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Database: UniProt
Entry: Q7N839
LinkDB: Q7N839
Original site: Q7N839 
ID   RLMD_PHOLL              Reviewed;         438 AA.
AC   Q7N839;
DT   19-JUL-2004, integrated into UniProtKB/Swiss-Prot.
DT   15-DEC-2003, sequence version 1.
DT   01-OCT-2014, entry version 67.
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=plu0909;
OS   Photorhabdus luminescens subsp. laumondii (strain TT01).
OC   Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales;
OC   Enterobacteriaceae; Photorhabdus.
OX   NCBI_TaxID=243265;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=TT01;
RX   PubMed=14528314; DOI=10.1038/nbt886;
RA   Duchaud E., Rusniok C., Frangeul L., Buchrieser C., Givaudan A.,
RA   Taourit S., Bocs S., Boursaux-Eude C., Chandler M., Charles J.-F.,
RA   Dassa E., Derose R., Derzelle S., Freyssinet G., Gaudriault S.,
RA   Medigue C., Lanois A., Powell K., Siguier P., Vincent R., Wingate V.,
RA   Zouine M., Glaser P., Boemare N., Danchin A., Kunst F.;
RT   "The genome sequence of the entomopathogenic bacterium Photorhabdus
RT   luminescens.";
RL   Nat. Biotechnol. 21:1307-1313(2003).
CC   -!- FUNCTION: Catalyzes the formation of 5-methyl-uridine at position
CC       1939 (m5U1939) in 23S rRNA. {ECO:0000255|HAMAP-Rule:MF_01010}.
CC   -!- CATALYTIC ACTIVITY: S-adenosyl-L-methionine + uracil(1939) in 23S
CC       rRNA = S-adenosyl-L-homocysteine + 5-methyluracil(1939) in 23S
CC       rRNA. {ECO:0000255|HAMAP-Rule:MF_01010}.
CC   -!- SIMILARITY: Belongs to the class I-like SAM-binding
CC       methyltransferase superfamily. RNA M5U methyltransferase family.
CC       RlmD subfamily. {ECO:0000255|HAMAP-Rule:MF_01010}.
CC   -!- SIMILARITY: Contains 1 TRAM domain. {ECO:0000255|HAMAP-
CC       Rule:MF_01010}.
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DR   EMBL; BX571862; CAE13204.1; -; Genomic_DNA.
DR   RefSeq; NP_928245.1; NC_005126.1.
DR   ProteinModelPortal; Q7N839; -.
DR   SMR; Q7N839; 16-438.
DR   STRING; 243265.plu0909; -.
DR   EnsemblBacteria; CAE13204; CAE13204; plu0909.
DR   GeneID; 2800872; -.
DR   KEGG; plu:plu0909; -.
DR   PATRIC; 20505455; VBIPhoLum48522_1001.
DR   GenoList; plu0909; -.
DR   eggNOG; COG2265; -.
DR   HOGENOM; HOG000029868; -.
DR   KO; K03215; -.
DR   OMA; DFIQVND; -.
DR   OrthoDB; EOG6V4GKM; -.
DR   GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IEA:UniProtKB-KW.
DR   GO; GO:0005506; F:iron ion binding; IEA:UniProtKB-HAMAP.
DR   GO; GO:0003723; F:RNA binding; IEA:InterPro.
DR   GO; GO:0070041; F:rRNA (uridine-C5-)-methyltransferase activity; IEA:UniProtKB-HAMAP.
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; IPR012340; NA-bd_OB-fold.
DR   InterPro; IPR029063; SAM-dependent_MTases-like.
DR   InterPro; IPR002792; TRAM_dom.
DR   InterPro; IPR010280; U5_MeTrfase_fam.
DR   Pfam; PF01938; TRAM; 1.
DR   Pfam; PF05958; tRNA_U5-meth_tr; 1.
DR   SUPFAM; SSF50249; SSF50249; 1.
DR   SUPFAM; SSF53335; SSF53335; 1.
DR   TIGRFAMs; TIGR00479; rumA; 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; Complete proteome; Iron; Iron-sulfur; Metal-binding;
KW   Methyltransferase; Reference proteome; rRNA processing;
KW   S-adenosyl-L-methionine; Transferase.
FT   CHAIN         1    438       23S rRNA (uracil(1939)-C(5))-
FT                                methyltransferase RlmD.
FT                                /FTId=PRO_0000161905.
FT   DOMAIN        9     68       TRAM. {ECO:0000255|HAMAP-Rule:MF_01010}.
FT   ACT_SITE    396    396       Nucleophile. {ECO:0000255|HAMAP-
FT                                Rule:MF_01010}.
FT   METAL        81     81       Iron-sulfur (4Fe-4S). {ECO:0000255|HAMAP-
FT                                Rule:MF_01010}.
FT   METAL        87     87       Iron-sulfur (4Fe-4S). {ECO:0000255|HAMAP-
FT                                Rule:MF_01010}.
FT   METAL        90     90       Iron-sulfur (4Fe-4S). {ECO:0000255|HAMAP-
FT                                Rule:MF_01010}.
FT   METAL       168    168       Iron-sulfur (4Fe-4S). {ECO:0000255|HAMAP-
FT                                Rule:MF_01010}.
FT   BINDING     272    272       S-adenosyl-L-methionine.
FT                                {ECO:0000255|HAMAP-Rule:MF_01010}.
FT   BINDING     301    301       S-adenosyl-L-methionine; via carbonyl
FT                                oxygen. {ECO:0000255|HAMAP-
FT                                Rule:MF_01010}.
FT   BINDING     306    306       S-adenosyl-L-methionine.
FT                                {ECO:0000255|HAMAP-Rule:MF_01010}.
FT   BINDING     322    322       S-adenosyl-L-methionine.
FT                                {ECO:0000255|HAMAP-Rule:MF_01010}.
FT   BINDING     349    349       S-adenosyl-L-methionine.
FT                                {ECO:0000255|HAMAP-Rule:MF_01010}.
FT   BINDING     370    370       S-adenosyl-L-methionine.
FT                                {ECO:0000255|HAMAP-Rule:MF_01010}.
SQ   SEQUENCE   438 AA;  49080 MW;  AA323B6ACF6BB2A9 CRC64;
     MVQFYSPNRR TVNRHIITVT ADNLDAQGQG VARHQGKTIF VAGLLPGEQA QVQLTEEKRQ
     FAKAKLVKRL SDSPYRVNPR CPHFGVCGGC QQQHVAPDLQ RESKASVLEH LIRRETGVTV
     SAKPVILGPE YGYRRRARLG LHYQIKQRQL VIGFRQNQSN ELVAIKECPV LRPELEQLLQ
     PLSQCLNSLK AVKRLGHVEL VLADNGPLMI LRHLDPLKRE DKEKLGTFSV QHNVAVYLAA
     DETSLESLNE LPEPWYQVDG LKLVFSPRDF IQVNDQVNQQ MVAQAIEWLD LQPNDNVLDL
     FCGMGNFTLP IGRIVQSVVG VEGVATLVAN GQYNAKINNL DNISFCHENL EADIHHQPWA
     KLGFNKVLLD PARAGAVGVM SHIVELVPEK VVYVSCNPTT LARDSKILLE AGYQIISVRM
     LDMFPHTGHL ESMALFSR
//
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