HAMAP rule MF_01010
General rule information
[?]
| Accession | MF_01010 |
| Dates | 25-MAR-2002 (Created)
1-JUN-2023 (Last updated, Version 33) |
| Name | 23SrRNA_methyltr_RlmD |
| Scope(s) |
Bacteria Pseudomonadota |
| Template(s) | P55135 (RLMD_ECOLI); [ Recover all ] |
| Triggered by |
HAMAP; MF_01010 (Get profile general information and statistics) |
Propagated annotation
[?]
Identifier, protein and gene names
[?]
| Identifier | RLMD |
| Protein name | RecName: Full=23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD; EC=2.1.1.190; AltName: Full=23S rRNA(m5U1939)-methyltransferase; |
| Gene name | Name=rlmD; |
Comments
[?]
| FUNCTION | Catalyzes the formation of 5-methyl-uridine at position 1939 (m5U1939) in 23S rRNA. |
| CATALYTIC ACTIVITY | Reaction=S-adenosyl-L-methionine + uridine(1939) in 23S rRNA = 5- methyluridine(1939) in 23S rRNA + H(+) + S-adenosyl-L-homocysteine; Xref=Rhea:RHEA:42908, Rhea:RHEA-COMP:10278, Rhea:RHEA-COMP:10279, ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789, ChEBI:CHEBI:65315, ChEBI:CHEBI:74447; EC=2.1.1.190; |
| SIMILARITY | Belongs to the class I-like SAM-binding methyltransferase superfamily. RNA M5U methyltransferase family. RlmD subfamily. |
Keywords
[?]
| Methyltransferase | |
| rRNA processing | |
| S-adenosyl-L-methionine | |
| Transferase | |
| case <FTGroup:1> | |
| 4Fe-4S | |
| Iron | |
| Iron-sulfur | |
| Metal-binding | |
| end case | |
Gene Ontology
[?]
| GO:0070041; Molecular function:rRNA (uridine-C5-)-methyltransferase activity | |
| case <FTGroup:1> | |
| GO:0005506; Molecular function:iron ion binding | |
| end case | |
| GO:0031167; Biological process:rRNA methylation | |
Cross-references
[?]
| Pfam | PF01938; TRAM; 1; |
| Pfam | PF05958; tRNA_U5-meth_tr; 1; |
| NCBIfam | TIGR00479; RumA; 1; |
| PROSITE | PS51687; SAM_MT_RNA_M5U; 1; |
| PROSITE | PS50926; TRAM; 0-1; |
| PROSITE | PS01230; TRMA_1; 1; |
| PROSITE | PS01231; TRMA_2; 1; |
Features
[?]
| From: RLMD_ECOLI (P55135) | ||||||||||||
| Key | From | To | Description | Tag | Condition | FTGroup | ||||||
| ACT_SITE | 389 | 389 | /note="Nucleophile" | C | ||||||||
| BINDING | 81 | 81 | /ligand="[4Fe-4S] cluster" /ligand_id="ChEBI:CHEBI:49883" |
C | 1 | |||||||
| BINDING | 87 | 87 | /ligand="[4Fe-4S] cluster" /ligand_id="ChEBI:CHEBI:49883" |
C | 1 | |||||||
| BINDING | 90 | 90 | /ligand="[4Fe-4S] cluster" /ligand_id="ChEBI:CHEBI:49883" |
C | 1 | |||||||
| BINDING | 162 | 162 | /ligand="[4Fe-4S] cluster" /ligand_id="ChEBI:CHEBI:49883" |
C | 1 | |||||||
| BINDING | 265 | 265 | /ligand="S-adenosyl-L-methionine" /ligand_id="ChEBI:CHEBI:59789" |
Q | ||||||||
| BINDING | 294 | 294 | /ligand="S-adenosyl-L-methionine" /ligand_id="ChEBI:CHEBI:59789" |
F | ||||||||
| BINDING | 299 | 299 | /ligand="S-adenosyl-L-methionine" /ligand_id="ChEBI:CHEBI:59789" |
N | ||||||||
| BINDING | 315 | 315 | /ligand="S-adenosyl-L-methionine" /ligand_id="ChEBI:CHEBI:59789" |
E | ||||||||
| BINDING | 342 | 342 | /ligand="S-adenosyl-L-methionine" /ligand_id="ChEBI:CHEBI:59789" |
[ND] | ||||||||
| BINDING | 363 | 363 | /ligand="S-adenosyl-L-methionine" /ligand_id="ChEBI:CHEBI:59789" |
D | ||||||||
Additional information
[?]
| Size range | 431-514 amino acids |
| Related rules |
MF_01011 |
| Fusion | Nter: None Cter: None |