RLMN_EXIS2
ID RLMN_EXIS2 Reviewed; 357 AA.
AC B1YG36;
DT 02-SEP-2008, integrated into UniProtKB/Swiss-Prot.
DT 20-MAY-2008, sequence version 1.
DT 03-AUG-2022, entry version 93.
DE RecName: Full=Probable 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}; OrderedLocusNames=Exig_2974;
OS Exiguobacterium sibiricum (strain DSM 17290 / CIP 109462 / JCM 13490 /
OS 255-15).
OC Bacteria; Firmicutes; Bacilli; Bacillales;
OC Bacillales Family XII. Incertae Sedis; Exiguobacterium.
OX NCBI_TaxID=262543;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DSM 17290 / CIP 109462 / JCM 13490 / 255-15;
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., Kiss H., Chertkov O., Monk C.,
RA Brettin T., Detter J.C., Han C., Kuske C.R., Schmutz J., Larimer F.,
RA Land M., Hauser L., Kyrpides N., Mikhailova N., Vishnivetskaya T.,
RA Rodrigues D.F., Gilichinsky D., Tiedje J., Richardson P.;
RT "Complete sequence of chromosome of Exiguobacterium sibiricum 255-15.";
RL Submitted (APR-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. {ECO:0000255|HAMAP-
CC 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}.
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DR EMBL; CP001022; ACB62420.1; -; Genomic_DNA.
DR RefSeq; WP_012371835.1; NC_010556.1.
DR AlphaFoldDB; B1YG36; -.
DR SMR; B1YG36; -.
DR STRING; 262543.Exig_2974; -.
DR EnsemblBacteria; ACB62420; ACB62420; Exig_2974.
DR KEGG; esi:Exig_2974; -.
DR eggNOG; COG0820; Bacteria.
DR HOGENOM; CLU_029101_0_1_9; -.
DR OMA; KVVFMGM; -.
DR OrthoDB; 1111428at2; -.
DR Proteomes; UP000001681; 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-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; 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..357
FT /note="Probable dual-specificity RNA methyltransferase
FT RlmN"
FT /id="PRO_0000350174"
FT DOMAIN 98..336
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 341
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 164..165
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01849"
FT BINDING 196
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01849"
FT BINDING 219..221
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01849"
FT BINDING 297
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01849"
FT DISULFID 105..341
FT /note="(transient)"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01849"
SQ SEQUENCE 357 AA; 40356 MW; B119F6076DBDB321 CRC64;
MNKPSIYGLT LEQMTEWLSH QGHKPFRAKQ VWDWLYRKRV TTFAEMTNVN KDCLELLDQS
FAIDSMTQAV KQESADGTIK FLFKLYDGSL IETVLMRHKY GLSVCVTTQV GCNIGCSFCA
SGLIKKSRDL SAGEIVEQIM NVQHHLDAVG KEERVSHVVV MGIGEPFDNF DNMVDFLNVI
KDHNGLAIGA RHITVSTSGL ADKIYKFADL KLQVNLAISL HAPNNELRTQ IMKINRAIPL
EKLMPAIDYY VKTTNRKITI EYILLRGVND QKAQAIELAK LFEDKRHLTY VNLIPYNPVD
EHGQYQRSTS EDISTFYDTL KKNGLNCGVR LEHGTDIDAA CGQLRSKQIK KDTVAAK
