RLMN_DESHD
ID RLMN_DESHD Reviewed; 357 AA.
AC B8FS78;
DT 22-SEP-2009, integrated into UniProtKB/Swiss-Prot.
DT 03-MAR-2009, sequence version 1.
DT 03-AUG-2022, entry version 69.
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=Dhaf_3850;
OS Desulfitobacterium hafniense (strain DSM 10664 / DCB-2).
OC Bacteria; Firmicutes; Clostridia; Eubacteriales; Desulfitobacteriaceae;
OC Desulfitobacterium.
OX NCBI_TaxID=272564;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DSM 10664 / DCB-2;
RX PubMed=22316246; DOI=10.1186/1471-2180-12-21;
RA Kim S.H., Harzman C., Davis J.K., Hutcheson R., Broderick J.B., Marsh T.L.,
RA Tiedje J.M.;
RT "Genome sequence of Desulfitobacterium hafniense DCB-2, a Gram-positive
RT anaerobe capable of dehalogenation and metal reduction.";
RL BMC Microbiol. 12:21-21(2012).
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}.
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; CP001336; ACL21866.1; -; Genomic_DNA.
DR AlphaFoldDB; B8FS78; -.
DR SMR; B8FS78; -.
DR EnsemblBacteria; ACL21866; ACL21866; Dhaf_3850.
DR KEGG; dhd:Dhaf_3850; -.
DR HOGENOM; CLU_029101_0_1_9; -.
DR OMA; QVGCSLD; -.
DR Proteomes; UP000007726; 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; rRNA processing; S-adenosyl-L-methionine; Transferase;
KW tRNA processing.
FT CHAIN 1..357
FT /note="Probable dual-specificity RNA methyltransferase
FT RlmN"
FT /id="PRO_1000216115"
FT DOMAIN 106..340
FT /note="Radical SAM core"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01266"
FT ACT_SITE 95
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01849"
FT ACT_SITE 345
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 172..173
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01849"
FT BINDING 204
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01849"
FT BINDING 227..229
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01849"
FT BINDING 302
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01849"
FT DISULFID 113..345
FT /note="(transient)"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01849"
SQ SEQUENCE 357 AA; 39911 MW; C70BA163896AC69D CRC64;
MNTMKRMDCR DLNQSELTQH CAELGLPKFR GRQVFQWVQQ KAVQNWEELR NIGAGDRQKL
QEGLFLQPLR KVREQIAQDG TRKFLFRCAD GETLECVLMD YDRRKNRDRH TVCVSTQIGC
AVGCAFCATG LGGWRRNLSP GEILGQVLDI TYLMRQEDPD FQVTNIVFMG MGEPLLNYEA
VLKAIELLND PEGQGIGMRR MTISTSGVAP KIRQLAKDNP QVGLAVSLHS AHNTTRDQLI
PMNRKYPLEE LMEACGDYTT LTNRRITFEI ALISGQATLE AAQAVGHLLK GQLAHVNLIP
VNPVAGTGMA RPTAKEVQQF AQSLESMGIP VSVREEKGTD IDAACGQLRR QLECEQK
