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Database: UniProt
Entry: RLMD_SHESH
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ID   RLMD_SHESH              Reviewed;         442 AA.
AC   A8FSS4;
DT   14-APR-2009, integrated into UniProtKB/Swiss-Prot.
DT   13-NOV-2007, sequence version 1.
DT   27-MAR-2024, entry version 91.
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=Ssed_1286;
OS   Shewanella sediminis (strain HAW-EB3).
OC   Bacteria; Pseudomonadota; Gammaproteobacteria; Alteromonadales;
OC   Shewanellaceae; Shewanella.
OX   NCBI_TaxID=425104;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=HAW-EB3;
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., Chertkov O., Brettin T., Bruce D., Detter J.C.,
RA   Han C., Schmutz J., Larimer F., Land M., Hauser L., Kyrpides N., Kim E.,
RA   Zhao J.-S., Richardson P.;
RT   "Complete sequence of Shewanella sediminis HAW-EB3.";
RL   Submitted (AUG-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; CP000821; ABV35897.1; -; Genomic_DNA.
DR   RefSeq; WP_012141633.1; NC_009831.1.
DR   AlphaFoldDB; A8FSS4; -.
DR   SMR; A8FSS4; -.
DR   STRING; 425104.Ssed_1286; -.
DR   KEGG; sse:Ssed_1286; -.
DR   eggNOG; COG2265; Bacteria.
DR   HOGENOM; CLU_014689_8_2_6; -.
DR   OrthoDB; 9804590at2; -.
DR   Proteomes; UP000002015; 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   CDD; cd02440; AdoMet_MTases; 1.
DR   Gene3D; 2.40.50.1070; -; 1.
DR   Gene3D; 2.40.50.140; Nucleic acid-binding proteins; 1.
DR   Gene3D; 3.40.50.150; Vaccinia Virus protein VP39; 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   NCBIfam; TIGR00479; rumA; 1.
DR   PANTHER; PTHR11061:SF49; 23S RRNA (URACIL(1939)-C(5))-METHYLTRANSFERASE RLMD; 1.
DR   PANTHER; PTHR11061; RNA M5U METHYLTRANSFERASE; 1.
DR   Pfam; PF01938; TRAM; 1.
DR   Pfam; PF05958; tRNA_U5-meth_tr; 1.
DR   SUPFAM; SSF50249; Nucleic acid-binding proteins; 1.
DR   SUPFAM; SSF53335; S-adenosyl-L-methionine-dependent methyltransferases; 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   Reference proteome; rRNA processing; S-adenosyl-L-methionine; Transferase.
FT   CHAIN           1..442
FT                   /note="23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD"
FT                   /id="PRO_1000200855"
FT   DOMAIN          12..70
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         83
FT                   /ligand="[4Fe-4S] cluster"
FT                   /ligand_id="ChEBI:CHEBI:49883"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01010"
FT   BINDING         89
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         171
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         373
FT                   /ligand="S-adenosyl-L-methionine"
FT                   /ligand_id="ChEBI:CHEBI:59789"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01010"
SQ   SEQUENCE   442 AA;  48872 MW;  8C96B2CE142CE461 CRC64;
     MAQFFKAKPN SSKQLSAKVT LEVTKLDHLG AGMAQHQGKI VFIPGALPNE KVTVQLTEQK
     KRHARAKLLK IESDSNDRVE PKCPHYQQCG GCDLQHLSID KQRSYKQSAL VDLMAKLSHT
     EAESLAPALI GQEWDYRRRA RLATHYNKES KQITLGFRAS ASKQVINIDV CPVLAKPLSD
     LIAPLSLLLN QLSGKKALGH LELIDADNGY FAVLRMTKAL SDKDAKKLTA FANEKSISLI
     VQGNEGEFTI LGDRNELPYY ALDDVKLNFT PGNFIQVNAA INESMVKQAV DWLSVKPNER
     VLDLFCGVGN FSLPLAKSGA EVIGVEGVPE MVKQARENAA DSGLDNVSFF HTDLSADLSK
     ETWLGKVDKL LLDPARAGAF ESLQWLKKMK PKAIVYVSCD PSSLARDSEP LLKHGYKLKK
     LGLIDMFPQT HHIEAMALFE LD
//
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