{"entryType":"UniProtKB reviewed (Swiss-Prot)","primaryAccession":"Q45601","uniProtkbId":"RLMH_BACSU","entryAudit":{"firstPublicDate":"2003-06-20","lastAnnotationUpdateDate":"2026-09-02","lastSequenceUpdateDate":"1996-11-01","entryVersion":143,"sequenceVersion":1},"annotationScore":3.0,"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":{"evidences":[{"evidenceCode":"ECO:0000255","source":"HAMAP-Rule","id":"MF_00658"}],"value":"Ribosomal RNA large subunit methyltransferase H"},"ecNumbers":[{"evidences":[{"evidenceCode":"ECO:0000255","source":"HAMAP-Rule","id":"MF_00658"}],"value":"2.1.1.177"}]},"alternativeNames":[{"fullName":{"evidences":[{"evidenceCode":"ECO:0000255","source":"HAMAP-Rule","id":"MF_00658"}],"value":"23S rRNA (pseudouridine1915-N3)-methyltransferase"}},{"fullName":{"evidences":[{"evidenceCode":"ECO:0000255","source":"HAMAP-Rule","id":"MF_00658"}],"value":"23S rRNA m3Psi1915 methyltransferase"}},{"fullName":{"evidences":[{"evidenceCode":"ECO:0000255","source":"HAMAP-Rule","id":"MF_00658"}],"value":"rRNA (pseudouridine-N3-)-methyltransferase RlmH"}}]},"genes":[{"geneName":{"evidences":[{"evidenceCode":"ECO:0000255","source":"HAMAP-Rule","id":"MF_00658"}],"value":"rlmH"},"synonyms":[{"value":"yydA"}],"orderedLocusNames":[{"value":"BSU40230"}]}],"comments":[{"texts":[{"evidences":[{"evidenceCode":"ECO:0000255","source":"HAMAP-Rule","id":"MF_00658"}],"value":"Specifically methylates the pseudouridine at position 1915 (m3Psi1915) in 23S rRNA"}],"commentType":"FUNCTION"},{"commentType":"CATALYTIC ACTIVITY","reaction":{"name":"pseudouridine(1915) in 23S rRNA + S-adenosyl-L-methionine = N(3)-methylpseudouridine(1915) in 23S rRNA + S-adenosyl-L-homocysteine + H(+)","reactionCrossReferences":[{"database":"Rhea","id":"RHEA:42752"},{"database":"Rhea","id":"RHEA-COMP:10221"},{"database":"Rhea","id":"RHEA-COMP:10222"},{"database":"ChEBI","id":"CHEBI:15378"},{"database":"ChEBI","id":"CHEBI:57856"},{"database":"ChEBI","id":"CHEBI:59789"},{"database":"ChEBI","id":"CHEBI:65314"},{"database":"ChEBI","id":"CHEBI:74486"}],"ecNumber":"2.1.1.177","evidences":[{"evidenceCode":"ECO:0000255","source":"HAMAP-Rule","id":"MF_00658"}]}},{"texts":[{"evidences":[{"evidenceCode":"ECO:0000255","source":"HAMAP-Rule","id":"MF_00658"}],"value":"Homodimer"}],"commentType":"SUBUNIT"},{"commentType":"SUBCELLULAR LOCATION","subcellularLocations":[{"location":{"evidences":[{"evidenceCode":"ECO:0000255","source":"HAMAP-Rule","id":"MF_00658"}],"value":"Cytoplasm","id":"SL-0086"}}]},{"texts":[{"evidences":[{"evidenceCode":"ECO:0000255","source":"HAMAP-Rule","id":"MF_00658"}],"value":"Belongs to the RNA methyltransferase RlmH family"}],"commentType":"SIMILARITY"}],"features":[{"type":"Chain","location":{"start":{"value":1,"modifier":"EXACT"},"end":{"value":159,"modifier":"EXACT"}},"description":"Ribosomal RNA large subunit methyltransferase H","featureId":"PRO_0000198090"},{"type":"Binding site","location":{"start":{"value":76,"modifier":"EXACT"},"end":{"value":76,"modifier":"EXACT"}},"description":"","featureCrossReferences":[{"database":"ChEBI","id":"CHEBI:59789"}],"evidences":[{"evidenceCode":"ECO:0000255","source":"HAMAP-Rule","id":"MF_00658"}],"ligand":{"name":"S-adenosyl-L-methionine","id":"ChEBI:CHEBI:59789"}},{"type":"Binding site","location":{"start":{"value":108,"modifier":"EXACT"},"end":{"value":108,"modifier":"EXACT"}},"description":"","featureCrossReferences":[{"database":"ChEBI","id":"CHEBI:59789"}],"evidences":[{"evidenceCode":"ECO:0000255","source":"HAMAP-Rule","id":"MF_00658"}],"ligand":{"name":"S-adenosyl-L-methionine","id":"ChEBI:CHEBI:59789"}},{"type":"Binding site","location":{"start":{"value":127,"modifier":"EXACT"},"end":{"value":132,"modifier":"EXACT"}},"description":"","featureCrossReferences":[{"database":"ChEBI","id":"CHEBI:59789"}],"evidences":[{"evidenceCode":"ECO:0000255","source":"HAMAP-Rule","id":"MF_00658"}],"ligand":{"name":"S-adenosyl-L-methionine","id":"ChEBI:CHEBI:59789"}},{"type":"Beta strand","location":{"start":{"value":2,"modifier":"EXACT"},"end":{"value":9,"modifier":"EXACT"}},"description":"","evidences":[{"evidenceCode":"ECO:0007829","source":"PDB","id":"1TO0"}]},{"type":"Helix","location":{"start":{"value":14,"modifier":"EXACT"},"end":{"value":27,"modifier":"EXACT"}},"description":"","evidences":[{"evidenceCode":"ECO:0007829","source":"PDB","id":"1TO0"}]},{"type":"Turn","location":{"start":{"value":28,"modifier":"EXACT"},"end":{"value":30,"modifier":"EXACT"}},"description":"","evidences":[{"evidenceCode":"ECO:0007829","source":"PDB","id":"1TO0"}]},{"type":"Beta strand","location":{"start":{"value":31,"modifier":"EXACT"},"end":{"value":38,"modifier":"EXACT"}},"description":"","evidences":[{"evidenceCode":"ECO:0007829","source":"PDB","id":"1TO0"}]},{"type":"Helix","location":{"start":{"value":54,"modifier":"EXACT"},"end":{"value":64,"modifier":"EXACT"}},"description":"","evidences":[{"evidenceCode":"ECO:0007829","source":"PDB","id":"1TO0"}]},{"type":"Beta strand","location":{"start":{"value":71,"modifier":"EXACT"},"end":{"value":82,"modifier":"EXACT"}},"description":"","evidences":[{"evidenceCode":"ECO:0007829","source":"PDB","id":"1TO0"}]},{"type":"Helix","location":{"start":{"value":85,"modifier":"EXACT"},"end":{"value":96,"modifier":"EXACT"}},"description":"","evidences":[{"evidenceCode":"ECO:0007829","source":"PDB","id":"1TO0"}]},{"type":"Turn","location":{"start":{"value":97,"modifier":"EXACT"},"end":{"value":99,"modifier":"EXACT"}},"description":"","evidences":[{"evidenceCode":"ECO:0007829","source":"PDB","id":"1TO0"}]},{"type":"Beta strand","location":{"start":{"value":102,"modifier":"EXACT"},"end":{"value":107,"modifier":"EXACT"}},"description":"","evidences":[{"evidenceCode":"ECO:0007829","source":"PDB","id":"1TO0"}]},{"type":"Helix","location":{"start":{"value":115,"modifier":"EXACT"},"end":{"value":120,"modifier":"EXACT"}},"description":"","evidences":[{"evidenceCode":"ECO:0007829","source":"PDB","id":"1TO0"}]},{"type":"Beta strand","location":{"start":{"value":122,"modifier":"EXACT"},"end":{"value":127,"modifier":"EXACT"}},"description":"","evidences":[{"evidenceCode":"ECO:0007829","source":"PDB","id":"1TO0"}]},{"type":"Helix","location":{"start":{"value":134,"modifier":"EXACT"},"end":{"value":152,"modifier":"EXACT"}},"description":"","evidences":[{"evidenceCode":"ECO:0007829","source":"PDB","id":"1TO0"}]}],"keywords":[{"id":"KW-0002","category":"Technical term","name":"3D-structure"},{"id":"KW-0963","category":"Cellular component","name":"Cytoplasm"},{"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":"9205843","citationType":"journal article","authors":["Kasahara Y.","Nakai S.","Ogasawara N."],"citationCrossReferences":[{"database":"PubMed","id":"9205843"},{"database":"DOI","id":"10.1093/dnares/4.2.155"}],"title":"Sequence analysis of the 36-kb region between gntZ and trnY genes of Bacillus subtilis genome.","publicationDate":"1997","journal":"DNA Res.","firstPage":"155","lastPage":"159","volume":"4"},"referencePositions":["NUCLEOTIDE SEQUENCE [GENOMIC DNA]"],"referenceComments":[{"value":"168","type":"STRAIN"}]},{"referenceNumber":2,"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":3,"citation":{"id":"16460560","citationType":"journal article","authors":["von Grotthuss M.","Plewczynski D.","Ginalski K.","Rychlewski L.","Shakhnovich E.I."],"citationCrossReferences":[{"database":"PubMed","id":"16460560"},{"database":"DOI","id":"10.1186/1471-2105-7-53"}],"title":"PDB-UF: database of predicted enzymatic functions for unannotated protein structures from structural genomics.","publicationDate":"2006","journal":"BMC Bioinformatics","firstPage":"53","lastPage":"53","volume":"7"},"referencePositions":["X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS)"]}],"uniProtKBCrossReferences":[{"database":"EMBL","id":"D78193","properties":[{"key":"ProteinId","value":"BAA11281.1"},{"key":"Status","value":"-"},{"key":"MoleculeType","value":"Genomic_DNA"}]},{"database":"EMBL","id":"AL009126","properties":[{"key":"ProteinId","value":"CAB16060.1"},{"key":"Status","value":"-"},{"key":"MoleculeType","value":"Genomic_DNA"}]},{"database":"PIR","id":"H70090","properties":[{"key":"EntryName","value":"H70090"}]},{"database":"RefSeq","id":"NP_391903.1","properties":[{"key":"NucleotideSequenceId","value":"NC_000964.3"}]},{"database":"RefSeq","id":"WP_003243164.1","properties":[{"key":"NucleotideSequenceId","value":"NC_000964.3"}]},{"database":"PDB","id":"1TO0","properties":[{"key":"Method","value":"X-ray"},{"key":"Resolution","value":"2.50 A"},{"key":"Chains","value":"A/B/C/D/E/F/G/H=1-159"}]},{"database":"PDBsum","id":"1TO0","properties":[{"key":"Description","value":"-"}]},{"database":"AlphaFoldDB","id":"Q45601","properties":[{"key":"Description","value":"-"}]},{"database":"SMR","id":"Q45601","properties":[{"key":"Description","value":"-"}]},{"database":"FunCoup","id":"Q45601","properties":[{"key":"Number of interactors","value":"218"}]},{"database":"STRING","id":"224308.BSU40230","properties":[{"key":"Description","value":"-"}]},{"database":"PaxDb","id":"224308-BSU40230","properties":[{"key":"Description","value":"-"}]},{"database":"EnsemblBacteria","id":"CAB16060","properties":[{"key":"ProteinId","value":"CAB16060"},{"key":"GeneId","value":"BSU_40230"}]},{"database":"GeneID","id":"937752","properties":[{"key":"Description","value":"-"}]},{"database":"KEGG","id":"bsu:BSU40230","properties":[{"key":"Description","value":"-"}]},{"database":"PATRIC","id":"fig|224308.179.peg.4351","properties":[{"key":"GeneDesignation","value":"-"}]},{"database":"eggNOG","id":"COG1576","properties":[{"key":"ToxonomicScope","value":"Bacteria"}]},{"database":"InParanoid","id":"Q45601","properties":[{"key":"Description","value":"-"}]},{"database":"OrthoDB","id":"9806643at2","properties":[{"key":"Description","value":"-"}]},{"database":"PhylomeDB","id":"Q45601","properties":[{"key":"Description","value":"-"}]},{"database":"BioCyc","id":"BSUB:BSU40230-MONOMER","properties":[{"key":"Description","value":"-"}]},{"database":"EvolutionaryTrace","id":"Q45601","properties":[{"key":"Description","value":"-"}]},{"database":"Proteomes","id":"UP000001570","properties":[{"key":"Component","value":"Chromosome"}]},{"database":"AbasyAtlas","id":"Q45601","properties":[{"key":"Description","value":"-"}]},{"database":"GO","id":"GO:0005737","properties":[{"key":"GoTerm","value":"C:cytoplasm"},{"key":"GoEvidenceType","value":"IEA:UniProtKB-SubCell"}]},{"database":"GO","id":"GO:0070038","properties":[{"key":"GoTerm","value":"F:rRNA (pseudouridine-N3-)-methyltransferase activity"},{"key":"GoEvidenceType","value":"IBA:GO_Central"}]},{"database":"GO","id":"GO:0070475","properties":[{"key":"GoTerm","value":"P:rRNA base methylation"},{"key":"GoEvidenceType","value":"IBA:GO_Central"}]},{"database":"CDD","id":"cd18081","properties":[{"key":"EntryName","value":"RlmH-like"},{"key":"MatchStatus","value":"1"}]},{"database":"Gene3D","id":"3.40.1280.10","properties":[{"key":"EntryName","value":"-"},{"key":"MatchStatus","value":"1"}]},{"database":"HAMAP","id":"MF_00658","properties":[{"key":"EntryName","value":"23SrRNA_methyltr_H"},{"key":"MatchStatus","value":"1"}]},{"database":"InterPro","id":"IPR029028","properties":[{"key":"EntryName","value":"Alpha/beta_knot_MTases"}]},{"database":"InterPro","id":"IPR003742","properties":[{"key":"EntryName","value":"RlmH-like"}]},{"database":"InterPro","id":"IPR029026","properties":[{"key":"EntryName","value":"tRNA_m1G_MTases_N"}]},{"database":"NCBIfam","id":"NF000985","properties":[{"key":"EntryName","value":"PRK00103.1-3"},{"key":"MatchStatus","value":"1"}]},{"database":"NCBIfam","id":"TIGR00246","properties":[{"key":"EntryName","value":"tRNA_RlmH_YbeA"},{"key":"MatchStatus","value":"1"}]},{"database":"PANTHER","id":"PTHR33603","properties":[{"key":"EntryName","value":"METHYLTRANSFERASE"},{"key":"MatchStatus","value":"1"}]},{"database":"PANTHER","id":"PTHR33603:SF1","properties":[{"key":"EntryName","value":"RIBOSOMAL RNA LARGE SUBUNIT METHYLTRANSFERASE H"},{"key":"MatchStatus","value":"1"}]},{"database":"Pfam","id":"PF02590","properties":[{"key":"EntryName","value":"SPOUT_MTase"},{"key":"MatchStatus","value":"1"}]},{"database":"PIRSF","id":"PIRSF004505","properties":[{"key":"EntryName","value":"MT_bac"},{"key":"MatchStatus","value":"1"}]},{"database":"SUPFAM","id":"SSF75217","properties":[{"key":"EntryName","value":"alpha/beta knot"},{"key":"MatchStatus","value":"1"}]}],"sequence":{"value":"MNINIVTIGKLKEKYLKQGIEEYTKRLSAYAKIDIIELPDEKAPENLSDQDMKIIKDKEGDRILSKISPDAHVIALAIEGKMKTSEELADTIDKLATYGKSKVTFVIGGSLGLSDTVMKRADEKLSFSKMTFPHQLMRLILVEQIYRAFRINRGEPYHK","length":159,"molWeight":18073,"crc64":"7438A57C259BD602","md5":"9E80D5B9771905535F90DF6F06782828"},"extraAttributes":{"countByCommentType":{"FUNCTION":1,"CATALYTIC ACTIVITY":1,"SUBUNIT":1,"SUBCELLULAR LOCATION":1,"SIMILARITY":1},"countByFeatureType":{"Chain":1,"Binding site":3,"Beta strand":5,"Helix":5,"Turn":2},"uniParcId":"UPI0000060CF4"}}