{"entryType":"UniProtKB reviewed (Swiss-Prot)","primaryAccession":"O31503","uniProtkbId":"RLMCD_BACSU","entryAudit":{"firstPublicDate":"2004-07-19","lastAnnotationUpdateDate":"2026-09-02","lastSequenceUpdateDate":"1998-01-01","entryVersion":129,"sequenceVersion":1},"annotationScore":4.0,"organism":{"scientificName":"Bacillus subtilis (strain 168)","taxonId":224308,"lineage":["Bacteria","Bacillati","Bacillota","Bacilli","Caryophanales","Bacillaceae","Bacillus"]},"proteinExistence":"1: Evidence at protein level","proteinDescription":{"recommendedName":{"fullName":{"value":"23S rRNA (uracil-C(5))-methyltransferase RlmCD"},"ecNumbers":[{"value":"2.1.1.189"},{"value":"2.1.1.190"}]},"alternativeNames":[{"fullName":{"value":"23S rRNA (uracil(1939)-C(5))-methyltransferase"}},{"fullName":{"value":"23S rRNA (uracil(747)-C(5))-methyltransferase"}}]},"genes":[{"geneName":{"value":"rlmCD"},"synonyms":[{"value":"yefA"},{"value":"yerS"}],"orderedLocusNames":[{"value":"BSU06730"}]}],"comments":[{"texts":[{"evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"21824914"}],"value":"Catalyzes the formation of 5-methyl-uridine at positions 747 (m5U747) and 1939 (m5U1939) in 23S rRNA"}],"commentType":"FUNCTION"},{"commentType":"CATALYTIC ACTIVITY","reaction":{"name":"uridine(747) in 23S rRNA + S-adenosyl-L-methionine = 5-methyluridine(747) in 23S rRNA + S-adenosyl-L-homocysteine + H(+)","reactionCrossReferences":[{"database":"Rhea","id":"RHEA:42628"},{"database":"Rhea","id":"RHEA-COMP:10154"},{"database":"Rhea","id":"RHEA-COMP:10155"},{"database":"ChEBI","id":"CHEBI:15378"},{"database":"ChEBI","id":"CHEBI:57856"},{"database":"ChEBI","id":"CHEBI:59789"},{"database":"ChEBI","id":"CHEBI:65315"},{"database":"ChEBI","id":"CHEBI:74447"}],"ecNumber":"2.1.1.189","evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"21824914"}]}},{"commentType":"CATALYTIC ACTIVITY","reaction":{"name":"uridine(1939) in 23S rRNA + S-adenosyl-L-methionine = 5-methyluridine(1939) in 23S rRNA + S-adenosyl-L-homocysteine + H(+)","reactionCrossReferences":[{"database":"Rhea","id":"RHEA:42908"},{"database":"Rhea","id":"RHEA-COMP:10278"},{"database":"Rhea","id":"RHEA-COMP:10279"},{"database":"ChEBI","id":"CHEBI:15378"},{"database":"ChEBI","id":"CHEBI:57856"},{"database":"ChEBI","id":"CHEBI:59789"},{"database":"ChEBI","id":"CHEBI:65315"},{"database":"ChEBI","id":"CHEBI:74447"}],"ecNumber":"2.1.1.190","evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"21824914"}]}},{"texts":[{"evidences":[{"evidenceCode":"ECO:0000255","source":"PROSITE-ProRule","id":"PRU01024"}],"value":"Belongs to the class I-like SAM-binding methyltransferase superfamily. RNA M5U methyltransferase family"}],"commentType":"SIMILARITY"}],"features":[{"type":"Chain","location":{"start":{"value":1,"modifier":"EXACT"},"end":{"value":459,"modifier":"EXACT"}},"description":"23S rRNA (uracil-C(5))-methyltransferase RlmCD","featureId":"PRO_0000161953"},{"type":"Domain","location":{"start":{"value":6,"modifier":"EXACT"},"end":{"value":64,"modifier":"EXACT"}},"description":"TRAM","evidences":[{"evidenceCode":"ECO:0000255","source":"PROSITE-ProRule","id":"PRU00208"}]},{"type":"Active site","location":{"start":{"value":415,"modifier":"EXACT"},"end":{"value":415,"modifier":"EXACT"}},"description":"Nucleophile","evidences":[{"evidenceCode":"ECO:0000255","source":"PROSITE-ProRule","id":"PRU01024"}]},{"type":"Binding site","location":{"start":{"value":77,"modifier":"EXACT"},"end":{"value":77,"modifier":"EXACT"}},"description":"","featureCrossReferences":[{"database":"ChEBI","id":"CHEBI:49883"}],"evidences":[{"evidenceCode":"ECO:0000250"}],"ligand":{"name":"[4Fe-4S] cluster","id":"ChEBI:CHEBI:49883"}},{"type":"Binding site","location":{"start":{"value":83,"modifier":"EXACT"},"end":{"value":83,"modifier":"EXACT"}},"description":"","featureCrossReferences":[{"database":"ChEBI","id":"CHEBI:49883"}],"evidences":[{"evidenceCode":"ECO:0000250"}],"ligand":{"name":"[4Fe-4S] cluster","id":"ChEBI:CHEBI:49883"}},{"type":"Binding site","location":{"start":{"value":86,"modifier":"EXACT"},"end":{"value":86,"modifier":"EXACT"}},"description":"","featureCrossReferences":[{"database":"ChEBI","id":"CHEBI:49883"}],"evidences":[{"evidenceCode":"ECO:0000250"}],"ligand":{"name":"[4Fe-4S] cluster","id":"ChEBI:CHEBI:49883"}},{"type":"Binding site","location":{"start":{"value":166,"modifier":"EXACT"},"end":{"value":166,"modifier":"EXACT"}},"description":"","featureCrossReferences":[{"database":"ChEBI","id":"CHEBI:49883"}],"evidences":[{"evidenceCode":"ECO:0000250"}],"ligand":{"name":"[4Fe-4S] cluster","id":"ChEBI:CHEBI:49883"}},{"type":"Binding site","location":{"start":{"value":290,"modifier":"EXACT"},"end":{"value":290,"modifier":"EXACT"}},"description":"","featureCrossReferences":[{"database":"ChEBI","id":"CHEBI:59789"}],"evidences":[{"evidenceCode":"ECO:0000255","source":"PROSITE-ProRule","id":"PRU01024"}],"ligand":{"name":"S-adenosyl-L-methionine","id":"ChEBI:CHEBI:59789"}},{"type":"Binding site","location":{"start":{"value":319,"modifier":"EXACT"},"end":{"value":319,"modifier":"EXACT"}},"description":"","featureCrossReferences":[{"database":"ChEBI","id":"CHEBI:59789"}],"evidences":[{"evidenceCode":"ECO:0000255","source":"PROSITE-ProRule","id":"PRU01024"}],"ligand":{"name":"S-adenosyl-L-methionine","id":"ChEBI:CHEBI:59789"}},{"type":"Binding site","location":{"start":{"value":340,"modifier":"EXACT"},"end":{"value":340,"modifier":"EXACT"}},"description":"","featureCrossReferences":[{"database":"ChEBI","id":"CHEBI:59789"}],"evidences":[{"evidenceCode":"ECO:0000255","source":"PROSITE-ProRule","id":"PRU01024"}],"ligand":{"name":"S-adenosyl-L-methionine","id":"ChEBI:CHEBI:59789"}},{"type":"Binding site","location":{"start":{"value":388,"modifier":"EXACT"},"end":{"value":388,"modifier":"EXACT"}},"description":"","featureCrossReferences":[{"database":"ChEBI","id":"CHEBI:59789"}],"evidences":[{"evidenceCode":"ECO:0000255","source":"PROSITE-ProRule","id":"PRU01024"}],"ligand":{"name":"S-adenosyl-L-methionine","id":"ChEBI:CHEBI:59789"}}],"keywords":[{"id":"KW-0004","category":"Ligand","name":"4Fe-4S"},{"id":"KW-0408","category":"Ligand","name":"Iron"},{"id":"KW-0411","category":"Ligand","name":"Iron-sulfur"},{"id":"KW-0479","category":"Ligand","name":"Metal-binding"},{"id":"KW-0489","category":"Molecular function","name":"Methyltransferase"},{"id":"KW-1185","category":"Technical term","name":"Reference proteome"},{"id":"KW-0698","category":"Biological process","name":"rRNA processing"},{"id":"KW-0949","category":"Ligand","name":"S-adenosyl-L-methionine"},{"id":"KW-0808","category":"Molecular function","name":"Transferase"}],"references":[{"referenceNumber":1,"citation":{"id":"9384377","citationType":"journal article","authors":["Kunst F.","Ogasawara N.","Moszer I.","Albertini A.M.","Alloni G.","Azevedo V.","Bertero M.G.","Bessieres P.","Bolotin A.","Borchert S.","Borriss R.","Boursier L.","Brans A.","Braun M.","Brignell S.C.","Bron S.","Brouillet S.","Bruschi C.V.","Caldwell B.","Capuano V.","Carter N.M.","Choi S.-K.","Codani J.-J.","Connerton I.F.","Cummings N.J.","Daniel R.A.","Denizot F.","Devine K.M.","Duesterhoeft A.","Ehrlich S.D.","Emmerson P.T.","Entian K.-D.","Errington J.","Fabret C.","Ferrari E.","Foulger D.","Fritz C.","Fujita M.","Fujita Y.","Fuma S.","Galizzi A.","Galleron N.","Ghim S.-Y.","Glaser P.","Goffeau A.","Golightly E.J.","Grandi G.","Guiseppi G.","Guy B.J.","Haga K.","Haiech J.","Harwood C.R.","Henaut A.","Hilbert H.","Holsappel S.","Hosono S.","Hullo M.-F.","Itaya M.","Jones L.-M.","Joris B.","Karamata D.","Kasahara Y.","Klaerr-Blanchard M.","Klein C.","Kobayashi Y.","Koetter P.","Koningstein G.","Krogh S.","Kumano M.","Kurita K.","Lapidus A.","Lardinois S.","Lauber J.","Lazarevic V.","Lee S.-M.","Levine A.","Liu H.","Masuda S.","Mauel C.","Medigue C.","Medina N.","Mellado R.P.","Mizuno M.","Moestl D.","Nakai S.","Noback M.","Noone D.","O'Reilly M.","Ogawa K.","Ogiwara A.","Oudega B.","Park S.-H.","Parro V.","Pohl T.M.","Portetelle D.","Porwollik S.","Prescott A.M.","Presecan E.","Pujic P.","Purnelle B.","Rapoport G.","Rey M.","Reynolds S.","Rieger M.","Rivolta C.","Rocha E.","Roche B.","Rose M.","Sadaie Y.","Sato T.","Scanlan E.","Schleich S.","Schroeter R.","Scoffone F.","Sekiguchi J.","Sekowska A.","Seror S.J.","Serror P.","Shin B.-S.","Soldo B.","Sorokin A.","Tacconi E.","Takagi T.","Takahashi H.","Takemaru K.","Takeuchi M.","Tamakoshi A.","Tanaka T.","Terpstra P.","Tognoni A.","Tosato V.","Uchiyama S.","Vandenbol M.","Vannier F.","Vassarotti A.","Viari A.","Wambutt R.","Wedler E.","Wedler H.","Weitzenegger T.","Winters P.","Wipat A.","Yamamoto H.","Yamane K.","Yasumoto K.","Yata K.","Yoshida K.","Yoshikawa H.-F.","Zumstein E.","Yoshikawa H.","Danchin A."],"citationCrossReferences":[{"database":"PubMed","id":"9384377"},{"database":"DOI","id":"10.1038/36786"}],"title":"The complete genome sequence of the Gram-positive bacterium Bacillus subtilis.","publicationDate":"1997","journal":"Nature","firstPage":"249","lastPage":"256","volume":"390"},"referencePositions":["NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]"],"referenceComments":[{"value":"168","type":"STRAIN"}]},{"referenceNumber":2,"citation":{"id":"21824914","citationType":"journal article","authors":["Desmolaize B.","Fabret C.","Bregeon D.","Rose S.","Grosjean H.","Douthwaite S."],"citationCrossReferences":[{"database":"PubMed","id":"21824914"},{"database":"DOI","id":"10.1093/nar/gkr626"}],"title":"A single methyltransferase YefA (RlmCD) catalyses both m5U747 and m5U1939 modifications in Bacillus subtilis 23S rRNA.","publicationDate":"2011","journal":"Nucleic Acids Res.","firstPage":"9368","lastPage":"9375","volume":"39"},"referencePositions":["FUNCTION","CATALYTIC ACTIVITY","GENE NAME"],"referenceComments":[{"value":"168","type":"STRAIN"}]}],"uniProtKBCrossReferences":[{"database":"EMBL","id":"AL009126","properties":[{"key":"ProteinId","value":"CAB12493.1"},{"key":"Status","value":"-"},{"key":"MoleculeType","value":"Genomic_DNA"}]},{"database":"PIR","id":"E69793","properties":[{"key":"EntryName","value":"E69793"}]},{"database":"RefSeq","id":"NP_388555.1","properties":[{"key":"NucleotideSequenceId","value":"NC_000964.3"}]},{"database":"RefSeq","id":"WP_003233892.1","properties":[{"key":"NucleotideSequenceId","value":"NC_000964.3"}]},{"database":"AlphaFoldDB","id":"O31503","properties":[{"key":"Description","value":"-"}]},{"database":"SMR","id":"O31503","properties":[{"key":"Description","value":"-"}]},{"database":"FunCoup","id":"O31503","properties":[{"key":"Number of interactors","value":"979"}]},{"database":"STRING","id":"224308.BSU06730","properties":[{"key":"Description","value":"-"}]},{"database":"PaxDb","id":"224308-BSU06730","properties":[{"key":"Description","value":"-"}]},{"database":"EnsemblBacteria","id":"CAB12493","properties":[{"key":"ProteinId","value":"CAB12493"},{"key":"GeneId","value":"BSU_06730"}]},{"database":"GeneID","id":"936060","properties":[{"key":"Description","value":"-"}]},{"database":"KEGG","id":"bsu:BSU06730","properties":[{"key":"Description","value":"-"}]},{"database":"PATRIC","id":"fig|224308.179.peg.731","properties":[{"key":"GeneDesignation","value":"-"}]},{"database":"eggNOG","id":"COG2265","properties":[{"key":"ToxonomicScope","value":"Bacteria"}]},{"database":"InParanoid","id":"O31503","properties":[{"key":"Description","value":"-"}]},{"database":"OrthoDB","id":"9804590at2","properties":[{"key":"Description","value":"-"}]},{"database":"PhylomeDB","id":"O31503","properties":[{"key":"Description","value":"-"}]},{"database":"BioCyc","id":"BSUB:BSU06730-MONOMER","properties":[{"key":"Description","value":"-"}]},{"database":"BRENDA","id":"2.1.1.189","properties":[{"key":"OrganismId","value":"658"}]},{"database":"BRENDA","id":"2.1.1.190","properties":[{"key":"OrganismId","value":"658"}]},{"database":"Proteomes","id":"UP000001570","properties":[{"key":"Component","value":"Chromosome"}]},{"database":"AbasyAtlas","id":"O31503","properties":[{"key":"Description","value":"-"}]},{"database":"GO","id":"GO:0070041","properties":[{"key":"GoTerm","value":"F:rRNA (uridine-C5-)-methyltransferase activity"},{"key":"GoEvidenceType","value":"IDA:UniProtKB"}],"evidences":[{"evidenceCode":"ECO:0000314","source":"PubMed","id":"21824914"}]},{"database":"GO","id":"GO:0070475","properties":[{"key":"GoTerm","value":"P:rRNA base methylation"},{"key":"GoEvidenceType","value":"IBA:GO_Central"}]},{"database":"GO","id":"GO:0031167","properties":[{"key":"GoTerm","value":"P:rRNA methylation"},{"key":"GoEvidenceType","value":"IDA:UniProtKB"}],"evidences":[{"evidenceCode":"ECO:0000314","source":"PubMed","id":"21824914"}]},{"database":"CDD","id":"cd02440","properties":[{"key":"EntryName","value":"AdoMet_MTases"},{"key":"MatchStatus","value":"1"}]},{"database":"FunFam","id":"3.40.50.150:FF:000009","properties":[{"key":"EntryName","value":"23S rRNA (Uracil(1939)-C(5))-methyltransferase RlmD"},{"key":"MatchStatus","value":"1"}]},{"database":"FunFam","id":"2.40.50.140:FF:000097","properties":[{"key":"EntryName","value":"23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD"},{"key":"MatchStatus","value":"1"}]},{"database":"FunFam","id":"2.40.50.1070:FF:000003","properties":[{"key":"EntryName","value":"23S rRNA (Uracil-5-)-methyltransferase RumA"},{"key":"MatchStatus","value":"1"}]},{"database":"Gene3D","id":"2.40.50.1070","properties":[{"key":"EntryName","value":"-"},{"key":"MatchStatus","value":"1"}]},{"database":"Gene3D","id":"2.40.50.140","properties":[{"key":"EntryName","value":"Nucleic acid-binding proteins"},{"key":"MatchStatus","value":"1"}]},{"database":"Gene3D","id":"3.40.50.150","properties":[{"key":"EntryName","value":"Vaccinia Virus protein VP39"},{"key":"MatchStatus","value":"1"}]},{"database":"InterPro","id":"IPR030390","properties":[{"key":"EntryName","value":"MeTrfase_TrmA_AS"}]},{"database":"InterPro","id":"IPR030391","properties":[{"key":"EntryName","value":"MeTrfase_TrmA_CS"}]},{"database":"InterPro","id":"IPR012340","properties":[{"key":"EntryName","value":"NA-bd_OB-fold"}]},{"database":"InterPro","id":"IPR029063","properties":[{"key":"EntryName","value":"SAM-dependent_MTases_sf"}]},{"database":"InterPro","id":"IPR002792","properties":[{"key":"EntryName","value":"TRAM_dom"}]},{"database":"InterPro","id":"IPR010280","properties":[{"key":"EntryName","value":"U5_MeTrfase_fam"}]},{"database":"NCBIfam","id":"TIGR00479","properties":[{"key":"EntryName","value":"rumA"},{"key":"MatchStatus","value":"1"}]},{"database":"PANTHER","id":"PTHR11061","properties":[{"key":"EntryName","value":"RNA M5U METHYLTRANSFERASE"},{"key":"MatchStatus","value":"1"}]},{"database":"PANTHER","id":"PTHR11061:SF30","properties":[{"key":"EntryName","value":"TRNA (URACIL(54)-C(5))-METHYLTRANSFERASE"},{"key":"MatchStatus","value":"1"}]},{"database":"Pfam","id":"PF01938","properties":[{"key":"EntryName","value":"TRAM"},{"key":"MatchStatus","value":"1"}]},{"database":"Pfam","id":"PF05958","properties":[{"key":"EntryName","value":"tRNA_U5-meth_tr"},{"key":"MatchStatus","value":"1"}]},{"database":"SUPFAM","id":"SSF50249","properties":[{"key":"EntryName","value":"Nucleic acid-binding proteins"},{"key":"MatchStatus","value":"1"}]},{"database":"SUPFAM","id":"SSF53335","properties":[{"key":"EntryName","value":"S-adenosyl-L-methionine-dependent methyltransferases"},{"key":"MatchStatus","value":"1"}]},{"database":"PROSITE","id":"PS51687","properties":[{"key":"EntryName","value":"SAM_MT_RNA_M5U"},{"key":"MatchStatus","value":"1"}]},{"database":"PROSITE","id":"PS50926","properties":[{"key":"EntryName","value":"TRAM"},{"key":"MatchStatus","value":"1"}]},{"database":"PROSITE","id":"PS01230","properties":[{"key":"EntryName","value":"TRMA_1"},{"key":"MatchStatus","value":"1"}]},{"database":"PROSITE","id":"PS01231","properties":[{"key":"EntryName","value":"TRMA_2"},{"key":"MatchStatus","value":"1"}]}],"sequence":{"value":"MKMKPPVEKNEYYDVTFEDLTHEGAGVAKVQGFPIFVPNALPEEKAQIKVTRVKKGFAFGRLIELKEESPHRTDAPCPIYKQCGGCQLQHMTYEGQLLFKQKQVKDVLERIGKLDLSKVTVHPTLGMEDPWNYRNKAQVPVGEREGGLVAGFYQQRSHDIIDMSACLIQQSKNDEAVQAVKDICANYGVKAYNEERHKGWLRHIMVRYGVVTGEMMIVFITRTSDFPHKAKIIEDITAQFPHVKSIVQNINPNKTNVIFGNETNVIWGEEYIYDLIGDVKFAISARSFYQVNPEQTKVLYDKALEYAELQGEETVIDAYCGIGTISLFLAKQAKKVYGVEIVPEAIEDAKRNAELNGNTNAEFAVGEAETVIPKWYEEGITADTLVVDPPRKGCDEALLRTIVEMKPKRVVYVSCNPGTLARDLRVLEDGGYVTREVQPVDMFPHTNHVECCVLIKLKE","length":459,"molWeight":51819,"crc64":"35E99547779421D5","md5":"4EF912523F0E6A4B92237338870A12DB"},"extraAttributes":{"countByCommentType":{"FUNCTION":1,"CATALYTIC ACTIVITY":2,"SIMILARITY":1},"countByFeatureType":{"Chain":1,"Domain":1,"Active site":1,"Binding site":8},"uniParcId":"UPI000006003B"}}