ID RLMD_VIBC3 Reviewed; 440 AA. AC A5F5I8; C3M4U3; DT 14-APR-2009, integrated into UniProtKB/Swiss-Prot. DT 12-JUN-2007, sequence version 1. DT 27-MAR-2024, entry version 88. 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=VC0395_A2030, VC395_2567; OS Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / OS O395). OC Bacteria; Pseudomonadota; Gammaproteobacteria; Vibrionales; Vibrionaceae; OC Vibrio. OX NCBI_TaxID=345073; RN [1] RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. RC STRAIN=ATCC 39541 / Classical Ogawa 395 / O395; RA Heidelberg J.; RL Submitted (MAR-2007) to the EMBL/GenBank/DDBJ databases. RN [2] RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. RC STRAIN=ATCC 39541 / Classical Ogawa 395 / O395; RX PubMed=19115014; DOI=10.1371/journal.pone.0004053; RA Feng L., Reeves P.R., Lan R., Ren Y., Gao C., Zhou Z., Ren Y., Cheng J., RA Wang W., Wang J., Qian W., Li D., Wang L.; RT "A recalibrated molecular clock and independent origins for the cholera RT pandemic clones."; RL PLoS ONE 3:E4053-E4053(2008). 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}. CC --------------------------------------------------------------------------- CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms CC Distributed under the Creative Commons Attribution (CC BY 4.0) License CC --------------------------------------------------------------------------- DR EMBL; CP000627; ABQ21286.1; -; Genomic_DNA. DR EMBL; CP001235; ACP10554.1; -; Genomic_DNA. DR RefSeq; WP_000090453.1; NZ_JAACZH010000010.1. DR AlphaFoldDB; A5F5I8; -. DR SMR; A5F5I8; -. DR KEGG; vco:VC0395_A2030; -. DR KEGG; vcr:VC395_2567; -. DR PATRIC; fig|345073.21.peg.2472; -. DR eggNOG; COG2265; Bacteria. DR HOGENOM; CLU_014689_8_2_6; -. DR OrthoDB; 9804590at2; -. DR Proteomes; UP000000249; Chromosome 2. 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 rRNA processing; S-adenosyl-L-methionine; Transferase. FT CHAIN 1..440 FT /note="23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD" FT /id="PRO_1000200859" FT DOMAIN 11..69 FT /note="TRAM" FT /evidence="ECO:0000255|HAMAP-Rule:MF_01010" FT ACT_SITE 396 FT /note="Nucleophile" FT /evidence="ECO:0000255|HAMAP-Rule:MF_01010" FT BINDING 82 FT /ligand="[4Fe-4S] cluster" FT /ligand_id="ChEBI:CHEBI:49883" FT /evidence="ECO:0000255|HAMAP-Rule:MF_01010" FT BINDING 88 FT /ligand="[4Fe-4S] cluster" FT /ligand_id="ChEBI:CHEBI:49883" FT /evidence="ECO:0000255|HAMAP-Rule:MF_01010" FT BINDING 91 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 272 FT /ligand="S-adenosyl-L-methionine" FT /ligand_id="ChEBI:CHEBI:59789" FT /evidence="ECO:0000255|HAMAP-Rule:MF_01010" FT BINDING 301 FT /ligand="S-adenosyl-L-methionine" FT /ligand_id="ChEBI:CHEBI:59789" FT /evidence="ECO:0000255|HAMAP-Rule:MF_01010" FT BINDING 306 FT /ligand="S-adenosyl-L-methionine" FT /ligand_id="ChEBI:CHEBI:59789" FT /evidence="ECO:0000255|HAMAP-Rule:MF_01010" FT BINDING 322 FT /ligand="S-adenosyl-L-methionine" FT /ligand_id="ChEBI:CHEBI:59789" FT /evidence="ECO:0000255|HAMAP-Rule:MF_01010" FT BINDING 349 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; 48939 MW; FEB85661F2C4210D CRC64; MARFFQPKKH STLDTKHQPV TIERLDHQGS GLAFLHKKPL FVDGALPGEE VLIQLTENKS KYARGQLIKV LKPSAERVAP FCAHYAQCGG CDLQHLDRAG QIHHKQQALS QLMVKFAGQS LALSAPVCSD DQGYRRRARL SLMWDKKTQQ LQLGFRRKQS KAIVNVTDCP VLEPSLNALL PDLNALLSEW SQPERLGHVE LVKGDNTRVL VLRHLGALIE QDQQRLTDFA SQNQLTLYLM LEAGELQHVQ GEAPYCEETG SRLSFLPSHF IQVNRAVNQH MVAQALNWLE VSPQEHVLDL FCGLGNFTLP LAKQAQAVVG VEGVDEMVQH ATHNAKLNQI NNVAFYQANL EQDMTSASWA QQKFAKVLLD PARAGAEGIV DQLSALGAKR VVYVSCNPAT LARDSQSLLS QGFRLEKLGM LDMFPHTSHL ESMALFVKKG //