ID A0A0M3AZW4_9SPHN Unreviewed; 419 AA. AC A0A0M3AZW4; DT 11-NOV-2015, integrated into UniProtKB/TrEMBL. DT 11-NOV-2015, sequence version 1. DT 24-JAN-2024, entry version 37. 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=YP76_00100 {ECO:0000313|EMBL:KKW94099.1}; OS Sphingobium chungbukense. OC Bacteria; Pseudomonadota; Alphaproteobacteria; Sphingomonadales; OC Sphingomonadaceae; Sphingobium. OX NCBI_TaxID=56193 {ECO:0000313|EMBL:KKW94099.1, ECO:0000313|Proteomes:UP000033874}; RN [1] {ECO:0000313|EMBL:KKW94099.1, ECO:0000313|Proteomes:UP000033874} RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. RC STRAIN=DJ77 {ECO:0000313|EMBL:KKW94099.1, RC ECO:0000313|Proteomes:UP000033874}; RA Kim Y.-C., Chae J.-C.; RT "Genome sequence of aromatic hydrocarbons-degrading Sphingobium RT chungbukense DJ77."; RL Submitted (APR-2015) 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: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|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:KKW94099.1}. 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; LBIC01000001; KKW94099.1; -; Genomic_DNA. DR RefSeq; WP_046762530.1; NZ_LBIC01000001.1. DR AlphaFoldDB; A0A0M3AZW4; -. DR STRING; 56193.YP76_00100; -. DR PATRIC; fig|56193.3.peg.21; -. DR Proteomes; UP000033874; 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(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 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; SFLDG01062; methyltransferase_(Class_A); 1. DR SUPFAM; SSF102114; Radical SAM enzymes; 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}; KW tRNA processing {ECO:0000256|ARBA:ARBA00022694, ECO:0000256|HAMAP- KW Rule:MF_01849}. FT DOMAIN 130..387 FT /note="Radical SAM core" FT /evidence="ECO:0000259|PROSITE:PS51918" FT ACT_SITE 124 FT /note="Proton acceptor" FT /evidence="ECO:0000256|HAMAP-Rule:MF_01849" FT ACT_SITE 392 FT /note="S-methylcysteine intermediate" FT /evidence="ECO:0000256|HAMAP-Rule:MF_01849" FT BINDING 144 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 148 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 151 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 216..217 FT /ligand="S-adenosyl-L-methionine" FT /ligand_id="ChEBI:CHEBI:59789" FT /evidence="ECO:0000256|HAMAP-Rule:MF_01849" FT BINDING 248 FT /ligand="S-adenosyl-L-methionine" FT /ligand_id="ChEBI:CHEBI:59789" FT /evidence="ECO:0000256|HAMAP-Rule:MF_01849" FT BINDING 270..272 FT /ligand="S-adenosyl-L-methionine" FT /ligand_id="ChEBI:CHEBI:59789" FT /evidence="ECO:0000256|HAMAP-Rule:MF_01849" FT BINDING 349 FT /ligand="S-adenosyl-L-methionine" FT /ligand_id="ChEBI:CHEBI:59789" FT /evidence="ECO:0000256|HAMAP-Rule:MF_01849" SQ SEQUENCE 419 AA; 46382 MW; 6C8356BA65450E6C CRC64; MQTAANPLMP IPGLIDPVPV PRAVTPREDG RVDLMGLSRP QIKGVLEEAG LDQKQAKLRS KQLFHWLYHR GETDFDAMTD LAKPMRGWMA ERFVVGRPEV VEAQVSSDGT RKWLLRSDDG QDYEMVFIPD ADRGTLCVSS QVGCTLNCRF CHTGTMRLVR NLTPGEIVGQ VMLARDALGE WPKGSMASAN DDEADDASQY SPDGRMLTNI VMMGMGEPLY NFDHVRDALK VVMDGDGLAL SKRRITLSTS GVVPMMARAG EEIGVNLAVS LHAVTKDVRD ELVPLNKKYG IEQLLQACAD YPNANNARRI TFEYVMIKDK NDSDDDAREL VRLLRQYKLP AKVNLIPFNP WPGTDYECST PERIRAFSTI VFEGGISAPV RTPRGRDIMA ACGQLKSASE KKSRAELDRL AAEKQAALG //