ID   Y2859_RHOPS             Reviewed;         359 AA.
AC   Q136A2;
DT   02-SEP-2008, integrated into UniProtKB/Swiss-Prot.
DT   31-OCT-2006, sequence version 1.
DT   03-AUG-2022, entry version 89.
DE   RecName: Full=Probable RNA methyltransferase RPD_2859;
DE            EC=2.1.1.-;
GN   OrderedLocusNames=RPD_2859;
OS   Rhodopseudomonas palustris (strain BisB5).
OC   Bacteria; Proteobacteria; Alphaproteobacteria; Hyphomicrobiales;
OC   Bradyrhizobiaceae; Rhodopseudomonas.
OX   NCBI_TaxID=316057;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=BisB5;
RG   US DOE Joint Genome Institute;
RA   Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C.,
RA   Glavina del Rio T., Hammon N., Israni S., Dalin E., Tice H., Pitluck S.,
RA   Chain P., Malfatti S., Shin M., Vergez L., Schmutz J., Larimer F., Land M.,
RA   Hauser L., Pelletier D.A., Kyrpides N., Lykidis A., Oda Y., Harwood C.S.,
RA   Richardson P.;
RT   "Complete sequence of Rhodopseudomonas palustris BisB5.";
RL   Submitted (MAR-2006) 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; CP000283; ABE40087.1; -; Genomic_DNA.
DR   AlphaFoldDB; Q136A2; -.
DR   SMR; Q136A2; -.
DR   STRING; 316057.RPD_2859; -.
DR   EnsemblBacteria; ABE40087; ABE40087; RPD_2859.
DR   KEGG; rpd:RPD_2859; -.
DR   eggNOG; COG0820; Bacteria.
DR   HOGENOM; CLU_029101_3_3_5; -.
DR   OMA; PANRMYP; -.
DR   OrthoDB; 1111428at2; -.
DR   BioCyc; RPAL316057:RPD_RS14365-MON; -.
DR   Proteomes; UP000001818; 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; IPR006638; Elp3/MiaB/NifB.
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   SFLD; SFLDS00029; Radical_SAM; 1.
DR   SMART; SM00729; Elp3; 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; S-adenosyl-L-methionine; Transferase.
FT   CHAIN           1..359
FT                   /note="Probable RNA methyltransferase RPD_2859"
FT                   /id="PRO_0000350372"
FT   DOMAIN          105..330
FT                   /note="Radical SAM core"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01266"
FT   ACT_SITE        99
FT                   /note="Proton acceptor"
FT                   /evidence="ECO:0000255"
FT   ACT_SITE        336
FT                   /note="S-methylcysteine intermediate"
FT                   /evidence="ECO:0000250"
FT   BINDING         119
FT                   /ligand="[4Fe-4S] cluster"
FT                   /ligand_id="ChEBI:CHEBI:49883"
FT                   /ligand_note="4Fe-4S-S-AdoMet"
FT                   /evidence="ECO:0000250"
FT   BINDING         123
FT                   /ligand="[4Fe-4S] cluster"
FT                   /ligand_id="ChEBI:CHEBI:49883"
FT                   /ligand_note="4Fe-4S-S-AdoMet"
FT                   /evidence="ECO:0000250"
FT   BINDING         126
FT                   /ligand="[4Fe-4S] cluster"
FT                   /ligand_id="ChEBI:CHEBI:49883"
FT                   /ligand_note="4Fe-4S-S-AdoMet"
FT                   /evidence="ECO:0000250"
FT   BINDING         162..163
FT                   /ligand="S-adenosyl-L-methionine"
FT                   /ligand_id="ChEBI:CHEBI:59789"
FT                   /evidence="ECO:0000250"
FT   BINDING         194
FT                   /ligand="S-adenosyl-L-methionine"
FT                   /ligand_id="ChEBI:CHEBI:59789"
FT                   /evidence="ECO:0000250"
FT   BINDING         217..219
FT                   /ligand="S-adenosyl-L-methionine"
FT                   /ligand_id="ChEBI:CHEBI:59789"
FT                   /evidence="ECO:0000250"
FT   BINDING         293
FT                   /ligand="S-adenosyl-L-methionine"
FT                   /ligand_id="ChEBI:CHEBI:59789"
FT                   /evidence="ECO:0000250"
FT   DISULFID        112..336
FT                   /note="(transient)"
FT                   /evidence="ECO:0000250"
SQ   SEQUENCE   359 AA;  39815 MW;  CBEDC1DC5F019B71 CRC64;
     MASAQRHSTP DLVRQRDPAG VSGLSLGLTS SEFAGLHEGA VPDVTYRELF FPHADPPRRL
     QNWARSRGVR LRTLTRIGRD QGGRSEKMLF GLHDGYAVES VLIRRFDGHT ACISSQVGCA
     FACRFCASGQ AGLMRNLEAG EIVEQVVRLG PKVNRIVFMG IGEPLNNYQQ VLKAIRILRD
     RQGMNFPTTG ITLSTIGIPK ALKQLREEHL AINLTISLHA TTQEVRDRLI PGARKHPLGE
     VVERACAWAR RHNRPVTFAY LVLPGINDSI ADARRLAAML RDSPARVNLM RWNPVDGVGL
     QRTPDRSLAH FRTTLENALV PVVVRDTQGR DISAACGQLW LRDLKGLPVG NRPRQGRMT