ultrafiltration, and gel filtration
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
gene rlmJ, sequence comparisons, recombinant expression of wild-type and mutant enzymes
gene yhiR, expression as C-terminally His6-tagged protein in escherichia coli strain AG1
gene yhiR, recombinant expresssion of C-terminally His6-tagged enzyme in Escherichia coli strain BL21(DE3)
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Golovina, A.Y.; Dzama, M.M.; Osterman, I.A.; Sergiev, P.V.; Serebryakova, M.V.; Bogdanov, A.A.; Dontsova, O.A.
The last rRNA methyltransferase of E. coli revealed: The yhiR gene encodes adenine-N6 methyltransferase specific for modification of A2030 of 23S ribosomal RNA
RNA
18
1725-1734
2012
Escherichia coli, Escherichia coli (P37634)
brenda
Punekar, A.S.; Selmer, M.
Purification, crystallization and preliminary X-ray diffraction analysis of the 23S rRNA methyltransferase RlmJ from Escherichia coli
Acta Crystallogr. Sect. F
69
1001-1003
2013
Escherichia coli (P37634)
brenda
Punekar, A.; Liljeruhm, J.; Shepherd, T.; Forster, A.; Selmer, M.
Structural and functional insights into the molecular mechanism of rRNA m6A methyltransferase RlmJ
Nucleic Acids Res.
41
9537-9548
2013
Escherichia coli (P37634), Escherichia coli
brenda
EXTERNAL LINKS (specific for EC-Number 2.1.1.266)
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