ID   Y2507_LEPCP             Reviewed;         347 AA.
AC   B1Y6D6;
DT   02-SEP-2008, integrated into UniProtKB/Swiss-Prot.
DT   20-MAY-2008, sequence version 1.
DT   03-AUG-2022, entry version 73.
DE   RecName: Full=Probable RNA methyltransferase Lcho_2507;
DE            EC=2.1.1.-;
GN   OrderedLocusNames=Lcho_2507;
OS   Leptothrix cholodnii (strain ATCC 51168 / LMG 8142 / SP-6) (Leptothrix
OS   discophora (strain SP-6)).
OC   Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales; Leptothrix.
OX   NCBI_TaxID=395495;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 51168 / LMG 8142 / SP-6;
RG   US DOE Joint Genome Institute;
RA   Copeland A., Lucas S., Lapidus A., Glavina del Rio T., Dalin E., Tice H.,
RA   Bruce D., Goodwin L., Pitluck S., Chertkov O., Brettin T., Detter J.C.,
RA   Han C., Kuske C.R., Schmutz J., Larimer F., Land M., Hauser L.,
RA   Kyrpides N., Lykidis A., Emerson D., Richardson P.;
RT   "Complete sequence of Leptothrix cholodnii SP-6.";
RL   Submitted (MAR-2008) to the EMBL/GenBank/DDBJ databases.
CC   -!- COFACTOR:
CC       Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883; Evidence={ECO:0000250};
CC       Note=Binds 1 [4Fe-4S] cluster. The cluster is coordinated with 3
CC       cysteines and an exchangeable S-adenosyl-L-methionine. {ECO:0000250};
CC   -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000305}.
CC   -!- SIMILARITY: Belongs to the radical SAM superfamily. RlmN family.
CC       {ECO:0000305}.
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DR   EMBL; CP001013; ACB34772.1; -; Genomic_DNA.
DR   RefSeq; WP_012347528.1; NC_010524.1.
DR   AlphaFoldDB; B1Y6D6; -.
DR   SMR; B1Y6D6; -.
DR   STRING; 395495.Lcho_2507; -.
DR   EnsemblBacteria; ACB34772; ACB34772; Lcho_2507.
DR   KEGG; lch:Lcho_2507; -.
DR   eggNOG; COG0820; Bacteria.
DR   HOGENOM; CLU_029101_3_3_4; -.
DR   OMA; KVVFMGM; -.
DR   OrthoDB; 1111428at2; -.
DR   Proteomes; UP000001693; Chromosome.
DR   GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR   GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IEA:UniProtKB-KW.
DR   GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR   GO; GO:0008173; F:RNA methyltransferase activity; IEA:InterPro.
DR   GO; GO:0006364; P:rRNA processing; IEA:InterPro.
DR   Gene3D; 3.20.20.70; -; 1.
DR   InterPro; IPR013785; Aldolase_TIM.
DR   InterPro; IPR040072; Methyltransferase_A.
DR   InterPro; IPR004383; rRNA_lsu_MTrfase_RlmN/Cfr.
DR   InterPro; IPR007197; rSAM.
DR   PANTHER; PTHR30544; PTHR30544; 1.
DR   Pfam; PF04055; Radical_SAM; 1.
DR   SFLD; SFLDF00275; adenosine_C2_methyltransferase; 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; S-adenosyl-L-methionine;
KW   Transferase.
FT   CHAIN           1..347
FT                   /note="Probable RNA methyltransferase Lcho_2507"
FT                   /id="PRO_0000350236"
FT   DOMAIN          92..318
FT                   /note="Radical SAM core"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01266"
FT   ACT_SITE        89
FT                   /note="Proton acceptor"
FT                   /evidence="ECO:0000255"
FT   ACT_SITE        323
FT                   /note="S-methylcysteine intermediate"
FT                   /evidence="ECO:0000250"
FT   BINDING         106
FT                   /ligand="[4Fe-4S] cluster"
FT                   /ligand_id="ChEBI:CHEBI:49883"
FT                   /ligand_note="4Fe-4S-S-AdoMet"
FT                   /evidence="ECO:0000250"
FT   BINDING         110
FT                   /ligand="[4Fe-4S] cluster"
FT                   /ligand_id="ChEBI:CHEBI:49883"
FT                   /ligand_note="4Fe-4S-S-AdoMet"
FT                   /evidence="ECO:0000250"
FT   BINDING         113
FT                   /ligand="[4Fe-4S] cluster"
FT                   /ligand_id="ChEBI:CHEBI:49883"
FT                   /ligand_note="4Fe-4S-S-AdoMet"
FT                   /evidence="ECO:0000250"
FT   BINDING         151..152
FT                   /ligand="S-adenosyl-L-methionine"
FT                   /ligand_id="ChEBI:CHEBI:59789"
FT                   /evidence="ECO:0000250"
FT   BINDING         181
FT                   /ligand="S-adenosyl-L-methionine"
FT                   /ligand_id="ChEBI:CHEBI:59789"
FT                   /evidence="ECO:0000250"
FT   BINDING         204..206
FT                   /ligand="S-adenosyl-L-methionine"
FT                   /ligand_id="ChEBI:CHEBI:59789"
FT                   /evidence="ECO:0000250"
FT   BINDING         280
FT                   /ligand="S-adenosyl-L-methionine"
FT                   /ligand_id="ChEBI:CHEBI:59789"
FT                   /evidence="ECO:0000250"
FT   DISULFID        99..323
FT                   /note="(transient)"
FT                   /evidence="ECO:0000250"
SQ   SEQUENCE   347 AA;  38067 MW;  B4B357F3D29AA83E CRC64;
     MRIDFIRQRL RAQGAKPCHE QRILRIWAQV LPTEGGRSRP DDFLPQAVRD AMPALLADLD
     GLARLRSQHP GEDGSARLLV ELADGQTVES VLLPRDGLCV STQVGCAVGC VFCMTGREGL
     LRQVGSAEIV AQVVLARRQR LVKKVVFMGM GEPAHNLDNV MEAIDFLGTT GAIGHKNLVF
     STVGDPRVFE RLPLGPVKPA LALSLHTTRA DLRAQLLPRA PRMDPADLVE RAEAYARATS
     YPIQYQWTLL EGINDGPDEV EGIVRLLHGK YAVLNMIPYN TVPDLPYTRP SWEAAAALAR
     TLHRRGILTK LRQSAGQDVE GGCGQLRARE LAPSARRIEI RPVASLP