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HAMAP rule MF_01849

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General rule information [?]

Accession MF_01849
Dates 11-JUL-2008 (Created)
1-JUN-2023 (Last updated, Version 21)
Name RNA_methyltr_RlmN
Scope
Bacteria
Archaea
Templates P36979 (RLMN_ECOLI); A6QGB8 (RLMN_STAAE): [Recover all]
Triggered by

Propagated annotation [?]


Identifier, protein and gene names [?]

Identifier
RLMN
case <OC:Pseudomonadota>
Protein name
RecName: Full=Dual-specificity RNA methyltransferase RlmN;
EC 2.1.1.192;
AltName: Full=23S rRNA (adenine(2503)-C(2))-methyltransferase;
AltName: Full=23S rRNA m2A2503 methyltransferase;
AltName: Full=Ribosomal RNA large subunit methyltransferase N;
AltName: Full=tRNA (adenine(37)-C(2))-methyltransferase;
AltName: Full=tRNA m2A37 methyltransferase;
else case <OC:Bacteria>
Protein name
RecName: Full=Probable dual-specificity RNA methyltransferase RlmN;
EC 2.1.1.192;
AltName: Full=23S rRNA (adenine(2503)-C(2))-methyltransferase;
AltName: Full=23S rRNA m2A2503 methyltransferase;
AltName: Full=Ribosomal RNA large subunit methyltransferase N;
AltName: Full=tRNA (adenine(37)-C(2))-methyltransferase;
AltName: Full=tRNA m2A37 methyltransferase;
else
Protein name
RecName: Full=Ribosomal RNA large subunit methyltransferase N;
EC 2.1.1.-;
AltName: Full=23S rRNA (adenine(2503)-C(2))-methyltransferase;
AltName: Full=23S rRNA m2A2503 methyltransferase;
end case
Gene name
rlmN

Comments [?]

case <OC:Pseudomonadota>
Function Specifically methylates position 2 of adenine 2503 in 23S rRNA and position 2 of adenine 37 in tRNAs. m2A2503 modification seems to play a crucial role in the proofreading step occurring at the peptidyl transferase center and thus would serve to optimize ribosomal fidelity.
else case <OC:Staphylococcus>
Function Specifically methylates position 2 of adenine 2503 in 23S rRNA and position 2 of adenine 37 in tRNAs. Confers resistance to some classes of antibiotics.
else case <OC:Bacteria>
Function Specifically methylates position 2 of adenine 2503 in 23S rRNA and position 2 of adenine 37 in tRNAs.
end case
case <OC:Archaea>
Function Specifically methylates position 2 of adenine 2503 in 23S rRNA.
end case
case <OC:Bacteria>
Catalytic activity RHEA:42916: adenosine(2503) in 23S rRNA + 2 reduced [2Fe-2S]-[ferredoxin] + 2 S-adenosyl-L-methionine = 2-methyladenosine(2503) in 23S rRNA + 5'-deoxyadenosine + L-methionine + 2 oxidized [2Fe-2S]-[ferredoxin] + S-adenosyl-L-homocysteine
EC 2.1.1.192
RHEA:43332: adenosine(37) in tRNA + 2 reduced [2Fe-2S]-[ferredoxin] + 2 S-adenosyl-L-methionine = 2-methyladenosine(37) in tRNA + 5'-deoxyadenosine + L-methionine + 2 oxidized [2Fe-2S]-[ferredoxin] + S-adenosyl-L-homocysteine
EC 2.1.1.192
end case
case <OC:Archaea>
Catalytic activity RHEA:42916: adenosine(2503) in 23S rRNA + 2 reduced [2Fe-2S]-[ferredoxin] + 2 S-adenosyl-L-methionine = 2-methyladenosine(2503) in 23S rRNA + 5'-deoxyadenosine + L-methionine + 2 oxidized [2Fe-2S]-[ferredoxin] + S-adenosyl-L-homocysteine
EC 2.1.1.192
end case
case <FTGroup:1>
Cofactor [4Fe-4S] cluster
Note: Binds 1 [4Fe-4S] cluster. The cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine.
end case
Subcellular location Cytoplasm.
Miscellaneous Reaction proceeds by a ping-pong mechanism involving intermediate methylation of a conserved cysteine residue.
Similarity Belongs to the radical SAM superfamily. RlmN family.

Keywords [?]

Cytoplasm
Disulfide bond
Methyltransferase
rRNA processing
S-adenosyl-L-methionine
Transferase
case <FTGroup:1>
4Fe-4S
Iron
Iron-sulfur
Metal-binding
end case
case <OC:Staphylococcus>
Antibiotic resistance
end case
case <OC:Bacteria>
tRNA processing
end case

Gene Ontology [?]

GO:0019843; Molecular function: rRNA binding.
GO:0070040; Molecular function: rRNA (adenine-C2-)-methyltransferase activity.
GO:0070475; Biological process: rRNA base methylation.
case <OC:Bacteria>
GO:0000049; Molecular function: tRNA binding.
GO:0002935; Molecular function: tRNA (adenine-C2-)-methyltransferase activity.
GO:0030488; Biological process: tRNA methylation.
end case
case <FTGroup:1>
GO:0051539; Molecular function: 4 iron, 4 sulfur cluster binding.
end case
GO:0005737; Cellular component: cytoplasm.

Cross-references [?]

Pfam PF04055; Radical_SAM; 1;
NCBIfam TIGR00048; TIGR00048; 1;
PIRSF PIRSF006004; CHP00048; 1;
PROSITE PS51918; RADICAL_SAM; 1; trigger=PRU01266;

Features [?]

From: RLMN_ECOLI (P36979)
Key     From     To       Description   Tag   Condition   FTGroup
BINDING     179     180       /ligand="S-adenosyl-L-methionine" /ligand_id="ChEBI:CHEBI:59789     G-E  
BINDING     233     235       /ligand="S-adenosyl-L-methionine" /ligand_id="ChEBI:CHEBI:59789     S-x-[HNT]  
ACT_SITE     105     105       Proton acceptor     E  
ACT_SITE     355     355       S-methylcysteine intermediate     C  
BINDING     125     125       /ligand="[4Fe-4S] cluster" /ligand_id="ChEBI:CHEBI:49883" /ligand_note="4Fe-4S-S-AdoMet     C   1
BINDING     129     129       /ligand="[4Fe-4S] cluster" /ligand_id="ChEBI:CHEBI:49883" /ligand_note="4Fe-4S-S-AdoMet     C   1
BINDING     132     132       /ligand="[4Fe-4S] cluster" /ligand_id="ChEBI:CHEBI:49883" /ligand_note="4Fe-4S-S-AdoMet     C   1
BINDING     211     211       /ligand="S-adenosyl-L-methionine" /ligand_id="ChEBI:CHEBI:59789     S  
BINDING     312     312       /ligand="S-adenosyl-L-methionine" /ligand_id="ChEBI:CHEBI:59789     [NTH]  
DISULFID     118     355       (transient)     C-x*-C  

Additional information [?]

Size range 318-431 amino acids
Related rules MF_01873 (CFR)
Fusion None
Comments Possible wrong starts.


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