Gene Ontology annotation through association of InterPro records with GO terms
Annotation inferences using phylogenetic trees
Electronic Gene Ontology annotations created by transferring manual GO annotations between related proteins based on shared sequence features
Electronic Gene Ontology annotations created by ARBA machine learning models
Combined Automated Annotation using Multiple IEA Methods
Identifying the methyltransferases for m(5)U747 and m(5)U1939 in 23S rRNA using MALDI mass spectrometry.
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Native rlmC disruption eliminates m5U747 without changing the other observed rRNA methylation sites.
"Comparison of the methylation patterns in 23S rRNAs from YbjF(+) and YbjF(-) strains showed that the latter differed only in the lack of the m(5)U747 modification"
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Failure of recombinant preparations leaves the physiological substrate state and activity-loss mechanism unresolved.
"We were unable to generate a recombinant version of YbjF that retained in vitro activity, so the function of this enzyme was defined in vivo by engineering a ybjF knockout strain"
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No competitive growth disadvantage was detected in the reported rich and minimal media; this is not universal dispensability.
"in competition experiments run in rich and minimal media, we have not been able to detect any growth disadvantage for ybjF ( rumB ) knockout strains compared to the wild type"
A single methyltransferase YefA (RlmCD) catalyses both m5U747 and m5U1939 modifications in Bacillus subtilis 23S rRNA.
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In B. subtilis, a single COG2265 enzyme (YefA/RlmCD) catalyzes both m5U747 and m5U1939 modifications, whereas E. coli uses separate enzymes RlmC and RlmD for these two sites.
"methylation of U747 and U1939 in B. subtilis rRNA is catalysed by a single enzyme, YefA that is a COG2265 member"
Specificity shifts in the rRNA and tRNA nucleotide targets of archaeal and bacterial m5U methyltransferases.
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RNA m5U methyltransferases arose in Bacteria and spread to Archaea and Eukaryota by horizontal gene transfer. The COG2265 enzymes have undergone target specificity shifts during evolution.
"The RNA m(5)U methyltransferases appear to have arisen in Bacteria and were then dispersed by horizontal transfer of an rlmD-type gene to the Archaea and Eukaryota"
Unveiling the structural features that determine the dual methyltransferase activities of Streptococcus pneumoniae RlmCD.
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Structural analysis of S. pneumoniae RlmCD in complex with U747-containing and U1939-containing RNA substrates reveals how the dual-specificity enzyme discriminates between the two substrates, providing insight into the dedicated specificity of E. coli RlmC for U747.
"RlmC is the dedicated enzyme for m5U747 in Escherichia coli"
Redox reactions of the iron-sulfur cluster in a ribosomal RNA methyltransferase, RumA: optical and EPR studies.
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RumA/RlmD provides the experimentally established Fe-S comparator; RlmC retains a separate curated sequence inference.
"An unprecedented [4Fe-4S] iron-sulfur cluster was found in RumA, the enzyme that methylates U1939 in Escherichia coli 23 S ribosomal RNA"
Amino acid residues of the Escherichia coli tRNA(m5U54)methyltransferase (TrmA) critical for stability, covalent binding of tRNA and enzymatic activity.
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Conserved residues in the COG2265 catalytic domain are shared across TrmA, RumA/RlmD, and RumB/RlmC, supporting modular evolution with a conserved catalytic domain combined with different RNA-binding domains.
"the amino acids F188, Q190, G220, D299, R302, C324 and E358, conserved in the C-terminal catalytic domain of several RNA(m5U)methyltransferases of the COG2265 family, are important for the formation of the TrmA-tRNA intermediate and/or the enzymatic activity"
UniProtKB record for Escherichia coli rlmC (P75817)
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RlmC has a HAMAP-inferred Fe-S ligand feature; its biological interpretation remains distinct from RlmD spectroscopy.
"FT BINDING 3
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01012""