RlmC catalyzes the formation of 5-methyluridine at position 747 (m5U747) in 23S rRNA, using S-adenosyl-L-methionine (SAM/AdoMet) as the methyl donor.
"Identifying the methyltransferases for m(5)U747 and m(5)U1939 in 23S rRNA using MALDI mass spectrometry."
This is the definitive paper establishing the function of RlmC (then called YbjF). Key findings:
- Three m5U sites in E. coli stable RNAs: U54 in tRNA (TrmA), U747 in 23S rRNA (YbjF/RumB/RlmC), and U1939 in 23S rRNA (YgcA/RumA/RlmD)
- YbjF function was defined in vivo by engineering a ybjF knockout strain PMID:12907714
- YbjF(-) strains showed ONLY the loss of m5U747 modification PMID:12907714
- Could not get recombinant YbjF to retain in vitro activity PMID:12907714
- Proposed the name RumB (RNA uridine methyltransferase B)
"A single methyltransferase YefA (RlmCD) catalyses both m5U747 and m5U1939 modifications in Bacillus subtilis 23S rRNA."
Key comparative finding:
- In E. coli: three separate COG2265 paralogs (TrmA, RlmC, RlmD) for three m5U sites
- In B. subtilis: a single enzyme YefA/RlmCD handles both m5U747 and m5U1939
- PMID:21824914
- PMID:21824914
- Suggests evolutionary specialization of COG2265 paralogs
"Specificity shifts in the rRNA and tRNA nucleotide targets of archaeal and bacterial m5U methyltransferases."
Key evolutionary findings:
- PMID:21051506
- RlmC (formerly RumB) specifically modifies m5U747 in 23S rRNA
- In Pyrococcus abyssi, PAB0760 has RlmC-like activity despite being more closely related to RlmD in sequence
"Unveiling the structural features that determine the dual methyltransferase activities of Streptococcus pneumoniae RlmCD."
"Crystal structure of RumA, an iron-sulfur cluster containing E. coli ribosomal RNA 5-methyluridine methyltransferase."
"Redox reactions of the iron-sulfur cluster in a ribosomal RNA methyltransferase, RumA."
Initial characterization of RumA, establishing the presence of a [4Fe-4S] cluster in this family.
"Erythromycin resistance mutations in ribosomal proteins L22 and L4 perturb the higher order structure of 23 S ribosomal RNA."
"Amino acid residues of the E. coli tRNA(m5U54)methyltransferase (TrmA) critical for stability, covalent binding of tRNA and enzymatic activity."
The TrmA/RlmC/RlmD family uses a common mechanism:
1. Nucleophilic Cys attacks C6 of the target uracil, forming a covalent Michael adduct
2. This activates C5 for electrophilic methyl transfer from SAM
3. Beta-elimination releases the methylated product (m5U) and regenerates the Cys
UniProt lists RlmC as containing a [4Fe-4S] cluster based on HAMAP rule MF_01012. The binding motif CX5CGGC is present in the N-terminal region (Cys3, Cys11, Cys14, Cys87). This is well-established for the paralog RumA/RlmD (PMID:12003490, PMID:15016356, PMID:15181002) but has not been directly demonstrated experimentally for RlmC. The annotation is based on sequence conservation and is likely correct given the high conservation of the cysteine motif. The role of the [4Fe-4S] cluster is structural rather than catalytic -- the methyltransferase reaction does not involve a redox step (PMID:15181002).
This section supersedes the earlier mechanistic, motif and growth claims where they differ. The original 13 annotation payloads and original UniProt/GOA files are retained byte-for-byte; only reviewer-authored content changes. Identity is P75817, rlmC/rumB/ybjF, K-12 locus b0859/JW0843. The existing genuine Falcon report (2026-06-01, Edison metadata and artifacts) was reused for discovery; BioReason and provider prose were removed as supporting evidence in favor of primary or curated independent sources. Neither report was rewritten.
Normally recovered full PMID:12907714 establishes native loss of m5U747 by MALDI-MS after ybjF disruption. Recombinant N-terminal-tagged and intein-derived preparations were inactive both on tested transcripts and on unmethylated full 23S rRNA. The authors considered inadvertent loss of enzyme activity during in-vitro handling. This does not establish a required assembly particle or exclude a naked-RNA substrate for an intact enzyme. U747 lies near the exit-tunnel constriction, not a demonstrated RlmC-specific peptidyl-transferase-center mechanism. Contrary to the older notes, the full paper explicitly describes rich/minimal-medium competition experiments with no detectable growth disadvantage: “we have not been able to detect any growth disadvantage for ybjF ( rumB ) knockout strains compared to the wild type”. No stress-response or translation-fidelity annotation is manufactured from proximity or a predicted physiological role.
The Fe-S refinement remains supported as a curated HAMAP inference from the target FT:BINDING features (Cys3/11/14/87). It is not a direct RlmC cofactor measurement. The raw RlmC sequence does not contain the exact CX5CGGC motif previously attributed to it, and the existence of an Fe-S cluster is not universal across RNA m5U enzymes. Normally recovered full PMID:15181002 experimentally studies RumA/RlmD; RumB appears in its sequence searches. Its potential oxidative-regulation interpretation is not an experimentally established RlmC process. The 2026 review PMID:42517620 reference185 resolves to that same RumA paper; its RlmC wording therefore must not upgrade comparative evidence into a target assay. Catalytic Cys334 remains a target HAMAP feature inference, not a measured RlmC covalent intermediate. Even the precise structural/functional role of the cluster in RumA is discussed as unresolved rather than settled solely because methyl transfer lacks a redox step.
Correct-but-general RNA activity/process rows are now MODIFY, not peripheral merely because broad. GO:0006396 RNA processing includes conversion to mature RNA and does not exclude methylation. Live QuickGO definitions were checked on 2026-10-26, including the C5 rRNA activity and base-methylation terms. The broad iron row is refined to the inferred cluster; no new annotation row is added. Direct native assignment and recombinant assay limitations are kept together in the core and questions.
just fetch-gene-pmids ECOLI rlmC completed. The actual FEBA lookup for keio/b0859 failed because neither local data nor the remote source was reachable; no fitness artifact or negative biological conclusion was fabricated. Source/access logs and the original payload/raw-hash snapshot are in .cache/module-audit-logs/rrna-three-*. Independent annotation-reviewer consultation agreed with the qualified cofactor inference and separate TrmA/RlmD substrate boundaries.
Validation: schema, term/ontology, source/quote and consistency checks pass with zero errors. Strict mode reports the available deep-research file is not cited in annotations; this is intentional, because primary and curated independent evidence replaces provider/prediction quotations. No artificial provider citation was added to clear the advisory.
The existing iron-ion-to-[4Fe-4S] MODIFY is explicitly a lateral correction supported by target HAMAP FT:BINDING features, not a GO descendant refinement or a direct RlmC spectroscopy assay. The RumA/RlmD motif and redox findings remain excluded from target experimental evidence. No action, payload or source byte changed.