RLMN_ACIAC
ID RLMN_ACIAC Reviewed; 373 AA.
AC A1TM24;
DT 02-SEP-2008, integrated into UniProtKB/Swiss-Prot.
DT 06-FEB-2007, sequence version 1.
DT 03-AUG-2022, entry version 90.
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=Aave_1421;
OS Acidovorax citrulli (strain AAC00-1) (Acidovorax avenae subsp. citrulli).
OC Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales;
OC Comamonadaceae; Acidovorax.
OX NCBI_TaxID=397945;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=AAC00-1;
RA Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C.,
RA Glavina del Rio T., Dalin E., Tice H., Pitluck S., Kiss H., Brettin T.,
RA Bruce D., Han C., Tapia R., Gilna P., Schmutz J., Larimer F., Land M.,
RA Hauser L., Kyrpides N., Kim E., Stahl D., Richardson P.;
RT "Complete sequence of Acidovorax avenae subsp. citrulli AAC00-1.";
RL Submitted (DEC-2006) 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: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; CP000512; ABM32012.1; -; Genomic_DNA.
DR RefSeq; WP_011794562.1; NC_008752.1.
DR AlphaFoldDB; A1TM24; -.
DR SMR; A1TM24; -.
DR STRING; 397945.Aave_1421; -.
DR EnsemblBacteria; ABM32012; ABM32012; Aave_1421.
DR KEGG; aav:Aave_1421; -.
DR eggNOG; COG0820; Bacteria.
DR HOGENOM; CLU_029101_0_0_4; -.
DR OMA; QVGCSLD; -.
DR OrthoDB; 1111428at2; -.
DR Proteomes; UP000002596; 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..373
FT /note="Dual-specificity RNA methyltransferase RlmN"
FT /id="PRO_0000349995"
FT DOMAIN 97..339
FT /note="Radical SAM core"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01266"
FT ACT_SITE 91
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 111
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 115
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 118
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 165..166
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01849"
FT BINDING 197
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 301
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01849"
FT DISULFID 104..344
FT /note="(transient)"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01849"
SQ SEQUENCE 373 AA; 41143 MW; EDB4F4BDB57E4D02 CRC64;
MTKNLLDFDL DGLAAFCEQL GEKRFRAVQL FRWIHQRGAS DFARMSDLAK SLREKLSGCA
HVAALPVISE HVSADGTVKW LFDVGDGNAV ESVFIPEDDR GTLCISSQAG CAVGCRFCST
GHQGFSRNLT SGEIVAQLWF AEHALRARLG TQERVISNVV MMGMGEPLQN YTALVPALRT
MLDDHGYGLS RRRLTVSTSG VVPMMDRLSQ DCAVAMAVSL HAPNDALRDQ LVPLNRKYPL
RELLDACTRY LEHAPRDFIT FEYCMLDGVN DQPEHARQLI DLVRPRGGEG VRCKFNLIPF
NPFPASGLHR SNPQQVAAFA KMLSDAGIVT TVRKTRGDDI DAACGQLAGD VKDRTRAAER
MARQRTIVLK PVA
