RLMD_LEGPC
ID RLMD_LEGPC Reviewed; 444 AA.
AC A5IBU7;
DT 20-MAY-2008, integrated into UniProtKB/Swiss-Prot.
DT 26-JUN-2007, sequence version 1.
DT 03-AUG-2022, entry version 81.
DE RecName: Full=23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD {ECO:0000255|HAMAP-Rule:MF_01010};
DE EC=2.1.1.190 {ECO:0000255|HAMAP-Rule:MF_01010};
DE AltName: Full=23S rRNA(m5U1939)-methyltransferase {ECO:0000255|HAMAP-Rule:MF_01010};
GN Name=rlmD {ECO:0000255|HAMAP-Rule:MF_01010}; Synonyms=rumA;
GN OrderedLocusNames=LPC_0871;
OS Legionella pneumophila (strain Corby).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Legionellales;
OC Legionellaceae; Legionella.
OX NCBI_TaxID=400673;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Corby;
RA Gloeckner G., Albert-Weissenberger C., Weinmann E., Jacobi S., Schunder E.,
RA Steinert M., Buchrieser C., Hacker J., Heuner K.;
RT "Identification and characterization of a new conjugation/ type IVA
RT secretion system (trb/tra) of L. pneumophila Corby localized on a mobile
RT genomic island.";
RL Submitted (NOV-2006) to the EMBL/GenBank/DDBJ databases.
CC -!- FUNCTION: Catalyzes the formation of 5-methyl-uridine at position 1939
CC (m5U1939) in 23S rRNA. {ECO:0000255|HAMAP-Rule:MF_01010}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=S-adenosyl-L-methionine + uridine(1939) in 23S rRNA = 5-
CC methyluridine(1939) in 23S rRNA + H(+) + S-adenosyl-L-homocysteine;
CC Xref=Rhea:RHEA:42908, Rhea:RHEA-COMP:10278, Rhea:RHEA-COMP:10279,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC ChEBI:CHEBI:65315, ChEBI:CHEBI:74447; EC=2.1.1.190;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01010};
CC -!- SIMILARITY: Belongs to the class I-like SAM-binding methyltransferase
CC superfamily. RNA M5U methyltransferase family. RlmD subfamily.
CC {ECO:0000255|HAMAP-Rule:MF_01010}.
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DR EMBL; CP000675; ABQ54847.1; -; Genomic_DNA.
DR RefSeq; WP_011946460.1; NC_009494.2.
DR AlphaFoldDB; A5IBU7; -.
DR SMR; A5IBU7; -.
DR KEGG; lpc:LPC_0871; -.
DR HOGENOM; CLU_014689_8_2_6; -.
DR OMA; FYAGDMK; -.
DR BioCyc; LPNE400673:LPC_RS07595-MON; -.
DR GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IEA:UniProtKB-KW.
DR GO; GO:0005506; F:iron ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0003723; F:RNA binding; IEA:InterPro.
DR GO; GO:0070041; F:rRNA (uridine-C5-)-methyltransferase activity; IEA:UniProtKB-UniRule.
DR Gene3D; 2.40.50.140; -; 1.
DR Gene3D; 3.40.50.150; -; 1.
DR HAMAP; MF_01010; 23SrRNA_methyltr_RlmD; 1.
DR InterPro; IPR001566; 23S_rRNA_MeTrfase_RlmD.
DR InterPro; IPR030390; MeTrfase_TrmA_AS.
DR InterPro; IPR030391; MeTrfase_TrmA_CS.
DR InterPro; IPR012340; NA-bd_OB-fold.
DR InterPro; IPR029063; SAM-dependent_MTases_sf.
DR InterPro; IPR002792; TRAM_dom.
DR InterPro; IPR010280; U5_MeTrfase_fam.
DR PANTHER; PTHR11061; PTHR11061; 1.
DR Pfam; PF01938; TRAM; 1.
DR Pfam; PF05958; tRNA_U5-meth_tr; 1.
DR SUPFAM; SSF50249; SSF50249; 1.
DR SUPFAM; SSF53335; SSF53335; 1.
DR PROSITE; PS51687; SAM_MT_RNA_M5U; 1.
DR PROSITE; PS50926; TRAM; 1.
DR PROSITE; PS01230; TRMA_1; 1.
DR PROSITE; PS01231; TRMA_2; 1.
PE 3: Inferred from homology;
KW 4Fe-4S; Iron; Iron-sulfur; Metal-binding; Methyltransferase;
KW rRNA processing; S-adenosyl-L-methionine; Transferase.
FT CHAIN 1..444
FT /note="23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD"
FT /id="PRO_1000084034"
FT DOMAIN 5..64
FT /note="TRAM"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01010"
FT ACT_SITE 400
FT /note="Nucleophile"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01010"
FT BINDING 77
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01010"
FT BINDING 83
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01010"
FT BINDING 86
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01010"
FT BINDING 166
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01010"
FT BINDING 276
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01010"
FT BINDING 305
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01010"
FT BINDING 310
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01010"
FT BINDING 326
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01010"
FT BINDING 353
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01010"
FT BINDING 374
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01010"
SQ SEQUENCE 444 AA; 50497 MW; 28E4F4D224D42636 CRC64;
MRKVKPKLNL TSQTARIVNL SHDGRGIARV NGKATFIQGA LPGEVVEFQY TRIKKDFDEG
KLLSIVEPST LRVEPKCPHY QMCGGCSLQH MSAEEQIRFK QSHLLDLLSR YGHTEPQSVL
SPLTSHHWNY RNKARLSTRF VEKKQSTMVG FRERNNPRFI TEINQCPILN SKIDTDIVHL
RKLIDTMEDK HCIAQIEVAA GDNEVALIFR NLSPLTEQDE LKIREFAQQF QYKVFLQPGG
LDSVFCFYPS DAHAYLSYEL PDYQITFQFH PNDFTQVNAE LNRKMVTQAI QLMELKNSDI
VLDLFCGLGN FSLPMAKHCS RVIGVEGNKN MVERAYMNAK SNHITNVDFY AANLDDVMEV
RNLVNTSFSK VLIDPPRSGA LEIVKQIDSI DPERIVYVSC NPITLARDTD ILVNQKGYVL
ITAGVMDMFP HTAHVESIAL FQKG
