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HAMAP rule MF_01849

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General rule information [?]

Accession MF_01849
Dates 11-JUL-2008 (Created)
13-OCT-2023 (Last updated, Version 22)
Name RNA_methyltr_RlmN
Scope(s) Bacteria
Archaea
Template(s) P36979 (RLMN_ECOLI); A6QGB8 (RLMN_STAAE); [ Recover all ]
Triggered by HAMAP; MF_01849 (Get profile general information and statistics)

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 Name=rlmN;

Comments [?]

case <OC:Pseudomonadota>
FUNCTIONSpecifically 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>
FUNCTIONSpecifically 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>
FUNCTIONSpecifically methylates position 2 of adenine 2503 in 23S rRNA and position 2 of adenine 37 in tRNAs.
end case
case <OC:Archaea>
FUNCTIONSpecifically methylates position 2 of adenine 2503 in 23S rRNA.
end case
case <OC:Bacteria>
CATALYTIC ACTIVITY Reaction=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; Xref=Rhea:RHEA:42916, Rhea:RHEA- COMP:10000, Rhea:RHEA-COMP:10001, Rhea:RHEA-COMP:10152, Rhea:RHEA- COMP:10282, ChEBI:CHEBI:17319, ChEBI:CHEBI:33737, ChEBI:CHEBI:33738, ChEBI:CHEBI:57844, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789, ChEBI:CHEBI:74411, ChEBI:CHEBI:74497; EC=2.1.1.192;
CATALYTIC ACTIVITY Reaction=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; Xref=Rhea:RHEA:43332, Rhea:RHEA-COMP:10000, Rhea:RHEA-COMP:10001, Rhea:RHEA-COMP:10162, Rhea:RHEA-COMP:10485, ChEBI:CHEBI:17319, ChEBI:CHEBI:33737, ChEBI:CHEBI:33738, ChEBI:CHEBI:57844, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789, ChEBI:CHEBI:74411, ChEBI:CHEBI:74497; EC=2.1.1.192;
end case
case <OC:Archaea>
CATALYTIC ACTIVITY Reaction=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; Xref=Rhea:RHEA:42916, Rhea:RHEA- COMP:10000, Rhea:RHEA-COMP:10001, Rhea:RHEA-COMP:10152, Rhea:RHEA- COMP:10282, ChEBI:CHEBI:17319, ChEBI:CHEBI:33737, ChEBI:CHEBI:33738, ChEBI:CHEBI:57844, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789, ChEBI:CHEBI:74411, ChEBI:CHEBI:74497; EC=2.1.1.192;
end case
case <FTGroup:1>
COFACTOR Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883; Note=Binds 1 [4Fe-4S] cluster. The cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine.;
end case
SUBCELLULAR LOCATIONCytoplasm.
MISCELLANEOUSReaction proceeds by a ping-pong mechanism involving intermediate methylation of a conserved cysteine residue.
SIMILARITYBelongs to the radical SAM superfamily. RlmN family.

Keywords [?]


Gene Ontology [?]

GO:0019843; Molecular function:rRNA binding
GO:0070040; Molecular function:rRNA (adenine(2503)-C2-)-methyltransferase activity
GO:0070475; Biological process:rRNA base methylation
case <OCellular component:Bacteria>
GO:0000049; Molecular function:tRNA binding
GO:0002935; Molecular function:tRNA (adenine(37)-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;

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 /note="Proton acceptor" E
ACT_SITE 355 355 /note="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 /note="(transient)" C-x*-C

Additional information [?]

Size range 318-431 amino acids
Related rules MF_01873
Fusion Nter: None Cter: None
Comments Possible wrong starts.



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