ID A0A059G7V9_9PROT Unreviewed; 389 AA. AC A0A059G7V9; DT 09-JUL-2014, integrated into UniProtKB/TrEMBL. DT 09-JUL-2014, sequence version 1. DT 12-OCT-2022, entry version 43. DE RecName: Full=Dual-specificity RNA methyltransferase RlmN {ECO:0000256|HAMAP-Rule:MF_01849}; DE EC=2.1.1.192 {ECO:0000256|HAMAP-Rule:MF_01849}; DE AltName: Full=23S rRNA (adenine(2503)-C(2))-methyltransferase {ECO:0000256|HAMAP-Rule:MF_01849}; DE AltName: Full=23S rRNA m2A2503 methyltransferase {ECO:0000256|HAMAP-Rule:MF_01849}; DE AltName: Full=Ribosomal RNA large subunit methyltransferase N {ECO:0000256|HAMAP-Rule:MF_01849}; DE AltName: Full=tRNA (adenine(37)-C(2))-methyltransferase {ECO:0000256|HAMAP-Rule:MF_01849}; DE AltName: Full=tRNA m2A37 methyltransferase {ECO:0000256|HAMAP-Rule:MF_01849}; GN Name=rlmN {ECO:0000256|HAMAP-Rule:MF_01849}; GN ORFNames=HOC_08959 {ECO:0000313|EMBL:KDA02814.1}; OS Hyphomonas oceanitis SCH89. OC Bacteria; Proteobacteria; Alphaproteobacteria; Hyphomonadales; OC Hyphomonadaceae; Hyphomonas. OX NCBI_TaxID=1280953 {ECO:0000313|EMBL:KDA02814.1, ECO:0000313|Proteomes:UP000024942}; RN [1] {ECO:0000313|EMBL:KDA02814.1, ECO:0000313|Proteomes:UP000024942} RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. RC STRAIN=SCH89 {ECO:0000313|EMBL:KDA02814.1, RC ECO:0000313|Proteomes:UP000024942}; RX PubMed=25070064; DOI=10.1007/s10482-014-0236-y; RA Li C., Lai Q., Li G., Dong C., Wang J., Liao Y., Shao Z.; RT "Hyphomonas beringensis sp. nov. and Hyphomonas chukchiensis sp. nov., RT isolated from surface seawater of the Bering Sea and Chukchi Sea."; RL Antonie Van Leeuwenhoek 106:657-665(2014). 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:0000256|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:0000256|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:0000256|HAMAP-Rule:MF_01849}; CC -!- COFACTOR: CC Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883; CC Evidence={ECO:0000256|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:0000256|HAMAP-Rule:MF_01849}; CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000256|ARBA:ARBA00004496, CC ECO:0000256|HAMAP-Rule:MF_01849}. CC -!- MISCELLANEOUS: Reaction proceeds by a ping-pong mechanism involving CC intermediate methylation of a conserved cysteine residue. CC {ECO:0000256|HAMAP-Rule:MF_01849}. CC -!- SIMILARITY: Belongs to the radical SAM superfamily. RlmN family. CC {ECO:0000256|ARBA:ARBA00007544, ECO:0000256|HAMAP-Rule:MF_01849}. CC -!- CAUTION: Lacks conserved residue(s) required for the propagation of CC feature annotation. {ECO:0000256|HAMAP-Rule:MF_01849}. CC -!- CAUTION: The sequence shown here is derived from an EMBL/GenBank/DDBJ CC whole genome shotgun (WGS) entry which is preliminary data. CC {ECO:0000313|EMBL:KDA02814.1}. 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; ARYL01000011; KDA02814.1; -; Genomic_DNA. DR RefSeq; WP_035537682.1; NZ_ARYL01000011.1. DR STRING; 1280953.HOC_08959; -. DR EnsemblBacteria; KDA02814; KDA02814; HOC_08959. DR PATRIC; fig|1280953.3.peg.1810; -. DR eggNOG; COG0820; Bacteria. DR OrthoDB; 1111428at2; -. DR Proteomes; UP000024942; Unassembled WGS sequence. 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-C2-)-methyltransferase activity; IEA:UniProtKB-UniRule. DR GO; GO:0019843; F:rRNA binding; IEA:UniProtKB-UniRule. DR GO; GO:0002935; F:tRNA (adenine-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 Gene3D; 3.20.20.70; -; 1. DR HAMAP; MF_01849; RNA_methyltr_RlmN; 1. DR InterPro; IPR013785; Aldolase_TIM. DR InterPro; IPR040072; Methyltransferase_A. DR InterPro; IPR027492; RNA_MTrfase_RlmN. DR InterPro; IPR004383; rRNA_lsu_MTrfase_RlmN/Cfr. DR InterPro; IPR007197; rSAM. DR PANTHER; PTHR30544; PTHR30544; 1. DR Pfam; PF04055; Radical_SAM; 1. DR PIRSF; PIRSF006004; CHP00048; 1. DR SFLD; SFLDF00275; adenosine_C2_methyltransferase; 1. DR SFLD; SFLDS00029; Radical_SAM; 1. DR TIGRFAMs; TIGR00048; rRNA_mod_RlmN; 1. DR PROSITE; PS51918; RADICAL_SAM; 1. PE 3: Inferred from homology; KW 4Fe-4S {ECO:0000256|ARBA:ARBA00022485, ECO:0000256|HAMAP-Rule:MF_01849}; KW Cytoplasm {ECO:0000256|ARBA:ARBA00022490, ECO:0000256|HAMAP-Rule:MF_01849}; KW Disulfide bond {ECO:0000256|ARBA:ARBA00023157, ECO:0000256|HAMAP- KW Rule:MF_01849}; KW Iron {ECO:0000256|ARBA:ARBA00023004, ECO:0000256|HAMAP-Rule:MF_01849}; KW Iron-sulfur {ECO:0000256|ARBA:ARBA00023014, ECO:0000256|HAMAP- KW Rule:MF_01849}; KW Metal-binding {ECO:0000256|ARBA:ARBA00022723, ECO:0000256|HAMAP- KW Rule:MF_01849}; KW Methyltransferase {ECO:0000256|ARBA:ARBA00022603, ECO:0000256|HAMAP- KW Rule:MF_01849}; KW rRNA processing {ECO:0000256|ARBA:ARBA00022552, ECO:0000256|HAMAP- KW Rule:MF_01849}; KW S-adenosyl-L-methionine {ECO:0000256|ARBA:ARBA00022691, ECO:0000256|HAMAP- KW Rule:MF_01849}; KW Transferase {ECO:0000256|ARBA:ARBA00022679, ECO:0000256|HAMAP- KW Rule:MF_01849}; tRNA processing {ECO:0000256|HAMAP-Rule:MF_01849}. FT DOMAIN 118..350 FT /note="Radical SAM core" FT /evidence="ECO:0000259|PROSITE:PS51918" FT REGION 1..21 FT /note="Disordered" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT REGION 368..389 FT /note="Disordered" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT COMPBIAS 1..15 FT /note="Polar residues" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT COMPBIAS 369..389 FT /note="Basic and acidic residues" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT ACT_SITE 110 FT /note="Proton acceptor" FT /evidence="ECO:0000256|HAMAP-Rule:MF_01849" FT ACT_SITE 361 FT /note="S-methylcysteine intermediate" FT /evidence="ECO:0000256|HAMAP-Rule:MF_01849" FT BINDING 132 FT /ligand="[4Fe-4S] cluster" FT /ligand_id="ChEBI:CHEBI:49883" FT /ligand_note="4Fe-4S-S-AdoMet" FT /evidence="ECO:0000256|HAMAP-Rule:MF_01849" FT BINDING 136 FT /ligand="[4Fe-4S] cluster" FT /ligand_id="ChEBI:CHEBI:49883" FT /ligand_note="4Fe-4S-S-AdoMet" FT /evidence="ECO:0000256|HAMAP-Rule:MF_01849" FT BINDING 139 FT /ligand="[4Fe-4S] cluster" FT /ligand_id="ChEBI:CHEBI:49883" FT /ligand_note="4Fe-4S-S-AdoMet" FT /evidence="ECO:0000256|HAMAP-Rule:MF_01849" FT BINDING 187..188 FT /ligand="S-adenosyl-L-methionine" FT /ligand_id="ChEBI:CHEBI:59789" FT /evidence="ECO:0000256|HAMAP-Rule:MF_01849" FT BINDING 219 FT /ligand="S-adenosyl-L-methionine" FT /ligand_id="ChEBI:CHEBI:59789" FT /evidence="ECO:0000256|HAMAP-Rule:MF_01849" FT BINDING 241..243 FT /ligand="S-adenosyl-L-methionine" FT /ligand_id="ChEBI:CHEBI:59789" FT /evidence="ECO:0000256|HAMAP-Rule:MF_01849" FT BINDING 318 FT /ligand="S-adenosyl-L-methionine" FT /ligand_id="ChEBI:CHEBI:59789" FT /evidence="ECO:0000256|HAMAP-Rule:MF_01849" SQ SEQUENCE 389 AA; 42516 MW; FD984BB05934370E CRC64; MTITLDLSRK PDQPQGQRSL AGMPLPALKA ELEAMGLDPK KASMRAKQIS RWSQYFGATS FEGMTDIGKE LRAELAARFT LDRPEIADHQ VSKDGTQKWL SRFQPGVEGE SVYIPSVGMD GGALCVSSQV GCTLNCTFCH TGTQALVRNL TAQEITAQVM IARDALNEWP SSIEARNLTN IVFMGMGEPL YNLDNVAAAI DTISDGDGIS IGRRRITVST AGVAPKIPEL GERTNAMLAI SLHATNDDLR NELVPINRKY DLQMLFEAIR AYPGSGNSRR VTFEYVMLKG INDTQAEARE LVRLLKGVPA KINLIPFNPW PGSPYECSDW ETIEAFAEIV NRAGYASPIR TPRGRDIDAA CGQLRSESVK KSAAEKRREA LEAAASPEA //