RLMN_SULDN
ID RLMN_SULDN Reviewed; 356 AA.
AC Q30NR4;
DT 02-SEP-2008, integrated into UniProtKB/Swiss-Prot.
DT 06-DEC-2005, sequence version 1.
DT 03-AUG-2022, entry version 102.
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}; OrderedLocusNames=Suden_2093;
OS Sulfurimonas denitrificans (strain ATCC 33889 / DSM 1251) (Thiomicrospira
OS denitrificans (strain ATCC 33889 / DSM 1251)).
OC Bacteria; Proteobacteria; Epsilonproteobacteria; Campylobacterales;
OC Thiovulaceae; Sulfurimonas.
OX NCBI_TaxID=326298;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 33889 / DSM 1251;
RX PubMed=18065616; DOI=10.1128/aem.01844-07;
RA Sievert S.M., Scott K.M., Klotz M.G., Chain P.S.G., Hauser L.J., Hemp J.,
RA Huegler M., Land M., Lapidus A., Larimer F.W., Lucas S., Malfatti S.A.,
RA Meyer F., Paulsen I.T., Ren Q., Simon J., Bailey K., Diaz E.,
RA Fitzpatrick K.A., Glover B., Gwatney N., Korajkic A., Long A.,
RA Mobberley J.M., Pantry S.N., Pazder G., Peterson S., Quintanilla J.D.,
RA Sprinkle R., Stephens J., Thomas P., Vaughn R., Weber M.J., Wooten L.L.;
RT "Genome of the epsilonproteobacterial chemolithoautotroph Sulfurimonas
RT denitrificans.";
RL Appl. Environ. Microbiol. 74:1145-1156(2008).
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}.
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DR EMBL; CP000153; ABB45367.1; -; Genomic_DNA.
DR RefSeq; WP_011373707.1; NC_007575.1.
DR AlphaFoldDB; Q30NR4; -.
DR SMR; Q30NR4; -.
DR STRING; 326298.Suden_2093; -.
DR EnsemblBacteria; ABB45367; ABB45367; Suden_2093.
DR KEGG; tdn:Suden_2093; -.
DR eggNOG; COG0820; Bacteria.
DR HOGENOM; CLU_029101_2_0_7; -.
DR OMA; QVGCSLD; -.
DR OrthoDB; 1111428at2; -.
DR Proteomes; UP000002714; 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; IPR006638; Elp3/MiaB/NifB.
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 SMART; SM00729; Elp3; 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..356
FT /note="Dual-specificity RNA methyltransferase RlmN"
FT /id="PRO_0000350476"
FT DOMAIN 106..339
FT /note="Radical SAM core"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01266"
FT ACT_SITE 87
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01849"
FT ACT_SITE 344
FT /note="S-methylcysteine intermediate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01849"
FT BINDING 120
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 124
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 127
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 170..171
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01849"
FT BINDING 202
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01849"
FT BINDING 225..227
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01849"
FT BINDING 301
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01849"
FT DISULFID 113..344
FT /note="(transient)"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01849"
SQ SEQUENCE 356 AA; 40303 MW; 3F260BFCB907448D CRC64;
MKPSLLDFRL KELQANIKPS FRAKQIYGWL YHNYAQSFDD MKNIPQQLKD ELAKSYVVNL
LKIVKKELSN DGTIKYLFEL QDGKTIETVW LKMKDEQIDE EGCVTQEAKY TICVSTQVGC
KVGCAFCLTA KGGFTRDLTA GEIVAQVVAL KKDNDHKHNR MINIVYMGMG EPLDNLDNLS
RAIEIFKEED GLCISGKRQT VSTSGLSNKI DRLGEMDLGV HIAISLHAVD DELRTELIPM
NKAHNISSII EAVKRFPIDT RKRVMFEYLV IKNKNDDLGS AKKLVKLLSG IKAKVNLIYF
NPYPDTPYER PQKSDMIAFQ EYLINHGLLC TIRDSKGIDI SAACGQLKEK TQSELQ
