ID   RLMD_PARXL              Reviewed;         472 AA.
AC   Q13Z67;
DT   03-APR-2007, integrated into UniProtKB/Swiss-Prot.
DT   03-APR-2007, sequence version 2.
DT   03-AUG-2022, entry version 95.
DE   RecName: Full=23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD {ECO:0000255|HAMAP-Rule:MF_01010};
DE            EC=2.1.1.190 {ECO:0000255|HAMAP-Rule:MF_01010};
DE   AltName: Full=23S rRNA(m5U1939)-methyltransferase {ECO:0000255|HAMAP-Rule:MF_01010};
GN   Name=rlmD {ECO:0000255|HAMAP-Rule:MF_01010}; Synonyms=rumA;
GN   OrderedLocusNames=Bxeno_A2084; ORFNames=Bxe_A2348;
OS   Paraburkholderia xenovorans (strain LB400).
OC   Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales;
OC   Burkholderiaceae; Paraburkholderia.
OX   NCBI_TaxID=266265;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=LB400;
RX   PubMed=17030797; DOI=10.1073/pnas.0606924103;
RA   Chain P.S.G., Denef V.J., Konstantinidis K.T., Vergez L.M., Agullo L.,
RA   Reyes V.L., Hauser L., Cordova M., Gomez L., Gonzalez M., Land M., Lao V.,
RA   Larimer F., LiPuma J.J., Mahenthiralingam E., Malfatti S.A., Marx C.J.,
RA   Parnell J.J., Ramette A., Richardson P., Seeger M., Smith D., Spilker T.,
RA   Sul W.J., Tsoi T.V., Ulrich L.E., Zhulin I.B., Tiedje J.M.;
RT   "Burkholderia xenovorans LB400 harbors a multi-replicon, 9.73-Mbp genome
RT   shaped for versatility.";
RL   Proc. Natl. Acad. Sci. U.S.A. 103:15280-15287(2006).
CC   -!- FUNCTION: Catalyzes the formation of 5-methyl-uridine at position 1939
CC       (m5U1939) in 23S rRNA. {ECO:0000255|HAMAP-Rule:MF_01010}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=S-adenosyl-L-methionine + uridine(1939) in 23S rRNA = 5-
CC         methyluridine(1939) in 23S rRNA + H(+) + S-adenosyl-L-homocysteine;
CC         Xref=Rhea:RHEA:42908, Rhea:RHEA-COMP:10278, Rhea:RHEA-COMP:10279,
CC         ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC         ChEBI:CHEBI:65315, ChEBI:CHEBI:74447; EC=2.1.1.190;
CC         Evidence={ECO:0000255|HAMAP-Rule:MF_01010};
CC   -!- SIMILARITY: Belongs to the class I-like SAM-binding methyltransferase
CC       superfamily. RNA M5U methyltransferase family. RlmD subfamily.
CC       {ECO:0000255|HAMAP-Rule:MF_01010}.
CC   -!- SEQUENCE CAUTION:
CC       Sequence=ABE30622.1; Type=Erroneous initiation; Evidence={ECO:0000305};
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DR   EMBL; CP000270; ABE30622.1; ALT_INIT; Genomic_DNA.
DR   RefSeq; WP_011488254.1; NZ_CP008760.1.
DR   AlphaFoldDB; Q13Z67; -.
DR   SMR; Q13Z67; -.
DR   STRING; 266265.Bxe_A2348; -.
DR   EnsemblBacteria; ABE30622; ABE30622; Bxe_A2348.
DR   KEGG; bxb:DR64_52; -.
DR   KEGG; bxe:Bxe_A2348; -.
DR   PATRIC; fig|266265.5.peg.2180; -.
DR   eggNOG; COG2265; Bacteria.
DR   OMA; FYAGDMK; -.
DR   OrthoDB; 1421660at2; -.
DR   Proteomes; UP000001817; Chromosome 1.
DR   GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IEA:UniProtKB-KW.
DR   GO; GO:0005506; F:iron ion binding; IEA:UniProtKB-UniRule.
DR   GO; GO:0003723; F:RNA binding; IEA:InterPro.
DR   GO; GO:0070041; F:rRNA (uridine-C5-)-methyltransferase activity; IEA:UniProtKB-UniRule.
DR   Gene3D; 2.40.50.140; -; 1.
DR   Gene3D; 3.40.50.150; -; 1.
DR   HAMAP; MF_01010; 23SrRNA_methyltr_RlmD; 1.
DR   InterPro; IPR001566; 23S_rRNA_MeTrfase_RlmD.
DR   InterPro; IPR030391; MeTrfase_TrmA_CS.
DR   InterPro; IPR012340; NA-bd_OB-fold.
DR   InterPro; IPR029063; SAM-dependent_MTases_sf.
DR   InterPro; IPR002792; TRAM_dom.
DR   InterPro; IPR010280; U5_MeTrfase_fam.
DR   PANTHER; PTHR11061; PTHR11061; 1.
DR   Pfam; PF05958; tRNA_U5-meth_tr; 1.
DR   SUPFAM; SSF50249; SSF50249; 1.
DR   SUPFAM; SSF53335; SSF53335; 1.
DR   PROSITE; PS51687; SAM_MT_RNA_M5U; 1.
DR   PROSITE; PS50926; TRAM; 1.
DR   PROSITE; PS01231; TRMA_2; 1.
PE   3: Inferred from homology;
KW   4Fe-4S; Iron; Iron-sulfur; Metal-binding; Methyltransferase;
KW   Reference proteome; rRNA processing; S-adenosyl-L-methionine; Transferase.
FT   CHAIN           1..472
FT                   /note="23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD"
FT                   /id="PRO_0000282036"
FT   DOMAIN          23..87
FT                   /note="TRAM"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01010"
FT   REGION          1..23
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   ACT_SITE        428
FT                   /note="Nucleophile"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01010"
FT   BINDING         100
FT                   /ligand="[4Fe-4S] cluster"
FT                   /ligand_id="ChEBI:CHEBI:49883"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01010"
FT   BINDING         106
FT                   /ligand="[4Fe-4S] cluster"
FT                   /ligand_id="ChEBI:CHEBI:49883"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01010"
FT   BINDING         109
FT                   /ligand="[4Fe-4S] cluster"
FT                   /ligand_id="ChEBI:CHEBI:49883"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01010"
FT   BINDING         188
FT                   /ligand="[4Fe-4S] cluster"
FT                   /ligand_id="ChEBI:CHEBI:49883"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01010"
FT   BINDING         296
FT                   /ligand="S-adenosyl-L-methionine"
FT                   /ligand_id="ChEBI:CHEBI:59789"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01010"
FT   BINDING         325
FT                   /ligand="S-adenosyl-L-methionine"
FT                   /ligand_id="ChEBI:CHEBI:59789"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01010"
FT   BINDING         330
FT                   /ligand="S-adenosyl-L-methionine"
FT                   /ligand_id="ChEBI:CHEBI:59789"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01010"
FT   BINDING         346
FT                   /ligand="S-adenosyl-L-methionine"
FT                   /ligand_id="ChEBI:CHEBI:59789"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01010"
FT   BINDING         374
FT                   /ligand="S-adenosyl-L-methionine"
FT                   /ligand_id="ChEBI:CHEBI:59789"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01010"
FT   BINDING         395
FT                   /ligand="S-adenosyl-L-methionine"
FT                   /ligand_id="ChEBI:CHEBI:59789"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01010"
SQ   SEQUENCE   472 AA;  52414 MW;  6EF5D2A341C1624F CRC64;
     MSRTAPHRRA PKRYKTPPPA PAHVVTGNEP VIEIISLDME ARGVGRTETE DGTPGKVIFV
     EGVLPGERVS YSTHRSKPKF EQAEVVQVLR ESVMRTKPKC TYFDICGGCS MQHLDIRAQV
     AVKQRVLEDN LQHLAKLRPE TVFRPIHGPS WGYRYRARLA VRFLPEKGGM RIGFHEKKSS
     YIADMKTCEV LPPHVSAMLM PLRFMVRKLS IYDRMPQLEL AVGSSVTALV VRNLEPITAA
     DEQVLRDFAD EHKVQFWLQP GGPDTVTPFY PLDVQLDYTL PEYGIRMPFK PTDFTQVNHA
     INRVLVSRAL RLLAPARTDR VLDLFCGIGN FTLPLARISK EVMGIEGSEV LTSRALANAG
     LNGVAGHTSF ECRNLFEVTA DDLRALGHFD KFLIDPPREG ALAVAKALAE IARSGNGPLP
     KRIVYVSCAP ATLARDAGLL VHEAGYRLVG AGVVNMFPHT SHVESIALFE RD