ID A0A1D9PBF6_9FLAO Unreviewed; 347 AA.
AC A0A1D9PBF6;
DT 15-FEB-2017, integrated into UniProtKB/TrEMBL.
DT 15-FEB-2017, sequence version 1.
DT 27-MAR-2024, entry version 31.
DE RecName: Full=Probable 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=BIW12_09600 {ECO:0000313|EMBL:AOZ99674.1};
OS Flavobacterium commune.
OC Bacteria; Bacteroidota; Flavobacteriia; Flavobacteriales;
OC Flavobacteriaceae; Flavobacterium.
OX NCBI_TaxID=1306519 {ECO:0000313|EMBL:AOZ99674.1, ECO:0000313|Proteomes:UP000178198};
RN [1] {ECO:0000313|EMBL:AOZ99674.1, ECO:0000313|Proteomes:UP000178198}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=PK15 {ECO:0000313|EMBL:AOZ99674.1,
RC ECO:0000313|Proteomes:UP000178198};
RA Ekwe A., Kim S.B.;
RT "Complete Genome Sequence of Flavobacterium sp. PK15.";
RL Submitted (OCT-2016) 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:0000256|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: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|HAMAP-Rule:MF_01849}.
CC -!- CAUTION: Lacks conserved residue(s) required for the propagation of
CC feature annotation. {ECO:0000256|HAMAP-Rule:MF_01849}.
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DR EMBL; CP017774; AOZ99674.1; -; Genomic_DNA.
DR RefSeq; WP_071184922.1; NZ_CP017774.1.
DR AlphaFoldDB; A0A1D9PBF6; -.
DR STRING; 1306519.BIW12_09600; -.
DR KEGG; fcm:BIW12_09600; -.
DR OrthoDB; 9793973at2; -.
DR Proteomes; UP000178198; 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(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 CORE 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; SFLDS00029; Radical_SAM; 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|HAMAP-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}; Reference proteome {ECO:0000313|Proteomes:UP000178198};
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 100..334
FT /note="Radical SAM core"
FT /evidence="ECO:0000259|PROSITE:PS51918"
FT ACT_SITE 94
FT /note="Proton acceptor"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01849"
FT ACT_SITE 339
FT /note="S-methylcysteine intermediate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01849"
FT BINDING 114
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 118
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 121
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 165..166
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01849"
FT BINDING 197
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01849"
FT BINDING 220..222
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01849"
FT BINDING 296
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01849"
SQ SEQUENCE 347 AA; 39454 MW; FAA6D54B1FBA3034 CRC64;
MQMEKKDIRA LSKEELRNFF VANRDKAFRG NQVYEWLWSK GAHTFEDMTN ISKGTRAMLE
DNFVINHIKV DTMQRSEDGT VKNAVRLHDG LVVESVLIPT ETRTTACVSS QVGCSLDCNF
CATARLKRMR NLEPGEIYDQ VLAIDRESRL YYNHPLSNIV FMGMGEPLMN YNNVIKAISM
ITSEEGLGMS PKRIMVSTSG IPKMIKKMAD DEVKFKLAVS LHSAIDEIRA RIMPFSKNFP
LADLREALEY WYRKTKSKIS YEYVVWKGIN DNKASVDALV KFCKYVPCKV NLIEYNPIDD
GEFQQASEES INAYIKALEA IGVVVKVRRS RGKDIDAACG QLANKEV
//
