ID A0A1Y4CEU2_9BACT Unreviewed; 337 AA.
AC A0A1Y4CEU2;
DT 30-AUG-2017, integrated into UniProtKB/TrEMBL.
DT 30-AUG-2017, sequence version 1.
DT 24-JAN-2024, entry version 22.
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=B5F81_06960 {ECO:0000313|EMBL:OUO42520.1};
OS Muribaculum sp. An287.
OC Bacteria; Bacteroidota; Bacteroidia; Bacteroidales; Muribaculaceae;
OC Muribaculum.
OX NCBI_TaxID=1965623 {ECO:0000313|EMBL:OUO42520.1, ECO:0000313|Proteomes:UP000243574};
RN [1] {ECO:0000313|Proteomes:UP000243574}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=An287 {ECO:0000313|Proteomes:UP000243574};
RA Medvecky M., Cejkova D., Polansky O., Karasova D., Kubasova T., Cizek A.,
RA Rychlik I.;
RT "Function of individual gut microbiota members based on whole genome
RT sequencing of pure cultures obtained from chicken caecum.";
RL Submitted (APR-2017) 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}.
CC -!- CAUTION: The sequence shown here is derived from an EMBL/GenBank/DDBJ
CC whole genome shotgun (WGS) entry which is preliminary data.
CC {ECO:0000313|EMBL:OUO42520.1}.
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DR EMBL; NFIX01000008; OUO42520.1; -; Genomic_DNA.
DR AlphaFoldDB; A0A1Y4CEU2; -.
DR OrthoDB; 9793973at2; -.
DR Proteomes; UP000243574; Unassembled WGS sequence.
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 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:UP000243574};
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 97..318
FT /note="Radical SAM core"
FT /evidence="ECO:0000259|PROSITE:PS51918"
FT ACT_SITE 91
FT /note="Proton acceptor"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01849"
FT ACT_SITE 329
FT /note="S-methylcysteine intermediate"
FT /evidence="ECO:0000256|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:0000256|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: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 156..157
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01849"
FT BINDING 188
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01849"
FT BINDING 210..212
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01849"
FT BINDING 286
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01849"
SQ SEQUENCE 337 AA; 37773 MW; 74B010BFF488B55C CRC64;
MKKKLLGKNL YELQDVVSSY GTPLYVAKQM ADWLYKKKVR DIGDMTNLSK QFRERLSEDY
EIGVTEYSAV YRSSDGTKKY VFPVTGGGSV ETVMIPEPDR ATLCVSSQNG CKMNCSFCMT
GRGGFRGNLD AAEIMSQYIA VDEADMLTNT VFMGMGEPLD NIDTVMRCLE ILVSDWGFGW
SPKRITVSTI GVLPALRRFL EESRCHLAIS LHNPFPAERE SMMPVEKAFP VSETIELLKK
YDFSGQRRVS FEYTMFAGVN DSGRHCNALM AMLSGLECRI NLIRFHKIPG SNLLPSPDVV
MERFRDKLNS HGFICTIRAS RGEDIMAACG MLAGKKD
//