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Information on EC 2.1.1.189 - 23S rRNA (uracil747-C5)-methyltransferase
for references in articles please use BRENDA:EC2.1.1.189
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EC Tree 2 Transferases
2.1 Transferring one-carbon groups
2.1.1 Methyltransferases
2.1.1.189 23S rRNA (uracil747-C5)-methyltransferase
IUBMB Comments
The enzyme specifically methylates uracil747 at C5 in 23S rRNA.
The expected taxonomic range for this enzyme is: Bacteria, Archaea
- 2.1.1.189
- rrnas
- pneumoniae
- archaea
- paralogues
-
renamed
- eukaryota
-
in-vitro
- s-adenosylmethionine
- thermococcales
-
archetypical
-
pyrococcus
- methyltransferases
-
5-methyl
Reaction Schemes
show+
=
+
+
uracil747 in 23S rRNA
=
+
5-methyluracil747 in 23S rRNA
Synonyms
rlmcd, pab0760, sp_1029, more
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
23S rRNA (uracil-C(5))-methyltransferase
archaeal RlmCD-like methyltransferase
Arm5U MTase
dual-specificity RlmCD
m5U methyltransferase
PAB0760
PH1259
PYRAB11450
RlmCD
RlmCD-like methyltransferase
rRNA-specific Arm5U MTase
RumB
SAM-dependent RNA methyltransferase
SP 1029
SP_1029
YefA
additional information
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
S-adenosyl-L-methionine + uracil747 in 23S rRNA = S-adenosyl-L-homocysteine + 5-methyluracil747 in 23S rRNA
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-
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SYSTEMATIC NAME
IUBMB Comments
S-adenosyl-L-methionine:23S rRNA (uracil747-C5)-methyltransferase
The enzyme specifically methylates uracil747 at C5 in 23S rRNA.
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
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 + 5'-740GGCACGUUGAAAAGUGCC757-3'
S-adenosyl-L-homocysteine + 5'-740GGCACGUm5UGAAAAGUGCC757-3'
S-adenosyl-L-methionine + uracil747 in 23S rRNA
S-adenosyl-L-homocysteine + 5-methyluracil747 in 23S rRNA
S-adenosyl-L-methionine + uracil875 in 23S rRNA
S-adenosyl-L-homocysteine + 5-methyluracil875 in 23S rRNA
S-adenosyl-L-methionine + 5'-740GGCACGUUGAAAAGUGCC757-3'
S-adenosyl-L-homocysteine + 5'-740GGCACGUm5UGAAAAGUGCC757-3'
Substrates: 18-mer RNA analogue of the 23S rRNA helix 35
Products: -
Products: -
?
S-adenosyl-L-methionine + 5'-740GGCACGUUGAAAAGUGCC757-3'
S-adenosyl-L-homocysteine + 5'-740GGCACGUm5UGAAAAGUGCC757-3'
Substrates: 18-mer RNA analogue of the 23S rRNA helix 35
Products: -
Products: -
?
S-adenosyl-L-methionine + uracil747 in 23S rRNA
S-adenosyl-L-homocysteine + 5-methyluracil747 in 23S rRNA
Substrates: -
Products: -
Products: -
?
S-adenosyl-L-methionine + uracil747 in 23S rRNA
S-adenosyl-L-homocysteine + 5-methyluracil747 in 23S rRNA
Substrates: -
Products: -
Products: -
?
S-adenosyl-L-methionine + uracil747 in 23S rRNA
S-adenosyl-L-homocysteine + 5-methyluracil747 in 23S rRNA
Substrates: it is not possible to generate a recombinant version of YbjF that retains in vitro activity, so the function of this enzyme is defined in vivo by engineering a ybjF knockout strain
Products: -
Products: -
?
S-adenosyl-L-methionine + uracil747 in 23S rRNA
S-adenosyl-L-homocysteine + 5-methyluracil747 in 23S rRNA
-
Substrates: -
Products: -
Products: -
?
S-adenosyl-L-methionine + uracil747 in 23S rRNA
S-adenosyl-L-homocysteine + 5-methyluracil747 in 23S rRNA
-
Substrates: RlmC recognizes a specific uridine within the loop of 23S rRNA hairpin 35
Products: -
Products: -
?
S-adenosyl-L-methionine + uracil747 in 23S rRNA
S-adenosyl-L-homocysteine + 5-methyluracil747 in 23S rRNA
-
Substrates: -
Products: -
Products: -
?
S-adenosyl-L-methionine + uracil747 in 23S rRNA
S-adenosyl-L-homocysteine + 5-methyluracil747 in 23S rRNA
-
Substrates: PAB0760 is a m5U methyltransferase and recognizes a specific uridine within the loop of 23S rRNA hairpin 35 in a highly specific manner
Products: product identification by reverse transcriptase primer extension and MALDI mass spectrometry
Products: product identification by reverse transcriptase primer extension and MALDI mass spectrometry
?
S-adenosyl-L-methionine + uracil747 in 23S rRNA
S-adenosyl-L-homocysteine + 5-methyluracil747 in 23S rRNA
Substrates: -
Products: -
Products: -
?
S-adenosyl-L-methionine + uracil747 in 23S rRNA
S-adenosyl-L-homocysteine + 5-methyluracil747 in 23S rRNA
Substrates: -
Products: -
Products: -
?
S-adenosyl-L-methionine + uracil747 in 23S rRNA
S-adenosyl-L-homocysteine + 5-methyluracil747 in 23S rRNA
Substrates: -
Products: -
Products: -
?
S-adenosyl-L-methionine + uracil747 in 23S rRNA
S-adenosyl-L-homocysteine + 5-methyluracil747 in 23S rRNA
Substrates: -
Products: -
Products: -
?
S-adenosyl-L-methionine + uracil747 in 23S rRNA
S-adenosyl-L-homocysteine + 5-methyluracil747 in 23S rRNA
Substrates: -
Products: -
Products: -
?
S-adenosyl-L-methionine + uracil747 in 23S rRNA
S-adenosyl-L-homocysteine + 5-methyluracil747 in 23S rRNA
Substrates: -
Products: -
Products: -
?
S-adenosyl-L-methionine + uracil747 in 23S rRNA
S-adenosyl-L-homocysteine + 5-methyluracil747 in 23S rRNA
Substrates: -
Products: -
Products: -
?
S-adenosyl-L-methionine + uracil747 in 23S rRNA
S-adenosyl-L-homocysteine + 5-methyluracil747 in 23S rRNA
Substrates: -
Products: -
Products: -
?
S-adenosyl-L-methionine + uracil747 in 23S rRNA
S-adenosyl-L-homocysteine + 5-methyluracil747 in 23S rRNA
-
Substrates: -
Products: -
Products: -
?
S-adenosyl-L-methionine + uracil747 in 23S rRNA
S-adenosyl-L-homocysteine + 5-methyluracil747 in 23S rRNA
-
Substrates: -
Products: -
Products: -
?
S-adenosyl-L-methionine + uracil875 in 23S rRNA
S-adenosyl-L-homocysteine + 5-methyluracil875 in 23S rRNA
Substrates: m5U methylation at U875 in Bacillus subtilis (U747 in Escherichia coli)
Products: -
Products: -
?
S-adenosyl-L-methionine + uracil875 in 23S rRNA
S-adenosyl-L-homocysteine + 5-methyluracil875 in 23S rRNA
Substrates: m5U methylation at U875 in Bacillus subtilis (U747 in Escherichia coli)
Products: -
Products: -
?
S-adenosyl-L-methionine + uracil875 in 23S rRNA
S-adenosyl-L-homocysteine + 5-methyluracil875 in 23S rRNA
Substrates: m5U methylation at U875 in Pyrococcus horikoshii (U747 in Escherichia coli)
Products: -
Products: -
?
S-adenosyl-L-methionine + uracil875 in 23S rRNA
S-adenosyl-L-homocysteine + 5-methyluracil875 in 23S rRNA
Substrates: m5U methylation at U875 in Pyrococcus horikoshii (U747 in Escherichia coli)
Products: -
Products: -
?
S-adenosyl-L-methionine + uracil875 in 23S rRNA
S-adenosyl-L-homocysteine + 5-methyluracil875 in 23S rRNA
Substrates: m5U methylation at U875 in Pyrococcus horikoshii (U747 in Escherichia coli)
Products: -
Products: -
?
S-adenosyl-L-methionine + uracil875 in 23S rRNA
S-adenosyl-L-homocysteine + 5-methyluracil875 in 23S rRNA
Substrates: m5U methylation at U875 in Pyrococcus horikoshii (U747 in Escherichia coli)
Products: -
Products: -
?
S-adenosyl-L-methionine + uracil875 in 23S rRNA
S-adenosyl-L-homocysteine + 5-methyluracil875 in 23S rRNA
Substrates: m5U methylation at U875 in Pyrococcus horikoshii (U747 in Escherichia coli)
Products: -
Products: -
?
S-adenosyl-L-methionine + uracil875 in 23S rRNA
S-adenosyl-L-homocysteine + 5-methyluracil875 in 23S rRNA
Substrates: m5U methylation at U875 in Pyrococcus horikoshii (U747 in Escherichia coli)
Products: -
Products: -
?
additional information
?
-
Substrates: methylation of U747 and U1939 in Bacillus subtilis rRNA is catalysed by a single enzyme, YefA, MALDI mass spectrometry product identification. YefA is not involved in tRNA methylation, or in 23S rRNA m554 methylation
Products: -
Products: -
?
additional information
?
-
-
Substrates: methylation of U747 and U1939 in Bacillus subtilis rRNA is catalysed by a single enzyme, YefA, MALDI mass spectrometry product identification. YefA is not involved in tRNA methylation, or in 23S rRNA m554 methylation
Products: -
Products: -
?
additional information
?
-
Substrates: methylation of U747 and U1939 in Bacillus subtilis rRNA is catalysed by a single enzyme, YefA, MALDI mass spectrometry product identification. YefA is not involved in tRNA methylation, or in 23S rRNA m554 methylation
Products: -
Products: -
?
additional information
?
-
-
Substrates: substrate specificity, overview
Products: -
Products: -
?
additional information
?
-
Substrates: in the archaeon Pyrococcus horikoshii, the m5U methylation sites in domains II and IV of 23S rRNA are located at U875 (U747 in Escherichia coli) and U2055 (U1939 in Escherichia coli) of the hairpin 35, cf. EC 2.1.1.190
Products: -
Products: -
-
additional information
?
-
Substrates: in the archaeon Pyrococcus horikoshii, the m5U methylation sites in domains II and IV of 23S rRNA are located at U875 (U747 in Escherichia coli) and U2055 (U1939 in Escherichia coli) of the hairpin 35, cf. EC 2.1.1.190
Products: -
Products: -
-
additional information
?
-
Substrates: in the archaeon Pyrococcus horikoshii, the m5U methylation sites in domains II and IV of 23S rRNA are located at U875 (U747 in Escherichia coli) and U2055 (U1939 in Escherichia coli) of the hairpin 35, cf. EC 2.1.1.190
Products: -
Products: -
-
additional information
?
-
Substrates: in the archaeon Pyrococcus horikoshii, the m5U methylation sites in domains II and IV of 23S rRNA are located at U875 (U747 in Escherichia coli) and U2055 (U1939 in Escherichia coli) of the hairpin 35, cf. EC 2.1.1.190
Products: -
Products: -
-
additional information
?
-
Substrates: in the archaeon Pyrococcus horikoshii, the m5U methylation sites in domains II and IV of 23S rRNA are located at U875 (U747 in Escherichia coli) and U2055 (U1939 in Escherichia coli) of the hairpin 35, cf. EC 2.1.1.190
Products: -
Products: -
-
additional information
?
-
Substrates: in the archaeon Pyrococcus horikoshii, the m5U methylation sites in domains II and IV of 23S rRNA are located at U875 (U747 in Escherichia coli) and U2055 (U1939 in Escherichia coli) of the hairpin 35, cf. EC 2.1.1.190
Products: -
Products: -
-
additional information
?
-
-
Substrates: the enzyme also methylates uracil1939 in 23S rRNA
Products: -
Products: -
?
additional information
?
-
Substrates: enzyme introduces C5 methylation at both U747 and U1939 of the 23S ribosomal RNA, i. e. catalyzes both the reactions of EC 2.18189 and 2.11.190
Products: -
Products: -
?
additional information
?
-
-
Substrates: enzyme introduces C5 methylation at both U747 and U1939 of the 23S ribosomal RNA, i. e. catalyzes both the reactions of EC 2.18189 and 2.11.190
Products: -
Products: -
?
additional information
?
-
Substrates: enzyme introduces C5 methylation at both U747 and U1939 of the 23S ribosomal RNA, i. e. catalyzes both the reactions of EC 2.1.1.189 and 2.1.1.190
Products: -
Products: -
?
additional information
?
-
-
Substrates: enzyme introduces C5 methylation at both U747 and U1939 of the 23S ribosomal RNA, i. e. catalyzes both the reactions of EC 2.1.1.189 and 2.1.1.190
Products: -
Products: -
?
additional information
?
-
Substrates: replacement of U747 in substrate 5'-740GGCACGUUGAAAAGUGCC757-3' by A, C, or G completely abolishes methylation
Products: -
Products: -
?
additional information
?
-
-
Substrates: replacement of U747 in substrate 5'-740GGCACGUUGAAAAGUGCC757-3' by A, C, or G completely abolishes methylation
Products: -
Products: -
?
additional information
?
-
Substrates: enzyme introduces C5 methylation at both U747 and U1939 of the 23S ribosomal RNA, i. e. catalyzes both the reactions of EC 2.18189 and 2.11.190
Products: -
Products: -
?
additional information
?
-
Substrates: enzyme introduces C5 methylation at both U747 and U1939 of the 23S ribosomal RNA, i. e. catalyzes both the reactions of EC 2.1.1.189 and 2.1.1.190
Products: -
Products: -
?
additional information
?
-
Substrates: replacement of U747 in substrate 5'-740GGCACGUUGAAAAGUGCC757-3' by A, C, or G completely abolishes methylation
Products: -
Products: -
?
additional information
?
-
-
Substrates: the enzyme also methylates uracil1939 in 23S rRNA
Products: -
Products: -
?
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
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 + uracil747 in 23S rRNA
S-adenosyl-L-homocysteine + 5-methyluracil747 in 23S rRNA
S-adenosyl-L-methionine + uracil875 in 23S rRNA
S-adenosyl-L-homocysteine + 5-methyluracil875 in 23S rRNA
S-adenosyl-L-methionine + uracil747 in 23S rRNA
S-adenosyl-L-homocysteine + 5-methyluracil747 in 23S rRNA
Substrates: -
Products: -
Products: -
?
S-adenosyl-L-methionine + uracil747 in 23S rRNA
S-adenosyl-L-homocysteine + 5-methyluracil747 in 23S rRNA
Substrates: -
Products: -
Products: -
?
S-adenosyl-L-methionine + uracil747 in 23S rRNA
S-adenosyl-L-homocysteine + 5-methyluracil747 in 23S rRNA
-
Substrates: -
Products: -
Products: -
?
S-adenosyl-L-methionine + uracil747 in 23S rRNA
S-adenosyl-L-homocysteine + 5-methyluracil747 in 23S rRNA
-
Substrates: -
Products: -
Products: -
?
S-adenosyl-L-methionine + uracil747 in 23S rRNA
S-adenosyl-L-homocysteine + 5-methyluracil747 in 23S rRNA
Substrates: -
Products: -
Products: -
?
S-adenosyl-L-methionine + uracil747 in 23S rRNA
S-adenosyl-L-homocysteine + 5-methyluracil747 in 23S rRNA
Substrates: -
Products: -
Products: -
?
S-adenosyl-L-methionine + uracil747 in 23S rRNA
S-adenosyl-L-homocysteine + 5-methyluracil747 in 23S rRNA
-
Substrates: -
Products: -
Products: -
?
S-adenosyl-L-methionine + uracil747 in 23S rRNA
S-adenosyl-L-homocysteine + 5-methyluracil747 in 23S rRNA
-
Substrates: -
Products: -
Products: -
?
S-adenosyl-L-methionine + uracil875 in 23S rRNA
S-adenosyl-L-homocysteine + 5-methyluracil875 in 23S rRNA
Substrates: m5U methylation at U875 in Bacillus subtilis (U747 in Escherichia coli)
Products: -
Products: -
?
S-adenosyl-L-methionine + uracil875 in 23S rRNA
S-adenosyl-L-homocysteine + 5-methyluracil875 in 23S rRNA
Substrates: m5U methylation at U875 in Bacillus subtilis (U747 in Escherichia coli)
Products: -
Products: -
?
S-adenosyl-L-methionine + uracil875 in 23S rRNA
S-adenosyl-L-homocysteine + 5-methyluracil875 in 23S rRNA
Substrates: m5U methylation at U875 in Pyrococcus horikoshii (U747 in Escherichia coli)
Products: -
Products: -
?
S-adenosyl-L-methionine + uracil875 in 23S rRNA
S-adenosyl-L-homocysteine + 5-methyluracil875 in 23S rRNA
Substrates: m5U methylation at U875 in Pyrococcus horikoshii (U747 in Escherichia coli)
Products: -
Products: -
?
S-adenosyl-L-methionine + uracil875 in 23S rRNA
S-adenosyl-L-homocysteine + 5-methyluracil875 in 23S rRNA
Substrates: m5U methylation at U875 in Pyrococcus horikoshii (U747 in Escherichia coli)
Products: -
Products: -
?
S-adenosyl-L-methionine + uracil875 in 23S rRNA
S-adenosyl-L-homocysteine + 5-methyluracil875 in 23S rRNA
Substrates: m5U methylation at U875 in Pyrococcus horikoshii (U747 in Escherichia coli)
Products: -
Products: -
?
S-adenosyl-L-methionine + uracil875 in 23S rRNA
S-adenosyl-L-homocysteine + 5-methyluracil875 in 23S rRNA
Substrates: m5U methylation at U875 in Pyrococcus horikoshii (U747 in Escherichia coli)
Products: -
Products: -
?
S-adenosyl-L-methionine + uracil875 in 23S rRNA
S-adenosyl-L-homocysteine + 5-methyluracil875 in 23S rRNA
Substrates: m5U methylation at U875 in Pyrococcus horikoshii (U747 in Escherichia coli)
Products: -
Products: -
?
additional information
?
-
Substrates: methylation of U747 and U1939 in Bacillus subtilis rRNA is catalysed by a single enzyme, YefA, MALDI mass spectrometry product identification. YefA is not involved in tRNA methylation, or in 23S rRNA m554 methylation
Products: -
Products: -
?
additional information
?
-
-
Substrates: methylation of U747 and U1939 in Bacillus subtilis rRNA is catalysed by a single enzyme, YefA, MALDI mass spectrometry product identification. YefA is not involved in tRNA methylation, or in 23S rRNA m554 methylation
Products: -
Products: -
?
additional information
?
-
Substrates: methylation of U747 and U1939 in Bacillus subtilis rRNA is catalysed by a single enzyme, YefA, MALDI mass spectrometry product identification. YefA is not involved in tRNA methylation, or in 23S rRNA m554 methylation
Products: -
Products: -
?
additional information
?
-
-
Substrates: the enzyme also methylates uracil1939 in 23S rRNA
Products: -
Products: -
?
additional information
?
-
Substrates: enzyme introduces C5 methylation at both U747 and U1939 of the 23S ribosomal RNA, i. e. catalyzes both the reactions of EC 2.18189 and 2.11.190
Products: -
Products: -
?
additional information
?
-
-
Substrates: enzyme introduces C5 methylation at both U747 and U1939 of the 23S ribosomal RNA, i. e. catalyzes both the reactions of EC 2.18189 and 2.11.190
Products: -
Products: -
?
additional information
?
-
Substrates: enzyme introduces C5 methylation at both U747 and U1939 of the 23S ribosomal RNA, i. e. catalyzes both the reactions of EC 2.18189 and 2.11.190
Products: -
Products: -
?
additional information
?
-
-
Substrates: the enzyme also methylates uracil1939 in 23S rRNA
Products: -
Products: -
?
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
iron-sulfur centre
presence of [4Fe-4S] or [3Fe-4S] clusters, residues Cys63, Cys69, Cys72 in the central domain are arranged in the coordination motif C-X (5,7)-C-X(2)-C
S-adenosyl-L-methionine
enzyme shows a stronger binding affinity of the cofactor SAM (kD about15 microM) compared to its product SAH (kD about 100 microM)
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
introduces C5 methylation at both U747 and U1939 of the 23S ribosomal RNA, i. e. catalyzes both the reactions of EC 2.1.1.189 and EC 2.1.1.190; serotype 4
UniProt
brenda
introduces C5 methylation at both U747 and U1939 of the 23S ribosomal RNA, i. e. catalyzes both the reactions of EC 2.1.1.189 and EC 2.1.1.190; serotype 4
UniProt
brenda
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
malfunction
metabolism
physiological function
additional information
evolution
-
PAB0760 originates as RlmD-type m5U methyltransferase and undergoes changes in target specificity after its acquisition by a Thermococcales ancestor from a bacterial source. PAB0760 possesses bacterial RlmC-like activity and specifically methylates the nucleotide equivalent to U747 in Pyrococcus abyssi 23S rRNA, but with a sequence most closely related to the bacterial RlmD, the archetypical enzyme that is specific for m5U1939 in 23S rRNA
evolution
YefA is a COG2265 member. During evolution, COG2265 enzymes have undergone a series of changes in target specificity and YefA is closer to an archetypical m5U methyltransferase. A functional shift has occurred during the evolution of the Bacillus subtilis YefA and YfjO methyltransferases.To reflect its dual specificity, YefA is renamed RlmCD
evolution
the gene PhRlmCD (PH1259) likely originates from a single horizontal gene transfer (HGT) event from Gram positive bacteria (RlmCD) rather than Gram-negative bacteria (RlmD or RumA). Phylogenetic analysis of PH1259 and its homologues, overview. The Arm5U MTase is horizontally acquired from Gram-positive bacteria
evolution
m5U tRNA or rRNA methyltransferases are members of the same superfamily (COG2265) and thus share a common ancestry, phylogenetic analysis. Reductive evolution and diversification of C5-uracil methylation in the nucleic acids of Mollicutes, a class of bacteria that has undergone extensive genome erosion. Many mollicutes have lost some of the m5U methyltransferases present in their common ancestor, overview. The C5-methylation of uracil to form 5-methyluracil (m5U) is a ubiquitous base modification of nucleic acids. Four enzyme families have converged to catalyze this methylation using different chemical solutions. Mollicutes modify 23S rRNA m5U1939 via either RlmD or RlmFO
evolution
-
YefA is a COG2265 member. During evolution, COG2265 enzymes have undergone a series of changes in target specificity and YefA is closer to an archetypical m5U methyltransferase. A functional shift has occurred during the evolution of the Bacillus subtilis YefA and YfjO methyltransferases.To reflect its dual specificity, YefA is renamed RlmCD
-
evolution
-
m5U tRNA or rRNA methyltransferases are members of the same superfamily (COG2265) and thus share a common ancestry, phylogenetic analysis. Reductive evolution and diversification of C5-uracil methylation in the nucleic acids of Mollicutes, a class of bacteria that has undergone extensive genome erosion. Many mollicutes have lost some of the m5U methyltransferases present in their common ancestor, overview. The C5-methylation of uracil to form 5-methyluracil (m5U) is a ubiquitous base modification of nucleic acids. Four enzyme families have converged to catalyze this methylation using different chemical solutions. Mollicutes modify 23S rRNA m5U1939 via either RlmD or RlmFO
-
evolution
-
the gene PhRlmCD (PH1259) likely originates from a single horizontal gene transfer (HGT) event from Gram positive bacteria (RlmCD) rather than Gram-negative bacteria (RlmD or RumA). Phylogenetic analysis of PH1259 and its homologues, overview. The Arm5U MTase is horizontally acquired from Gram-positive bacteria
-
evolution
-
the gene PhRlmCD (PH1259) likely originates from a single horizontal gene transfer (HGT) event from Gram positive bacteria (RlmCD) rather than Gram-negative bacteria (RlmD or RumA). Phylogenetic analysis of PH1259 and its homologues, overview. The Arm5U MTase is horizontally acquired from Gram-positive bacteria
-
evolution
-
the gene PhRlmCD (PH1259) likely originates from a single horizontal gene transfer (HGT) event from Gram positive bacteria (RlmCD) rather than Gram-negative bacteria (RlmD or RumA). Phylogenetic analysis of PH1259 and its homologues, overview. The Arm5U MTase is horizontally acquired from Gram-positive bacteria
-
evolution
-
the gene PhRlmCD (PH1259) likely originates from a single horizontal gene transfer (HGT) event from Gram positive bacteria (RlmCD) rather than Gram-negative bacteria (RlmD or RumA). Phylogenetic analysis of PH1259 and its homologues, overview. The Arm5U MTase is horizontally acquired from Gram-positive bacteria
-
evolution
-
the gene PhRlmCD (PH1259) likely originates from a single horizontal gene transfer (HGT) event from Gram positive bacteria (RlmCD) rather than Gram-negative bacteria (RlmD or RumA). Phylogenetic analysis of PH1259 and its homologues, overview. The Arm5U MTase is horizontally acquired from Gram-positive bacteria
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malfunction
comparison of the methylation patterns in 23S rRNAs from YbjF+ and YbjF- strains shows that the latter differs only in the lack of the 5-methyluracil747 modification
malfunction
-
enzyme inactivation reduces N1-methylated level of G748 by RlmAII in vivo, leading to telithromycin resistance when the nucleotide A2058, located in domain V of 23S rRNA, is dimethylated by the dimethyltransferase Erm(B)
malfunction
the structural investigation reveals crucial structural alterations induced by substituting the iron-sulfur cluster with disulfide bonds, raising the possibility that iron loss due to cysteine oxidation may be a regulatory mechanism controlling rRNA methylation
malfunction
-
the structural investigation reveals crucial structural alterations induced by substituting the iron-sulfur cluster with disulfide bonds, raising the possibility that iron loss due to cysteine oxidation may be a regulatory mechanism controlling rRNA methylation
-
malfunction
-
the structural investigation reveals crucial structural alterations induced by substituting the iron-sulfur cluster with disulfide bonds, raising the possibility that iron loss due to cysteine oxidation may be a regulatory mechanism controlling rRNA methylation
-
malfunction
-
the structural investigation reveals crucial structural alterations induced by substituting the iron-sulfur cluster with disulfide bonds, raising the possibility that iron loss due to cysteine oxidation may be a regulatory mechanism controlling rRNA methylation
-
malfunction
-
enzyme inactivation reduces N1-methylated level of G748 by RlmAII in vivo, leading to telithromycin resistance when the nucleotide A2058, located in domain V of 23S rRNA, is dimethylated by the dimethyltransferase Erm(B)
-
malfunction
-
the structural investigation reveals crucial structural alterations induced by substituting the iron-sulfur cluster with disulfide bonds, raising the possibility that iron loss due to cysteine oxidation may be a regulatory mechanism controlling rRNA methylation
-
malfunction
-
the structural investigation reveals crucial structural alterations induced by substituting the iron-sulfur cluster with disulfide bonds, raising the possibility that iron loss due to cysteine oxidation may be a regulatory mechanism controlling rRNA methylation
-
metabolism
-
methylation of uridine747 by the enzyme enhances adjacent guanine748 methylation by RlmAII leading to telithromycin-susceptibility
metabolism
-
methylation of uridine747 by the enzyme enhances adjacent guanine748 methylation by RlmAII leading to telithromycin-susceptibility
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physiological function
5-methyluridine (m5U) rRNA modifications frequently occur at U747 (Escherichia coli numbering) in domain II of the 23S rRNA in Gram-negative bacteria, with the help of S-adenosyl-L-methionine (SAM)-dependent rRNA methyltransferase (MTase), RlmC
physiological function
5-methyluridine (m5U) rRNA modifications frequently occur at U747 (Escherichia coli numbering) in domain II of the 23S rRNA in Gram-negative bacteria, with the help of S-adenosyl-L-methionine (SAM)-dependent rRNA methyltransferase (MTase), RlmC. In the archaeon Pyrococcus horikoshii, the m5U methylation sites in domains II and IV of 23S rRNA are located at U875 (U747 in Escherichia coli) and U2055 (U1939 in Escherichia coli) of the hairpin 35
physiological function
-
5-methyluridine (m5U) rRNA modifications frequently occur at U747 (Escherichia coli numbering) in domain II of the 23S rRNA in Gram-negative bacteria, with the help of S-adenosyl-L-methionine (SAM)-dependent rRNA methyltransferase (MTase), RlmC. In the archaeon Pyrococcus horikoshii, the m5U methylation sites in domains II and IV of 23S rRNA are located at U875 (U747 in Escherichia coli) and U2055 (U1939 in Escherichia coli) of the hairpin 35
-
physiological function
-
5-methyluridine (m5U) rRNA modifications frequently occur at U747 (Escherichia coli numbering) in domain II of the 23S rRNA in Gram-negative bacteria, with the help of S-adenosyl-L-methionine (SAM)-dependent rRNA methyltransferase (MTase), RlmC. In the archaeon Pyrococcus horikoshii, the m5U methylation sites in domains II and IV of 23S rRNA are located at U875 (U747 in Escherichia coli) and U2055 (U1939 in Escherichia coli) of the hairpin 35
-
physiological function
-
5-methyluridine (m5U) rRNA modifications frequently occur at U747 (Escherichia coli numbering) in domain II of the 23S rRNA in Gram-negative bacteria, with the help of S-adenosyl-L-methionine (SAM)-dependent rRNA methyltransferase (MTase), RlmC
-
physiological function
-
5-methyluridine (m5U) rRNA modifications frequently occur at U747 (Escherichia coli numbering) in domain II of the 23S rRNA in Gram-negative bacteria, with the help of S-adenosyl-L-methionine (SAM)-dependent rRNA methyltransferase (MTase), RlmC. In the archaeon Pyrococcus horikoshii, the m5U methylation sites in domains II and IV of 23S rRNA are located at U875 (U747 in Escherichia coli) and U2055 (U1939 in Escherichia coli) of the hairpin 35
-
physiological function
-
5-methyluridine (m5U) rRNA modifications frequently occur at U747 (Escherichia coli numbering) in domain II of the 23S rRNA in Gram-negative bacteria, with the help of S-adenosyl-L-methionine (SAM)-dependent rRNA methyltransferase (MTase), RlmC. In the archaeon Pyrococcus horikoshii, the m5U methylation sites in domains II and IV of 23S rRNA are located at U875 (U747 in Escherichia coli) and U2055 (U1939 in Escherichia coli) of the hairpin 35
-
physiological function
-
5-methyluridine (m5U) rRNA modifications frequently occur at U747 (Escherichia coli numbering) in domain II of the 23S rRNA in Gram-negative bacteria, with the help of S-adenosyl-L-methionine (SAM)-dependent rRNA methyltransferase (MTase), RlmC. In the archaeon Pyrococcus horikoshii, the m5U methylation sites in domains II and IV of 23S rRNA are located at U875 (U747 in Escherichia coli) and U2055 (U1939 in Escherichia coli) of the hairpin 35
-
additional information
enzyme catalytic mechanism, overview. A simple mechanism is used based on direct transfer of the methyl group from the electrophilic carbon of the SAM cofactor to the activated C5-uracil. This carbon is activated by a conserved cysteine that plays the role of nucleophile
additional information
-
enzyme catalytic mechanism, overview. A simple mechanism is used based on direct transfer of the methyl group from the electrophilic carbon of the SAM cofactor to the activated C5-uracil. This carbon is activated by a conserved cysteine that plays the role of nucleophile
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Show AA Sequence and Transmembrane Helices (1800 entries)
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PDB
SCOP
CATH
UNIPROT
ORGANISM
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SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
?
x * 50608, mass spectrometry, x * 50639, calculated from sequence
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x * 50608, mass spectrometry, x * 50639, calculated from sequence
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?
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x * 50608, mass spectrometry, x * 50639, calculated from sequence
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?
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x * 50608, mass spectrometry, x * 50639, calculated from sequence
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?
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x * 50608, mass spectrometry, x * 50639, calculated from sequence
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additional information
the crystal structure of PhRlmCD unveils the existence of three distinct and well-organized (TRAM, central, and catalytic) domain
additional information
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the crystal structure of PhRlmCD unveils the existence of three distinct and well-organized (TRAM, central, and catalytic) domain
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additional information
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the crystal structure of PhRlmCD unveils the existence of three distinct and well-organized (TRAM, central, and catalytic) domain
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additional information
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the crystal structure of PhRlmCD unveils the existence of three distinct and well-organized (TRAM, central, and catalytic) domain
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additional information
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the crystal structure of PhRlmCD unveils the existence of three distinct and well-organized (TRAM, central, and catalytic) domain
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additional information
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the crystal structure of PhRlmCD unveils the existence of three distinct and well-organized (TRAM, central, and catalytic) domain
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POSTTRANSLATIONAL MODIFICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
side-chain modification
side-chain modification
formation of disulfide bonds Cys63-Cys69 (right-handed) and Cys72-Cys139 (left-handed)
side-chain modification
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formation of disulfide bonds Cys63-Cys69 (right-handed) and Cys72-Cys139 (left-handed)
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side-chain modification
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formation of disulfide bonds Cys63-Cys69 (right-handed) and Cys72-Cys139 (left-handed)
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side-chain modification
-
formation of disulfide bonds Cys63-Cys69 (right-handed) and Cys72-Cys139 (left-handed)
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side-chain modification
-
formation of disulfide bonds Cys63-Cys69 (right-handed) and Cys72-Cys139 (left-handed)
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side-chain modification
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formation of disulfide bonds Cys63-Cys69 (right-handed) and Cys72-Cys139 (left-handed)
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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
purified recombinant His-tagged enzyme, microbatch-under-oil technique by mixing 0.002 ml of each of protein and buffer solution (1:1 ratio) at 4°C and 20°C, initial crystal hits of the protein PhRlmCD are obtained in three different buffer conditions: (1) 0.5 M ammonium sulfate, 0.1 M sodium citrate tribasic dihydrate, pH 5.6, and 1.0 M lithium sulfate monohydrate, (2) 0.1 M Bis-Tris, pH 5.5, and 2.0 M ammonium sulfate, (3) 0.1 M HEPES sodium, pH 7.5, 2% v/v PEG 400, and 2.0 M ammonium sulfate, at 20°C, crystal structure analysis at 3.2 A resolution, PDB ID 8Z62, overview
structure to 3.2 A resolution in the space group P212121 with two protomers in each asymmetric unit
crystal structures of apo-form RlmCD and its complex with SAH. A long linker in the central domain of RlmCD is the key factor in determining its substrate selectivity
structure of RlmCD in complex with its cofactor and the RNA substrate containing U747 at 2.00 A or U1939 at 3.10 A. The side-chain rearrangement of F145 displays an unusual mechanism through which RlmCD can discriminate between U747- and U1939-containing RNA substrate by switching the intermolecular aromatic stacking between protein and RNA on/off
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
D381A
2% residual activity towards U747 RNA substrate, 40% residual activity towards U1939 RNA substrate, reaction of EC 2.11.190
F145A
5% residual activity towards U747 RNA substrate, 120% activity towards U1939 RNA substrate, reaction of EC 2.11.190
H151A
5% residual activity towards U747 RNA substrate, 55% activity towards U1939 RNA substrate, reaction of EC 2.11.190
N249A
35% residual activity towards U747 RNA substrate, 55% residual activity towards U1939 RNA substrate, reaction of EC 2.11.190
Q162A
18% residual activity towards U747 RNA substrate, 160% activity towards U1939 RNA substrate, reaction of EC 2.11.190
Q283A
8% residual activity towards U747 RNA substrate, 50% residual activity towards U1939 RNA substrate, reaction of EC 2.11.190
R127A
8% residual activity towards U747 RNA substrate, 2% residual activity towards U1939 RNA substrate, reaction of EC 2.11.190
D381A
-
2% residual activity towards U747 RNA substrate, 40% residual activity towards U1939 RNA substrate, reaction of EC 2.11.190
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N249A
-
35% residual activity towards U747 RNA substrate, 55% residual activity towards U1939 RNA substrate, reaction of EC 2.11.190
-
Q162A
-
18% residual activity towards U747 RNA substrate, 160% activity towards U1939 RNA substrate, reaction of EC 2.11.190
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Q283A
-
8% residual activity towards U747 RNA substrate, 50% residual activity towards U1939 RNA substrate, reaction of EC 2.11.190
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R127A
-
8% residual activity towards U747 RNA substrate, 2% residual activity towards U1939 RNA substrate, reaction of EC 2.11.190
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additional information
additional information
both full-length RlmCD and its shorter construct RlmCDs (residue 1-454) exhibit strong U74 methyltransferase activity when compared with the glutamine mutant of E443
additional information
-
both full-length RlmCD and its shorter construct RlmCDs (residue 1-454) exhibit strong U74 methyltransferase activity when compared with the glutamine mutant of E443
additional information
-
both full-length RlmCD and its shorter construct RlmCDs (residue 1-454) exhibit strong U74 methyltransferase activity when compared with the glutamine mutant of E443
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PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant His-tagged enzyme from Escherichia coli by nickel affinity chromatography, followed by ultrafiltration and dialysis
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
gene PH1259, cloning, and DNA and amino acid sequence determination, phylogenetic analysis of PH1259 and its homologues, the gene PH1259 likely originates from a single horizontal gene transfer (HGT) event from Gram positive bacteria (RlmCD) rather than Gram-negative bacteria (RlmD or RumA), thus, it is referred to as PhRlmCD. Recombinant expression of His-tagged enzyme in Escherichia coli
gene yefA, phylogenetic analysis, functional complementation of Bacillus subtilis knockout strain BG12826 yefA::pMutin2 and DELTAyefA::Cm deletion mutant, and of Escherichia coli enzyme-deficient BW 25113 DELTAtrmA/DELTArlmC/DELTArlmD strain
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Madsen, C.T.; Mengel-Jorgensen, J.; Kirpekar, F.; Douthwaite, S.
Identifying the methyltransferases for m(5)U747 and m(5)U1939 in 23S rRNA using MALDI mass spectrometry
Nucleic Acids Res.
31
4738-4746
2003
Escherichia coli (P75817)
brenda
Desmolaize, B.; Fabret, C.; Bregeon, D.; Rose, S.; Grosjean, H.; Douthwaite, S.
A single methyltransferase YefA (RlmCD) catalyses both m5U747 and m5U1939 modifications in Bacillus subtilis 23S rRNA
Nucleic Acids Res.
39
9368-9375
2011
Bacillus subtilis (O31503), Bacillus subtilis, Bacillus subtilis 168 (O31503)
brenda
Auxilien, S.; Rasmussen, A.; Rose, S.; Brochier-Armanet, C.; Husson, C.; Fourmy, D.; Grosjean, H.; Douthwaite, S.
Specificity shifts in the rRNA and tRNA nucleotide targets of archaeal and bacterial m5U methyltransferases
RNA
17
45-53
2011
Escherichia coli, Pyrococcus abyssi
brenda
Shoji, T.; Takaya, A.; Sato, Y.; Kimura, S.; Suzuki, T.; Yamamoto, T.
RlmCD-mediated U747 methylation promotes efficient G748 methylation by methyltransferase RlmAII in 23S rRNA in Streptococcus pneumoniae; interplay between two rRNA methylations responsible for telithromycin susceptibility
Nucleic Acids Res.
43
8964-8972
2015
Streptococcus pneumoniae, Streptococcus pneumoniae S1
brenda
Jiang, Y.; Li, F.; Wu, J.; Shi, Y.; Gong, Q.
Structural insights into substrate selectivity of ribosomal RNA methyltransferase RlmCD
PLoS ONE
12
e0185226
2017
Streptococcus pneumoniae (Q97R12), Streptococcus pneumoniae, Streptococcus pneumoniae ATCC BAA-334 (Q97R12)
brenda
Jiang, Y.; Yu, H.; Li, F.; Cheng, L.; Zhu, L.; Shi, Y.; Gong, Q.
Unveiling the structural features that determine the dual methyltransferase activities of Streptococcus pneumoniae RlmCD
PLoS Pathog.
14
e1007379
2018
Streptococcus pneumoniae (Q97R12), Streptococcus pneumoniae, Streptococcus pneumoniae ATCC BAA-334 (Q97R12)
brenda
Saha, S.; Kanaujia, S.P.
Decoding substrate selectivity of an archaeal RlmCD-like methyltransferase through its salient traits
Biochemistry
63
2477-2492
2024
Pyrococcus abyssi (Q9UZK1), Pyrococcus abyssi Orsay (Q9UZK1), Pyrococcus horikoshii (O58994), Pyrococcus horikoshii ATCC 700860 (O58994), Pyrococcus horikoshii DSM 12428 (O58994), Pyrococcus horikoshii JCM 9974 (O58994), Pyrococcus horikoshii NBRC 100139 (O58994), Pyrococcus horikoshii OT-3 (O58994)
brenda
Sirand-Pugnet, P.; Bregeon, D.; Beven, L.; Goyenvalle, C.; Blanchard, A.; Rose, S.; Grosjean, H.; Douthwaite, S.; Hamdane, D.; Crecy-Lagard, V.
Reductive evolution and diversification of C5-uracil methylation in the nucleic acids of Mollicutes
Biomolecules
10
587
2020
Bacillus subtilis (O31503), Bacillus subtilis 168 (O31503)
brenda
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