RLMD_METFK
ID RLMD_METFK Reviewed; 445 AA.
AC Q1H069;
DT 03-APR-2007, integrated into UniProtKB/Swiss-Prot.
DT 27-JUN-2006, sequence version 1.
DT 03-AUG-2022, entry version 86.
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=Mfla_1851;
OS Methylobacillus flagellatus (strain KT / ATCC 51484 / DSM 6875).
OC Bacteria; Proteobacteria; Betaproteobacteria; Nitrosomonadales;
OC Methylophilaceae; Methylobacillus.
OX NCBI_TaxID=265072;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=KT / ATCC 51484 / DSM 6875;
RG US DOE Joint Genome Institute;
RA Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C.,
RA Glavina del Rio T., Hammon N., Israni S., Dalin E., Tice H., Pitluck S.,
RA Brettin T., Bruce D., Han C., Tapia R., Saunders E., Gilna P., Schmutz J.,
RA Larimer F., Land M., Kyrpides N., Anderson I., Richardson P.;
RT "Complete sequence of Methylobacillus flagellatus KT.";
RL Submitted (MAR-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; CP000284; ABE50118.1; -; Genomic_DNA.
DR RefSeq; WP_011480072.1; NC_007947.1.
DR AlphaFoldDB; Q1H069; -.
DR SMR; Q1H069; -.
DR STRING; 265072.Mfla_1851; -.
DR EnsemblBacteria; ABE50118; ABE50118; Mfla_1851.
DR KEGG; mfa:Mfla_1851; -.
DR eggNOG; COG2265; Bacteria.
DR HOGENOM; CLU_014689_8_2_4; -.
DR OMA; FYAGDMK; -.
DR OrthoDB; 1421660at2; -.
DR Proteomes; UP000002440; Chromosome.
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; 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; PS01231; TRMA_2; 1.
PE 3: Inferred from homology;
KW 4Fe-4S; Iron; Iron-sulfur; Metal-binding; Methyltransferase;
KW Reference proteome; rRNA processing; S-adenosyl-L-methionine; Transferase.
FT CHAIN 1..445
FT /note="23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD"
FT /id="PRO_0000282049"
FT DOMAIN 1..55
FT /note="TRAM"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01010"
FT ACT_SITE 399
FT /note="Nucleophile"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01010"
FT BINDING 68
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01010"
FT BINDING 74
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
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 156
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01010"
FT BINDING 265
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01010"
FT BINDING 294
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01010"
FT BINDING 299
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01010"
FT BINDING 315
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01010"
FT BINDING 343
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01010"
FT BINDING 364
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01010"
SQ SEQUENCE 445 AA; 49009 MW; 69ABC8FF4E6C1C3E CRC64;
MSTPIALVES LDQEGRGVAH VEGKTIFIDG ALPGEQVTYK VRRRKERYEV ADVLDVLQAS
HLRTQPGCEH FGVCGGCAIQ HLEFSGQVAA KQRMLESNLW HIGKTRSERM LPPIYGPAWG
YRHKARLRVR HVAKKGGVLV GFNEKSSSFV ADMDSCRVLP PHVSNLIVPM KELVGQLSIR
DRLPQIEVAV GELATVLVLR ILEPLQPQDA APIKAFADRY GVEVWTQSKG PDTVQPFYPL
QGPGLSYSLP EFNLTYPFKP TEFTQVNPYI NRVMLRRAMQ LLQPQPGERI ADFFCGLGNF
TLPIARSGAS VFGMEGSAAL VARANESAAL NSLAGQVEFQ EADLFKMTPA LLQSLGRFDK
WLIDPPRDGA IELVKALPDI EDADADTSHV PQRIVYVSCN PATLARDAGI LVHTKGYRLL
ASGVINMFPH TSHVESIALF EKASP
