RLMD_MARMS
ID RLMD_MARMS Reviewed; 440 AA.
AC A6VUQ2;
DT 25-JAN-2012, integrated into UniProtKB/Swiss-Prot.
DT 21-AUG-2007, sequence version 1.
DT 03-AUG-2022, entry version 76.
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}; OrderedLocusNames=Mmwyl1_1252;
OS Marinomonas sp. (strain MWYL1).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Oceanospirillales;
OC Oceanospirillaceae; Marinomonas.
OX NCBI_TaxID=400668;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=MWYL1;
RG US DOE Joint Genome Institute;
RA Copeland A., Lucas S., Lapidus A., Barry K., Glavina del Rio T., Dalin E.,
RA Tice H., Pitluck S., Kiss H., Brettin T., Bruce D., Detter J.C., Han C.,
RA Schmutz J., Larimer F., Land M., Hauser L., Kyrpides N., Kim E.,
RA Johnston A.W.B., Todd J.D., Rogers R., Wexler M., Bond P.L., Li Y.,
RA Richardson P.;
RT "Complete sequence of Marinomonas sp. MWYL1.";
RL Submitted (JUN-2007) 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; CP000749; ABR70181.1; -; Genomic_DNA.
DR RefSeq; WP_012068966.1; NC_009654.1.
DR AlphaFoldDB; A6VUQ2; -.
DR SMR; A6VUQ2; -.
DR STRING; 400668.Mmwyl1_1252; -.
DR EnsemblBacteria; ABR70181; ABR70181; Mmwyl1_1252.
DR KEGG; mmw:Mmwyl1_1252; -.
DR eggNOG; COG2265; Bacteria.
DR HOGENOM; CLU_014689_8_2_6; -.
DR OMA; FYAGDMK; -.
DR OrthoDB; 1421660at2; -.
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..440
FT /note="23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD"
FT /id="PRO_0000414808"
FT DOMAIN 15..73
FT /note="TRAM"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01010"
FT REGION 1..21
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 396
FT /note="Nucleophile"
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 92
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01010"
FT BINDING 95
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01010"
FT BINDING 169
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01010"
FT BINDING 273
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01010"
FT BINDING 302
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01010"
FT BINDING 307
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01010"
FT BINDING 323
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01010"
FT BINDING 350
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01010"
FT BINDING 370
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01010"
SQ SEQUENCE 440 AA; 49183 MW; 3A0DEC595FBAF96B CRC64;
MRRRTSPRRT TTSKPQPIGP IQTFEVDGLT HEAKGVARLQ GKVTFIEGAL PGETVEAQVN
KAGRRFDEAV LVNIIEPSVY RVEPSCQHFN LCGGCSFQHL ANEQQLSAKA DWLQGQLRNL
ITTQELETLS DTPTGYRRRA RLAIDIKKGR MVLGFRGKAS KEIISIDQCV VLTPNLQSTF
LLLKLKLLEN DLAGVLGHVE LLEDTKGVSA LFRLTSPISD ELKNAWEDWA EKGRVALYWQ
APKVGKAEVA LEKMRYYDLG DLRLKYHPQD FIQVNAAMNQ KMVVQAMDWL NPSKQDVILD
LFCGVGNFSL PLAVHAQAVI GVEVQETMVE AARENARVNG FDNLSFVAAD LTKPVNNELF
KQTITKVLLD PPRAGAFEFL DSIIKIGPTQ ILYVSCNAST LARDAEYLVA KGYRVLRVSL
MDMFPQTSHV ETMMLLQKKK
