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Literature summary for 2.1.1.224 extracted from

  • Fitzsimmons, C.M.; Fujimori, D.G.
    Determinants of tRNA recognition by the radical SAM enzyme RlmN (2016), PLoS ONE, 11, e0167298 .
    View publication on PubMedView publication on EuropePMC
Search for more literature for 2.1.1.224

Cloned(Commentary)

Cloned (Comment) Organism
gene cfr, sequence comparisons and phylogenetic analysis and tree, overview Bacillus amyloliquefaciens
gene cfr, sequence comparisons and phylogenetic analysis and tree, overview Enterococcus faecalis
gene cfr, sequence comparisons and phylogenetic analysis and tree, overview Paenibacillus lautus
gene cfr, sequence comparisons and phylogenetic analysis and tree, overview Clostridioides difficile

KM Value [mM]

KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
additional information
-
 additional information kinetic analysis, overview Bacillus amyloliquefaciens
additional information
-
 additional information kinetic analysis, overview Enterococcus faecalis
additional information
-
 additional information kinetic analysis, overview Paenibacillus lautus
additional information
-
 additional information kinetic analysis, overview Clostridioides difficile

Metals/Ions

Metals/Ions Comment Organism Structure
Fe2+ Clostridioides difficile Cfr contains an additional Cys-rich C-terminal domain that binds a mononuclear Fe2+ ion in a rubredoxin-type Cys4 motif. The rate of turnover is decreased upon disruption of the Fe2+-binding site by Zn2+ substitution or ligand mutation Clostridioides difficile
Mg2+ required Bacillus amyloliquefaciens
Mg2+ required Enterococcus faecalis
Mg2+ required Paenibacillus lautus
Mg2+ required Clostridioides difficile

Natural Substrates/ Products (Substrates)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
2 S-adenosyl-L-methionine + adenine2503 in 23S rRNA + 2 reduced [2Fe-2S] ferredoxin Bacillus amyloliquefaciens
-
 S-adenosyl-L-homocysteine + L-methionine + 5'-deoxyadenosine + 8-methyladenine2503 in 23S rRNA + 2 oxidized [2Fe-2S] ferredoxin
-
 ?
2 S-adenosyl-L-methionine + adenine2503 in 23S rRNA + 2 reduced [2Fe-2S] ferredoxin Enterococcus faecalis
-
 S-adenosyl-L-homocysteine + L-methionine + 5'-deoxyadenosine + 8-methyladenine2503 in 23S rRNA + 2 oxidized [2Fe-2S] ferredoxin
-
 ?
2 S-adenosyl-L-methionine + adenine2503 in 23S rRNA + 2 reduced [2Fe-2S] ferredoxin Paenibacillus lautus
-
 S-adenosyl-L-homocysteine + L-methionine + 5'-deoxyadenosine + 8-methyladenine2503 in 23S rRNA + 2 oxidized [2Fe-2S] ferredoxin
-
 ?
2 S-adenosyl-L-methionine + adenine2503 in 23S rRNA + 2 reduced [2Fe-2S] ferredoxin Clostridioides difficile
-
 S-adenosyl-L-homocysteine + L-methionine + 5'-deoxyadenosine + 8-methyladenine2503 in 23S rRNA + 2 oxidized [2Fe-2S] ferredoxin
-
 ?
2 S-adenosyl-L-methionine + adenine2503 in 23S rRNA + 2 reduced [2Fe-2S] ferredoxin Bacillus amyloliquefaciens DSM-7
-
 S-adenosyl-L-homocysteine + L-methionine + 5'-deoxyadenosine + 8-methyladenine2503 in 23S rRNA + 2 oxidized [2Fe-2S] ferredoxin
-
 ?
2 S-adenosyl-L-methionine + adenine2503 in 23S rRNA + 2 reduced [2Fe-2S] ferredoxin Paenibacillus lautus Y412MC10
-
 S-adenosyl-L-homocysteine + L-methionine + 5'-deoxyadenosine + 8-methyladenine2503 in 23S rRNA + 2 oxidized [2Fe-2S] ferredoxin
-
 ?
2 S-adenosyl-L-methionine + adenine2503 in 23S rRNA + 2 reduced [2Fe-2S] ferredoxin Enterococcus faecalis TX0645
-
 S-adenosyl-L-homocysteine + L-methionine + 5'-deoxyadenosine + 8-methyladenine2503 in 23S rRNA + 2 oxidized [2Fe-2S] ferredoxin
-
 ?
2 S-adenosyl-L-methionine + adenine2503 in 23S rRNA + 2 reduced [2Fe-2S] ferredoxin Clostridioides difficile QCD63q42
-
 S-adenosyl-L-homocysteine + L-methionine + 5'-deoxyadenosine + 8-methyladenine2503 in 23S rRNA + 2 oxidized [2Fe-2S] ferredoxin
-
 ?

Organism

Organism UniProt Comment Textmining
Bacillus amyloliquefaciens A0A4V7TJX0
-
-
Bacillus amyloliquefaciens DSM-7 A0A4V7TJX0
-
-
Clostridioides difficile V5ZEQ2
-
-
Clostridioides difficile QCD63q42 V5ZEQ2
-
-
Enterococcus faecalis A0A2Z6BLR4
-
-
Enterococcus faecalis TX0645 A0A2Z6BLR4
-
-
Paenibacillus lautus D3EIG6
-
-
Paenibacillus lautus Y412MC10 D3EIG6
-
-

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
2 S-adenosyl-L-methionine + adenine2503 in 23S rRNA + 2 reduced [2Fe-2S] ferredoxin
-
 Bacillus amyloliquefaciens S-adenosyl-L-homocysteine + L-methionine + 5'-deoxyadenosine + 8-methyladenine2503 in 23S rRNA + 2 oxidized [2Fe-2S] ferredoxin
-
 ?
2 S-adenosyl-L-methionine + adenine2503 in 23S rRNA + 2 reduced [2Fe-2S] ferredoxin
-
 Enterococcus faecalis S-adenosyl-L-homocysteine + L-methionine + 5'-deoxyadenosine + 8-methyladenine2503 in 23S rRNA + 2 oxidized [2Fe-2S] ferredoxin
-
 ?
2 S-adenosyl-L-methionine + adenine2503 in 23S rRNA + 2 reduced [2Fe-2S] ferredoxin
-
 Paenibacillus lautus S-adenosyl-L-homocysteine + L-methionine + 5'-deoxyadenosine + 8-methyladenine2503 in 23S rRNA + 2 oxidized [2Fe-2S] ferredoxin
-
 ?
2 S-adenosyl-L-methionine + adenine2503 in 23S rRNA + 2 reduced [2Fe-2S] ferredoxin
-
 Clostridioides difficile S-adenosyl-L-homocysteine + L-methionine + 5'-deoxyadenosine + 8-methyladenine2503 in 23S rRNA + 2 oxidized [2Fe-2S] ferredoxin
-
 ?
2 S-adenosyl-L-methionine + adenine2503 in 23S rRNA + 2 reduced [2Fe-2S] ferredoxin
-
 Bacillus amyloliquefaciens DSM-7 S-adenosyl-L-homocysteine + L-methionine + 5'-deoxyadenosine + 8-methyladenine2503 in 23S rRNA + 2 oxidized [2Fe-2S] ferredoxin
-
 ?
2 S-adenosyl-L-methionine + adenine2503 in 23S rRNA + 2 reduced [2Fe-2S] ferredoxin
-
 Paenibacillus lautus Y412MC10 S-adenosyl-L-homocysteine + L-methionine + 5'-deoxyadenosine + 8-methyladenine2503 in 23S rRNA + 2 oxidized [2Fe-2S] ferredoxin
-
 ?
2 S-adenosyl-L-methionine + adenine2503 in 23S rRNA + 2 reduced [2Fe-2S] ferredoxin
-
 Enterococcus faecalis TX0645 S-adenosyl-L-homocysteine + L-methionine + 5'-deoxyadenosine + 8-methyladenine2503 in 23S rRNA + 2 oxidized [2Fe-2S] ferredoxin
-
 ?
2 S-adenosyl-L-methionine + adenine2503 in 23S rRNA + 2 reduced [2Fe-2S] ferredoxin
-
 Clostridioides difficile QCD63q42 S-adenosyl-L-homocysteine + L-methionine + 5'-deoxyadenosine + 8-methyladenine2503 in 23S rRNA + 2 oxidized [2Fe-2S] ferredoxin
-
 ?
additional information kinetic analysis of methylation of a 155mer rRNA substrate by Cfr enzymes under limiting and under excess substrate conditions initiated with a protein-based reductant, substrate sequence, overview Bacillus amyloliquefaciens ?
-
-
additional information kinetic analysis of methylation of a 155mer rRNA substrate by Cfr enzymes under limiting and under excess substrate conditions initiated with a protein-based reductant, substrate sequence, overview Enterococcus faecalis ?
-
-
additional information kinetic analysis of methylation of a 155mer rRNA substrate by Cfr enzymes under limiting and under excess substrate conditions initiated with a protein-based reductant, substrate sequence, overview Paenibacillus lautus ?
-
-
additional information kinetic analysis of methylation of a 155mer rRNA substrate by Cfr enzymes under limiting and under excess substrate conditions initiated with a protein-based reductant, substrate sequence, overview Clostridioides difficile ?
-
-
additional information kinetic analysis of methylation of a 155mer rRNA substrate by Cfr enzymes under limiting and under excess substrate conditions initiated with a protein-based reductant, substrate sequence, overview Bacillus amyloliquefaciens DSM-7 ?
-
-
additional information kinetic analysis of methylation of a 155mer rRNA substrate by Cfr enzymes under limiting and under excess substrate conditions initiated with a protein-based reductant, substrate sequence, overview Paenibacillus lautus Y412MC10 ?
-
-
additional information kinetic analysis of methylation of a 155mer rRNA substrate by Cfr enzymes under limiting and under excess substrate conditions initiated with a protein-based reductant, substrate sequence, overview Enterococcus faecalis TX0645 ?
-
-
additional information kinetic analysis of methylation of a 155mer rRNA substrate by Cfr enzymes under limiting and under excess substrate conditions initiated with a protein-based reductant, substrate sequence, overview Clostridioides difficile QCD63q42 ?
-
-

Synonyms

Synonyms Comment Organism
Ba Cfr
-
 Bacillus amyloliquefaciens
C8 adenine RNA methylase
-
 Bacillus amyloliquefaciens
C8 adenine RNA methylase
-
 Enterococcus faecalis
C8 adenine RNA methylase
-
 Paenibacillus lautus
C8 adenine RNA methylase
-
 Clostridioides difficile
Cd Cfr
-
 Clostridioides difficile
Cfr
-
 Bacillus amyloliquefaciens
Cfr
-
 Enterococcus faecalis
Cfr
-
 Paenibacillus lautus
Cfr
-
 Clostridioides difficile
Ef Cfr
-
 Enterococcus faecalis
Pl Cfr
-
 Paenibacillus lautus

Temperature Optimum [°C]

Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
37
-
 assay at Bacillus amyloliquefaciens
37
-
 assay at Enterococcus faecalis
37
-
 assay at Paenibacillus lautus
37
-
 assay at Clostridioides difficile

pH Optimum

pH Optimum Minimum pH Optimum Maximum Comment Organism
8
-
 assay at Bacillus amyloliquefaciens
8
-
 assay at Enterococcus faecalis
8
-
 assay at Paenibacillus lautus
8
-
 assay at Clostridioides difficile

Cofactor

Cofactor Comment Organism Structure
reduced [2Fe-2S] ferredoxin
-
 Bacillus amyloliquefaciens
reduced [2Fe-2S] ferredoxin
-
 Enterococcus faecalis
reduced [2Fe-2S] ferredoxin
-
 Paenibacillus lautus
reduced [2Fe-2S] ferredoxin
-
 Clostridioides difficile
S-adenosyl-L-methionine
-
 Bacillus amyloliquefaciens
S-adenosyl-L-methionine
-
 Enterococcus faecalis
S-adenosyl-L-methionine
-
 Paenibacillus lautus
S-adenosyl-L-methionine
-
 Clostridioides difficile

General Information

General Information Comment Organism
evolution analysis of RNA methylation by phylogenetically diverse Cfr radical SAM enzymes reveals an ironbinding accessory domain in a clostridial enzyme. Sequence comparisons and phylogenetic analysis and tree, overview. Cfr homologues from Bacillus amyloliquefaciens, Enterococcus faecalis, Paenibacillus lautus, and Clostridioides difficile act as C8 adenine RNA methylases in biochemical assays Bacillus amyloliquefaciens
evolution analysis of RNA methylation by phylogenetically diverse Cfr radical SAM enzymes reveals an ironbinding accessory domain in a clostridial enzyme. Sequence comparisons and phylogenetic analysis and tree, overview. Cfr homologues from Bacillus amyloliquefaciens, Enterococcus faecalis, Paenibacillus lautus, and Clostridioides difficile act as C8 adenine RNA methylases in biochemical assays Enterococcus faecalis
evolution analysis of RNA methylation by phylogenetically diverse Cfr radical SAM enzymes reveals an ironbinding accessory domain in a clostridial enzyme. Sequence comparisons and phylogenetic analysis and tree, overview. Cfr homologues from Bacillus amyloliquefaciens, Enterococcus faecalis, Paenibacillus lautus, and Clostridioides difficile act as C8 adenine RNA methylases in biochemical assays Paenibacillus lautus
evolution analysis of RNA methylation by phylogenetically diverse Cfr radical SAM enzymes reveals an ironbinding accessory domain in a clostridial enzyme. Sequence comparisons and phylogenetic analysis and tree, overview. Cfr homologues from Bacillus amyloliquefaciens, Enterococcus faecalis, Paenibacillus lautus, and Clostridioides difficile act as C8 adenine RNA methylases in biochemical assays. Clostridioides difficile Cfr contains an additional Cys-rich C-terminal domain that binds a mononuclear Fe2+ ion in a rubredoxin-type Cys4 motif, which has an important purpose for the observed C-terminal iron in the native fusion protein. Bioinformatic analysis of the Clostridioides difficile Cfr Cys-rich domain shows that it is widespread (about 1400 homologues) as a stand-alone gene in pathogenic or commensal Bacilli and Clostridia, with >10% encoded adjacent to a predicted radical SAM RNA methylase Clostridioides difficile
malfunction Clostridioides difficile Cfr contains an additional Cys-rich C-terminal domain that binds a mononuclear Fe2+ ion in a rubredoxin-type Cys4 motif. The C-terminal domain can be truncated with minimal impact on Cfr activity, but the rate of turnover is decreased upon disruption of the Fe2+-binding site by Zn2+ substitution or ligand mutation Clostridioides difficile
physiological function Cfr is a radical S-adenosylmethionine (SAM) RNA methylase linked to multidrug antibiotic resistance in bacterial pathogens. It catalyzes a chemically challenging C-C bond-forming reaction to methylate C8 of A2503 (Escherichia coli numbering) of 23S rRNA during ribosome assembly Bacillus amyloliquefaciens
physiological function Cfr is a radical S-adenosylmethionine (SAM) RNA methylase linked to multidrug antibiotic resistance in bacterial pathogens. It catalyzes a chemically challenging C-C bond-forming reaction to methylate C8 of A2503 (Escherichia coli numbering) of 23S rRNA during ribosome assembly Enterococcus faecalis
physiological function Cfr is a radical S-adenosylmethionine (SAM) RNA methylase linked to multidrug antibiotic resistance in bacterial pathogens. It catalyzes a chemically challenging C-C bond-forming reaction to methylate C8 of A2503 (Escherichia coli numbering) of 23S rRNA during ribosome assembly Paenibacillus lautus
physiological function Cfr is a radical S-adenosylmethionine (SAM) RNA methylase linked to multidrug antibiotic resistance in bacterial pathogens. It catalyzes a chemically challenging C-C bond-forming reaction to methylate C8 of A2503 (Escherichia coli numbering) of 23S rRNA during ribosome assembly Clostridioides difficile