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-MAY-2013, entry version 60.
DE RecName: Full=23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD;
DE EC=2.1.1.190;
DE AltName: Full=23S rRNA(m5U1939)-methyltransferase;
GN Name=rlmD; Synonyms=rumA; 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 (By similarity).
CC -!- CATALYTIC ACTIVITY: S-adenosyl-L-methionine + uracil(1939) in 23S
CC rRNA = S-adenosyl-L-homocysteine + 5-methyluracil(1939) in 23S
CC rRNA.
CC -!- SIMILARITY: Belongs to the methyltransferase superfamily. RNA M5U
CC methyltransferase family. RlmD subfamily.
CC -!- SIMILARITY: Contains 1 TRAM domain.
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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; YSPNRRT; -.
DR ProtClustDB; PRK13168; -.
DR GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IEA:UniProtKB-KW.
DR GO; GO:0005506; F:iron ion binding; IEA:HAMAP.
DR GO; GO:0003723; F:RNA binding; IEA:InterPro.
DR GO; GO:0070041; F:rRNA (uridine-C5-)-methyltransferase activity; IEA:HAMAP.
DR Gene3D; 2.40.50.140; -; 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; IPR002792; TRAM_dom.
DR InterPro; IPR010280; U5_MeTrfase.
DR Pfam; PF01938; TRAM; 1.
DR Pfam; PF05958; tRNA_U5-meth_tr; 1.
DR SUPFAM; SSF50249; Nucleic_acid_OB; 1.
DR TIGRFAMs; TIGR00479; rumA; 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; rRNA processing; S-adenosyl-L-methionine;
KW Transferase.
FT CHAIN 1 438 23S rRNA (uracil(1939)-C(5))-
FT methyltransferase RlmD.
FT /FTId=PRO_0000161905.
FT DOMAIN 9 68 TRAM.
FT ACT_SITE 396 396 Nucleophile (By similarity).
FT METAL 81 81 Iron-sulfur (4Fe-4S) (By similarity).
FT METAL 87 87 Iron-sulfur (4Fe-4S) (By similarity).
FT METAL 90 90 Iron-sulfur (4Fe-4S) (By similarity).
FT METAL 168 168 Iron-sulfur (4Fe-4S) (By similarity).
FT BINDING 272 272 S-adenosyl-L-methionine (By similarity).
FT BINDING 301 301 S-adenosyl-L-methionine; via carbonyl
FT oxygen (By similarity).
FT BINDING 306 306 S-adenosyl-L-methionine (By similarity).
FT BINDING 322 322 S-adenosyl-L-methionine (By similarity).
FT BINDING 349 349 S-adenosyl-L-methionine (By similarity).
FT BINDING 370 370 S-adenosyl-L-methionine (By similarity).
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
//
