ID RLMN_LEPCP Reviewed; 393 AA. AC B1XXL6; DT 02-SEP-2008, integrated into UniProtKB/Swiss-Prot. DT 20-MAY-2008, sequence version 1. DT 27-MAR-2024, entry version 81. DE RecName: Full=Dual-specificity RNA methyltransferase RlmN {ECO:0000255|HAMAP-Rule:MF_01849}; DE EC=2.1.1.192 {ECO:0000255|HAMAP-Rule:MF_01849}; DE AltName: Full=23S rRNA (adenine(2503)-C(2))-methyltransferase {ECO:0000255|HAMAP-Rule:MF_01849}; DE AltName: Full=23S rRNA m2A2503 methyltransferase {ECO:0000255|HAMAP-Rule:MF_01849}; DE AltName: Full=Ribosomal RNA large subunit methyltransferase N {ECO:0000255|HAMAP-Rule:MF_01849}; DE AltName: Full=tRNA (adenine(37)-C(2))-methyltransferase {ECO:0000255|HAMAP-Rule:MF_01849}; DE AltName: Full=tRNA m2A37 methyltransferase {ECO:0000255|HAMAP-Rule:MF_01849}; GN Name=rlmN {ECO:0000255|HAMAP-Rule:MF_01849}; GN OrderedLocusNames=Lcho_2871; OS Leptothrix cholodnii (strain ATCC 51168 / LMG 8142 / SP-6) (Leptothrix OS discophora (strain SP-6)). OC Bacteria; Pseudomonadota; Betaproteobacteria; Burkholderiales; OC Sphaerotilaceae; Leptothrix. OX NCBI_TaxID=395495; RN [1] RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. RC STRAIN=ATCC 51168 / LMG 8142 / SP-6; RG US DOE Joint Genome Institute; RA Copeland A., Lucas S., Lapidus A., Glavina del Rio T., Dalin E., Tice H., RA Bruce D., Goodwin L., Pitluck S., Chertkov O., Brettin T., Detter J.C., RA Han C., Kuske C.R., Schmutz J., Larimer F., Land M., Hauser L., RA Kyrpides N., Lykidis A., Emerson D., Richardson P.; RT "Complete sequence of Leptothrix cholodnii SP-6."; RL Submitted (MAR-2008) to the EMBL/GenBank/DDBJ databases. CC -!- FUNCTION: Specifically methylates position 2 of adenine 2503 in 23S CC rRNA and position 2 of adenine 37 in tRNAs. m2A2503 modification seems CC to play a crucial role in the proofreading step occurring at the CC peptidyl transferase center and thus would serve to optimize ribosomal CC fidelity. {ECO:0000255|HAMAP-Rule:MF_01849}. CC -!- CATALYTIC ACTIVITY: CC Reaction=adenosine(2503) in 23S rRNA + 2 reduced [2Fe-2S]-[ferredoxin] CC + 2 S-adenosyl-L-methionine = 2-methyladenosine(2503) in 23S rRNA + CC 5'-deoxyadenosine + L-methionine + 2 oxidized [2Fe-2S]-[ferredoxin] + CC S-adenosyl-L-homocysteine; Xref=Rhea:RHEA:42916, Rhea:RHEA- CC COMP:10000, Rhea:RHEA-COMP:10001, Rhea:RHEA-COMP:10152, Rhea:RHEA- CC COMP:10282, ChEBI:CHEBI:17319, ChEBI:CHEBI:33737, ChEBI:CHEBI:33738, CC ChEBI:CHEBI:57844, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789, CC ChEBI:CHEBI:74411, ChEBI:CHEBI:74497; EC=2.1.1.192; CC Evidence={ECO:0000255|HAMAP-Rule:MF_01849}; CC -!- CATALYTIC ACTIVITY: CC Reaction=adenosine(37) in tRNA + 2 reduced [2Fe-2S]-[ferredoxin] + 2 S- CC adenosyl-L-methionine = 2-methyladenosine(37) in tRNA + 5'- CC deoxyadenosine + L-methionine + 2 oxidized [2Fe-2S]-[ferredoxin] + S- CC adenosyl-L-homocysteine; Xref=Rhea:RHEA:43332, Rhea:RHEA-COMP:10000, CC Rhea:RHEA-COMP:10001, Rhea:RHEA-COMP:10162, Rhea:RHEA-COMP:10485, CC ChEBI:CHEBI:17319, ChEBI:CHEBI:33737, ChEBI:CHEBI:33738, CC ChEBI:CHEBI:57844, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789, CC ChEBI:CHEBI:74411, ChEBI:CHEBI:74497; EC=2.1.1.192; CC Evidence={ECO:0000255|HAMAP-Rule:MF_01849}; CC -!- COFACTOR: CC Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883; CC Evidence={ECO:0000255|HAMAP-Rule:MF_01849}; CC Note=Binds 1 [4Fe-4S] cluster. The cluster is coordinated with 3 CC cysteines and an exchangeable S-adenosyl-L-methionine. CC {ECO:0000255|HAMAP-Rule:MF_01849}; CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_01849}. CC -!- MISCELLANEOUS: Reaction proceeds by a ping-pong mechanism involving CC intermediate methylation of a conserved cysteine residue. CC {ECO:0000255|HAMAP-Rule:MF_01849}. CC -!- SIMILARITY: Belongs to the radical SAM superfamily. RlmN family. CC {ECO:0000255|HAMAP-Rule:MF_01849}. 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; CP001013; ACB35136.1; -; Genomic_DNA. DR RefSeq; WP_012347890.1; NC_010524.1. DR AlphaFoldDB; B1XXL6; -. DR SMR; B1XXL6; -. DR STRING; 395495.Lcho_2871; -. DR KEGG; lch:Lcho_2871; -. DR eggNOG; COG0820; Bacteria. DR HOGENOM; CLU_029101_0_0_4; -. DR OrthoDB; 9793973at2; -. DR Proteomes; UP000001693; Chromosome. DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell. DR GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IEA:UniProtKB-UniRule. DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW. DR GO; GO:0070040; F:rRNA (adenine(2503)-C2-)-methyltransferase activity; IEA:UniProtKB-UniRule. DR GO; GO:0019843; F:rRNA binding; IEA:UniProtKB-UniRule. DR GO; GO:0002935; F:tRNA (adenine(37)-C2)-methyltransferase activity; IEA:UniProtKB-UniRule. DR GO; GO:0000049; F:tRNA binding; IEA:UniProtKB-UniRule. DR GO; GO:0070475; P:rRNA base methylation; IEA:UniProtKB-UniRule. DR GO; GO:0030488; P:tRNA methylation; IEA:UniProtKB-UniRule. DR CDD; cd01335; Radical_SAM; 1. DR Gene3D; 1.10.150.530; -; 1. DR Gene3D; 3.20.20.70; Aldolase class I; 1. DR HAMAP; MF_01849; RNA_methyltr_RlmN; 1. DR InterPro; IPR013785; Aldolase_TIM. DR InterPro; IPR040072; Methyltransferase_A. DR InterPro; IPR048641; RlmN_N. DR InterPro; IPR027492; RNA_MTrfase_RlmN. DR InterPro; IPR004383; rRNA_lsu_MTrfase_RlmN/Cfr. DR InterPro; IPR007197; rSAM. DR NCBIfam; TIGR00048; rRNA_mod_RlmN; 1. DR PANTHER; PTHR30544; 23S RRNA METHYLTRANSFERASE; 1. DR PANTHER; PTHR30544:SF5; RADICAL SAM CORE DOMAIN-CONTAINING PROTEIN; 1. DR Pfam; PF04055; Radical_SAM; 1. DR Pfam; PF21016; RlmN_N; 1. DR PIRSF; PIRSF006004; CHP00048; 1. DR SFLD; SFLDF00275; adenosine_C2_methyltransferase; 1. DR SFLD; SFLDS00029; Radical_SAM; 1. DR SUPFAM; SSF102114; Radical SAM enzymes; 1. DR PROSITE; PS51918; RADICAL_SAM; 1. PE 3: Inferred from homology; KW 4Fe-4S; Cytoplasm; Disulfide bond; Iron; Iron-sulfur; Metal-binding; KW Methyltransferase; Reference proteome; rRNA processing; KW S-adenosyl-L-methionine; Transferase; tRNA processing. FT CHAIN 1..393 FT /note="Dual-specificity RNA methyltransferase RlmN" FT /id="PRO_0000350237" FT DOMAIN 98..354 FT /note="Radical SAM core" FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01266" FT ACT_SITE 92 FT /note="Proton acceptor" FT /evidence="ECO:0000255|HAMAP-Rule:MF_01849" FT ACT_SITE 359 FT /note="S-methylcysteine intermediate" FT /evidence="ECO:0000255|HAMAP-Rule:MF_01849" FT BINDING 112 FT /ligand="[4Fe-4S] cluster" FT /ligand_id="ChEBI:CHEBI:49883" FT /ligand_note="4Fe-4S-S-AdoMet" FT /evidence="ECO:0000255|HAMAP-Rule:MF_01849" FT BINDING 116 FT /ligand="[4Fe-4S] cluster" FT /ligand_id="ChEBI:CHEBI:49883" FT /ligand_note="4Fe-4S-S-AdoMet" FT /evidence="ECO:0000255|HAMAP-Rule:MF_01849" FT BINDING 119 FT /ligand="[4Fe-4S] cluster" FT /ligand_id="ChEBI:CHEBI:49883" FT /ligand_note="4Fe-4S-S-AdoMet" FT /evidence="ECO:0000255|HAMAP-Rule:MF_01849" FT BINDING 179..180 FT /ligand="S-adenosyl-L-methionine" FT /ligand_id="ChEBI:CHEBI:59789" FT /evidence="ECO:0000255|HAMAP-Rule:MF_01849" FT BINDING 211 FT /ligand="S-adenosyl-L-methionine" FT /ligand_id="ChEBI:CHEBI:59789" FT /evidence="ECO:0000255|HAMAP-Rule:MF_01849" FT BINDING 233..235 FT /ligand="S-adenosyl-L-methionine" FT /ligand_id="ChEBI:CHEBI:59789" FT /evidence="ECO:0000255|HAMAP-Rule:MF_01849" FT BINDING 316 FT /ligand="S-adenosyl-L-methionine" FT /ligand_id="ChEBI:CHEBI:59789" FT /evidence="ECO:0000255|HAMAP-Rule:MF_01849" FT DISULFID 105..359 FT /note="(transient)" FT /evidence="ECO:0000255|HAMAP-Rule:MF_01849" SQ SEQUENCE 393 AA; 42738 MW; 34A9397DB5B1FA23 CRC64; MTAVNLLDFD LDALAAYCEQ LGEKRFRAVQ LFRWIHQRGA ADFGQMSDLA KSLRSKLADV ACIAPLRVLS EHRSSDGTIK WLFDVGDGNA VETVYIPEDD RATLCISSQA GCAVGCRFCS TGHQGFSRNL STAEILAQLW YAEHSLRRER AEGVSVGARA ATGPASERII SNVVMMGMGE PLQNYAAVLP ALRVMLDDHG YGLSRRRVTV STSGVVPMID RLAADLPVAL AVSLHACDDA LRDVLVPLNR KYPLAELLGA CQAYLASAPR DFITFEYCML DGVNDSDEQA RALLKLVGDK GPVGRLPCKF NLIPFNPFPE SGLKRSGNER VQAFAQVLID GGLVTTVRKT RGDDIDAACG QLAGEVQDRT RVQERMTRSP IRVIRSAAQP DAA //