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RLMD_ALCBS
ID   RLMD_ALCBS              Reviewed;         445 AA.
AC   Q0VP26;
DT   03-APR-2007, integrated into UniProtKB/Swiss-Prot.
DT   05-SEP-2006, sequence version 1.
DT   03-AUG-2022, entry version 91.
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=ABO_1624;
OS   Alcanivorax borkumensis (strain ATCC 700651 / DSM 11573 / NCIMB 13689 /
OS   SK2).
OC   Bacteria; Proteobacteria; Gammaproteobacteria; Oceanospirillales;
OC   Alcanivoracaceae; Alcanivorax.
OX   NCBI_TaxID=393595;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 700651 / DSM 11573 / NCIMB 13689 / SK2;
RX   PubMed=16878126; DOI=10.1038/nbt1232;
RA   Schneiker S., Martins dos Santos V.A.P., Bartels D., Bekel T., Brecht M.,
RA   Buhrmester J., Chernikova T.N., Denaro R., Ferrer M., Gertler C.,
RA   Goesmann A., Golyshina O.V., Kaminski F., Khachane A.N., Lang S., Linke B.,
RA   McHardy A.C., Meyer F., Nechitaylo T., Puehler A., Regenhardt D., Rupp O.,
RA   Sabirova J.S., Selbitschka W., Yakimov M.M., Timmis K.N., Vorhoelter F.-J.,
RA   Weidner S., Kaiser O., Golyshin P.N.;
RT   "Genome sequence of the ubiquitous hydrocarbon-degrading marine bacterium
RT   Alcanivorax borkumensis.";
RL   Nat. Biotechnol. 24:997-1004(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}.
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DR   EMBL; AM286690; CAL17072.1; -; Genomic_DNA.
DR   RefSeq; WP_011588905.1; NC_008260.1.
DR   AlphaFoldDB; Q0VP26; -.
DR   SMR; Q0VP26; -.
DR   STRING; 393595.ABO_1624; -.
DR   PRIDE; Q0VP26; -.
DR   EnsemblBacteria; CAL17072; CAL17072; ABO_1624.
DR   KEGG; abo:ABO_1624; -.
DR   eggNOG; COG2265; Bacteria.
DR   HOGENOM; CLU_014689_8_2_6; -.
DR   OMA; FYAGDMK; -.
DR   OrthoDB; 1421660at2; -.
DR   Proteomes; UP000008871; Chromosome.
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; IPR030390; MeTrfase_TrmA_AS.
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; PS01230; TRMA_1; 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..445
FT                   /note="23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD"
FT                   /id="PRO_0000282027"
FT   DOMAIN          5..64
FT                   /note="TRAM"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01010"
FT   REGION          1..21
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   ACT_SITE        399
FT                   /note="Nucleophile"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01010"
FT   BINDING         77
FT                   /ligand="[4Fe-4S] cluster"
FT                   /ligand_id="ChEBI:CHEBI:49883"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01010"
FT   BINDING         83
FT                   /ligand="[4Fe-4S] cluster"
FT                   /ligand_id="ChEBI:CHEBI:49883"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01010"
FT   BINDING         86
FT                   /ligand="[4Fe-4S] cluster"
FT                   /ligand_id="ChEBI:CHEBI:49883"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01010"
FT   BINDING         165
FT                   /ligand="[4Fe-4S] cluster"
FT                   /ligand_id="ChEBI:CHEBI:49883"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01010"
FT   BINDING         275
FT                   /ligand="S-adenosyl-L-methionine"
FT                   /ligand_id="ChEBI:CHEBI:59789"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01010"
FT   BINDING         304
FT                   /ligand="S-adenosyl-L-methionine"
FT                   /ligand_id="ChEBI:CHEBI:59789"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01010"
FT   BINDING         309
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         352
FT                   /ligand="S-adenosyl-L-methionine"
FT                   /ligand_id="ChEBI:CHEBI:59789"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01010"
FT   BINDING         373
FT                   /ligand="S-adenosyl-L-methionine"
FT                   /ligand_id="ChEBI:CHEBI:59789"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01010"
SQ   SEQUENCE   445 AA;  49770 MW;  89FCF1329BDADF03 CRC64;
     MARRRKQLPE TPEPASIETL SHDGRGIARR DGKTTFIDNA LPGEEVMFKF TYMRRKFDEG
     KAVEIVTASP DRVTPPCEHS TLCGGCSLQH MSPEVQVSRK QAVLREQLAH FGGLEPEEWL
     APLTGPVTGY RSKARMGVKY VEAKGETLVG FREKRNSFIA QLHTCEVLIP DVGHRIDELR
     TLMHGLESRS RIPQIELAAG DDDVALIIRH LDPLSEADQQ ALLGFCQNLG WHCYLQPGNE
     STVHRIWPQE GEQRLYYKHP SAGVELAFHP TDFTQVNAEI NRKMVPLALD LLDISPDHTV
     LDLFCGLGNF TIPAAKRAGK VVGVEVSQAM VERGYENARR NSLENLEFHA WDLSQDVSGQ
     AWARQTYDRI LIDPPRTGAL EMVKLMPRLG ASKIVYVSCN PATLARDAGE LMALGYRLKA
     AGVMDMFPHT THVESIAVFE KMKKK
 
 
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