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RLMN_BORPA
ID   RLMN_BORPA              Reviewed;         382 AA.
AC   Q7W6P5;
DT   02-SEP-2008, integrated into UniProtKB/Swiss-Prot.
DT   01-OCT-2003, sequence version 1.
DT   03-AUG-2022, entry version 108.
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=BPP2857;
OS   Bordetella parapertussis (strain 12822 / ATCC BAA-587 / NCTC 13253).
OC   Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales;
OC   Alcaligenaceae; Bordetella.
OX   NCBI_TaxID=257311;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=12822 / ATCC BAA-587 / NCTC 13253;
RX   PubMed=12910271; DOI=10.1038/ng1227;
RA   Parkhill J., Sebaihia M., Preston A., Murphy L.D., Thomson N.R.,
RA   Harris D.E., Holden M.T.G., Churcher C.M., Bentley S.D., Mungall K.L.,
RA   Cerdeno-Tarraga A.-M., Temple L., James K.D., Harris B., Quail M.A.,
RA   Achtman M., Atkin R., Baker S., Basham D., Bason N., Cherevach I.,
RA   Chillingworth T., Collins M., Cronin A., Davis P., Doggett J., Feltwell T.,
RA   Goble A., Hamlin N., Hauser H., Holroyd S., Jagels K., Leather S.,
RA   Moule S., Norberczak H., O'Neil S., Ormond D., Price C., Rabbinowitsch E.,
RA   Rutter S., Sanders M., Saunders D., Seeger K., Sharp S., Simmonds M.,
RA   Skelton J., Squares R., Squares S., Stevens K., Unwin L., Whitehead S.,
RA   Barrell B.G., Maskell D.J.;
RT   "Comparative analysis of the genome sequences of Bordetella pertussis,
RT   Bordetella parapertussis and Bordetella bronchiseptica.";
RL   Nat. Genet. 35:32-40(2003).
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; BX640431; CAE38149.1; -; Genomic_DNA.
DR   RefSeq; WP_010928770.1; NC_002928.3.
DR   AlphaFoldDB; Q7W6P5; -.
DR   SMR; Q7W6P5; -.
DR   EnsemblBacteria; CAE38149; CAE38149; BPP2857.
DR   KEGG; bpa:BPP2857; -.
DR   HOGENOM; CLU_029101_0_0_4; -.
DR   OMA; QVGCSLD; -.
DR   Proteomes; UP000001421; 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   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..382
FT                   /note="Dual-specificity RNA methyltransferase RlmN"
FT                   /id="PRO_0000350056"
FT   DOMAIN          101..348
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        353
FT                   /note="S-methylcysteine intermediate"
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         119
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         122
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         179..180
FT                   /ligand="S-adenosyl-L-methionine"
FT                   /ligand_id="ChEBI:CHEBI:59789"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01849"
FT   BINDING         211
FT                   /ligand="S-adenosyl-L-methionine"
FT                   /ligand_id="ChEBI:CHEBI:59789"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01849"
FT   BINDING         233..235
FT                   /ligand="S-adenosyl-L-methionine"
FT                   /ligand_id="ChEBI:CHEBI:59789"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01849"
FT   BINDING         310
FT                   /ligand="S-adenosyl-L-methionine"
FT                   /ligand_id="ChEBI:CHEBI:59789"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01849"
FT   DISULFID        108..353
FT                   /note="(transient)"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01849"
SQ   SEQUENCE   382 AA;  42396 MW;  79DA463C286EA535 CRC64;
     MESVERVNLL GLDGAALSEL VGQWGGKPFR ARQLQRWVHQ RGADSFDAMT DLARDFRAQL
     ARDCVIEALP VNTEQRSSDG TRKWLFDVGQ GNAIETVFIP EDDRGTLCIS SQAGCVVNCR
     FCSTGHQGFN RNLRASEIIG QLWWAKRVLE AAADTARLPG GKAGEDTRVI SNVVMMGMGE
     PLLNYDQVLP ALRLMLDDNA YGLSRRRVTV STSGVVPMMD RLSQDCPLAL AVSLHAPNDA
     LRDELVPLNR KYPLNALLAA CERYLAHAPR DFITFEYCML DGINDTDQHA RELIQLARQV
     RCKLNLIPFN PFPASGLKRS PSARVRVFAQ RLMDAGIVTT VRKTRGDDID AACGQLAGEV
     RDRTRITERN ATRTIPIQQV HA
 
 
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