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HAMAP rule MF_01849
General rule information
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| 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
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Identifier, protein and gene names
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| 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
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| 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 | 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 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
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| 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
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| 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
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| Pfam | PF04055; Radical_SAM; 1; |
| NCBIfam | TIGR00048; TIGR00048; 1; |
| PIRSF | PIRSF006004; CHP00048; 1; |
| PROSITE | PS51918; RADICAL_SAM; 1; |
Features
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| 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
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| Size range | 318-431 amino acids |
| Related rules |
MF_01873 |
| Fusion | Nter: None Cter: None |
| Comments | Possible wrong starts. |