ID   Y6963_RHOBA             Reviewed;         379 AA.
AC   Q7UPG1;
DT   02-SEP-2008, integrated into UniProtKB/Swiss-Prot.
DT   01-OCT-2003, sequence version 1.
DT   03-AUG-2022, entry version 106.
DE   RecName: Full=Probable RNA methyltransferase RB6963;
DE            EC=2.1.1.-;
GN   OrderedLocusNames=RB6963;
OS   Rhodopirellula baltica (strain DSM 10527 / NCIMB 13988 / SH1).
OC   Bacteria; Planctomycetes; Planctomycetia; Pirellulales; Pirellulaceae;
OC   Rhodopirellula.
OX   NCBI_TaxID=243090;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=DSM 10527 / NCIMB 13988 / SH1;
RX   PubMed=12835416; DOI=10.1073/pnas.1431443100;
RA   Gloeckner F.O., Kube M., Bauer M., Teeling H., Lombardot T., Ludwig W.,
RA   Gade D., Beck A., Borzym K., Heitmann K., Rabus R., Schlesner H., Amann R.,
RA   Reinhardt R.;
RT   "Complete genome sequence of the marine planctomycete Pirellula sp. strain
RT   1.";
RL   Proc. Natl. Acad. Sci. U.S.A. 100:8298-8303(2003).
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; BX294145; CAD75101.1; -; Genomic_DNA.
DR   RefSeq; NP_867554.1; NC_005027.1.
DR   RefSeq; WP_011121180.1; NC_005027.1.
DR   AlphaFoldDB; Q7UPG1; -.
DR   SMR; Q7UPG1; -.
DR   STRING; 243090.RB6963; -.
DR   EnsemblBacteria; CAD75101; CAD75101; RB6963.
DR   KEGG; rba:RB6963; -.
DR   PATRIC; fig|243090.15.peg.3371; -.
DR   eggNOG; COG0820; Bacteria.
DR   HOGENOM; CLU_029101_0_2_0; -.
DR   InParanoid; Q7UPG1; -.
DR   OMA; RIFFEWT; -.
DR   OrthoDB; 1111428at2; -.
DR   Proteomes; UP000001025; 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:0070475; P:rRNA base methylation; IBA:GO_Central.
DR   GO; GO:0030488; P:tRNA methylation; IBA:GO_Central.
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   SFLD; SFLDS00029; Radical_SAM; 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..379
FT                   /note="Probable RNA methyltransferase RB6963"
FT                   /id="PRO_0000350366"
FT   DOMAIN          96..332
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        335
FT                   /note="S-methylcysteine intermediate"
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         114
FT                   /ligand="[4Fe-4S] cluster"
FT                   /ligand_id="ChEBI:CHEBI:49883"
FT                   /ligand_note="4Fe-4S-S-AdoMet"
FT                   /evidence="ECO:0000250"
FT   BINDING         117
FT                   /ligand="[4Fe-4S] cluster"
FT                   /ligand_id="ChEBI:CHEBI:49883"
FT                   /ligand_note="4Fe-4S-S-AdoMet"
FT                   /evidence="ECO:0000250"
FT   BINDING         160..161
FT                   /ligand="S-adenosyl-L-methionine"
FT                   /ligand_id="ChEBI:CHEBI:59789"
FT                   /evidence="ECO:0000250"
FT   BINDING         192
FT                   /ligand="S-adenosyl-L-methionine"
FT                   /ligand_id="ChEBI:CHEBI:59789"
FT                   /evidence="ECO:0000250"
FT   BINDING         215..217
FT                   /ligand="S-adenosyl-L-methionine"
FT                   /ligand_id="ChEBI:CHEBI:59789"
FT                   /evidence="ECO:0000250"
FT   BINDING         291
FT                   /ligand="S-adenosyl-L-methionine"
FT                   /ligand_id="ChEBI:CHEBI:59789"
FT                   /evidence="ECO:0000250"
FT   DISULFID        103..335
FT                   /note="(transient)"
FT                   /evidence="ECO:0000250"
SQ   SEQUENCE   379 AA;  42264 MW;  AE137ADA6C57550D CRC64;
     MTAAPASVRL FQTHEMEALR RDRRLDPQVF RKLRNDLLKK FESDEAVLEK YPVAEAIELH
     SLKLYQRMDS EIDGATKLLF ETESGMLIES VILRIATGRT TLCVSSQIGC AAACDFCATG
     KMGIAKNLAT EEILDQVVQA GQILRGEDRR LSNIVFMGMG EPLHNEVNVT EAIELLTAPD
     HFARSPSTVL VSTVGVPAGM LRLAKRFPNL NLALSLHSAD QTTREKIIPL GKKASLAQLH
     DAIHEIQTIQ DREFMIEYLM LRDVNDSAKD ADRLIDWIGD LRVHVNLIPY NTIEASPHLH
     ASSRPVIESF ADILKASGLK TTVRYSLGND IEAACGQLIR QENRQRAMQA RRTESESDSH
     VGFLDVRQVV DGLESQKNK