ID R5A8E6_9CLOT Unreviewed; 352 AA.
AC R5A8E6;
DT 24-JUL-2013, integrated into UniProtKB/TrEMBL.
DT 24-JUL-2013, sequence version 1.
DT 27-MAR-2024, entry version 46.
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=BN452_00579 {ECO:0000313|EMBL:CCX38973.1};
OS Clostridium sp. CAG:1013.
OC Bacteria; Bacillota; Clostridia; Eubacteriales; Clostridiaceae;
OC Clostridium.
OX NCBI_TaxID=1262769 {ECO:0000313|EMBL:CCX38973.1, ECO:0000313|Proteomes:UP000018382};
RN [1] {ECO:0000313|EMBL:CCX38973.1, ECO:0000313|Proteomes:UP000018382}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=MGS:1013 {ECO:0000313|Proteomes:UP000018382};
RA Nielsen H.B., Almeida M., Juncker A.S., Rasmussen S., Li J., Sunagawa S.,
RA Plichta D., Gautier L., Le Chatelier E., Peletier E., Bonde I., Nielsen T.,
RA Manichanh C., Arumugam M., Batto J., Santos M.B.Q.D., Blom N., Borruel N.,
RA Burgdorf K.S., Boumezbeur F., Casellas F., Dore J., Guarner F., Hansen T.,
RA Hildebrand F., Kaas R.S., Kennedy S., Kristiansen K., Kultima J.R.,
RA Leonard P., Levenez F., Lund O., Moumen B., Le Paslier D., Pons N.,
RA Pedersen O., Prifti E., Qin J., Raes J., Tap J., Tims S., Ussery D.W.,
RA Yamada T., MetaHit consortium, Renault P., Sicheritz-Ponten T., Bork P.,
RA Wang J., Brunak S., Ehrlich S.D.;
RT "Dependencies among metagenomic species, viruses, plasmids and units of
RT genetic variation.";
RL Submitted (NOV-2012) 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:CCX38973.1}.
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DR EMBL; CAWF010000320; CCX38973.1; -; Genomic_DNA.
DR AlphaFoldDB; R5A8E6; -.
DR Proteomes; UP000018382; 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 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:UP000018382};
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 102..332
FT /note="Radical SAM core"
FT /evidence="ECO:0000259|PROSITE:PS51918"
FT ACT_SITE 96
FT /note="Proton acceptor"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01849"
FT ACT_SITE 337
FT /note="S-methylcysteine intermediate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01849"
FT BINDING 116
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 120
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 123
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 163..164
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01849"
FT BINDING 195
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01849"
FT BINDING 218..220
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01849"
FT BINDING 294
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01849"
SQ SEQUENCE 352 AA; 39770 MW; 753F5EBC85D54199 CRC64;
MNTEFLNPRD IKSKTLPELR EELGELGLPK YRAEQVYRWL HRGVTDFSQM SDLSKALREE
LSQKYDIYYA QVERKQVSKD GTVKYLFRLP DGEYVESVLM HYHHGSSICI STQVGCKMNC
SFCATGKSGF SRNLAASEIL SQVQAASLDA GERISHIVLM GMGEPLDNYE NVLRFLELVT
SPEGLNIGMR HISLSTCGLV DRIYDLADKR LQLTLSISLH APNDEIRSQT MPVNKRWNME
ELLRACKYYS DKTGRRISFE YAMISGVNDM DWCAKELAGR LRGILAHVNL IPVNDVTGTG
YKKSGLDRQK RFVALLEERG VTATVRRTLG SDIDASCGQL RRKVEGGTEH ES
//
