ID RLMD_POLNA Reviewed; 490 AA.
AC A1VQF1;
DT 28-JUL-2009, integrated into UniProtKB/Swiss-Prot.
DT 06-FEB-2007, sequence version 1.
DT 01-MAY-2013, entry version 48.
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=Pnap_2576;
OS Polaromonas naphthalenivorans (strain CJ2).
OC Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales;
OC Comamonadaceae; Polaromonas.
OX NCBI_TaxID=365044;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=CJ2;
RG US DOE Joint Genome Institute;
RA Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C.,
RA Glavina del Rio T., Hammon N., Israni S., Dalin E., Tice H.,
RA Pitluck S., Sims D.R., Brettin T., Bruce D., Han C., Tapia R.,
RA Brainard J., Schmutz J., Larimer F., Land M., Hauser L., Kyrpides N.,
RA Kim E., Madsen E.L., Richardson P.;
RT "Complete sequence of chromosome 1 of Polaromonas naphthalenivorans
RT CJ2.";
RL Submitted (DEC-2006) to the EMBL/GenBank/DDBJ databases.
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; CP000529; ABM37879.1; -; Genomic_DNA.
DR RefSeq; YP_982800.1; NC_008781.1.
DR ProteinModelPortal; A1VQF1; -.
DR STRING; 365044.Pnap_2576; -.
DR EnsemblBacteria; ABM37879; ABM37879; Pnap_2576.
DR GeneID; 4688529; -.
DR KEGG; pna:Pnap_2576; -.
DR PATRIC; 22949823; VBIPolNap76733_3444.
DR eggNOG; COG2265; -.
DR HOGENOM; HOG000029868; -.
DR KO; K03215; -.
DR OMA; YSIANSE; -.
DR ProtClustDB; PRK13168; -.
DR BioCyc; PNAP365044:GJ8X-2612-MONOMER; -.
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; IPR010280; U5_MeTrfase.
DR Pfam; PF05958; tRNA_U5-meth_tr; 2.
DR SUPFAM; SSF50249; Nucleic_acid_OB; 1.
DR TIGRFAMs; TIGR00479; rumA; 1.
DR PROSITE; PS50926; TRAM; FALSE_NEG.
DR PROSITE; PS01230; TRMA_1; FALSE_NEG.
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 1 490 23S rRNA (uracil(1939)-C(5))-
FT methyltransferase RlmD.
FT /FTId=PRO_1000148880.
FT DOMAIN 14 75 TRAM.
FT ACT_SITE 446 446 Nucleophile (By similarity).
FT METAL 88 88 Iron-sulfur (4Fe-4S) (By similarity).
FT METAL 98 98 Iron-sulfur (4Fe-4S) (By similarity).
FT METAL 101 101 Iron-sulfur (4Fe-4S) (By similarity).
FT METAL 180 180 Iron-sulfur (4Fe-4S) (By similarity).
FT BINDING 289 289 S-adenosyl-L-methionine (By similarity).
FT BINDING 318 318 S-adenosyl-L-methionine; via carbonyl
FT oxygen (By similarity).
FT BINDING 323 323 S-adenosyl-L-methionine (By similarity).
FT BINDING 339 339 S-adenosyl-L-methionine (By similarity).
FT BINDING 374 374 S-adenosyl-L-methionine (By similarity).
FT BINDING 395 395 S-adenosyl-L-methionine (By similarity).
SQ SEQUENCE 490 AA; 53770 MW; C0ABB81C779BA648 CRC64;
MIEETQTPSP PAPAPAPAEY PIDLLTVESL DIEAQGIAHR ADGKVVFIEG ALPFEQVTAN
VYRKKSSFEK ATLTAIYRES SQRVTPACPH FGMHTGACGG CKMQHLHIGA QVAVKQRVLE
DNLRFIGKVK ADNLLRPIEG PAWHYRYRAR LSVRYVRKKG TALVGFHERK SAYVADMTEC
HVVPQHVSDM LVPLRGLISS MDARETIPQI ELACGDDLTA MVLRHMEPLS VADLARLRAF
AAANAGLQWW VQSGGLDTVK LLDAQVAELS YGLPEFGITM PFKPTDFTQV NPHINQVLVS
RALRLLGVQP TERVIDWFCG LGNFTLPLAT RAREVLGIEG SEVLVARSRE NYERNKASSH
VRPALEATKF VARNLFEMTP AMLVKDGAAE KWLVDPPREG AFELFKSLAA LHQQVVTGVP
CDDGIHQQSL ALGGWTPPSR IVYVSCNPAT LARDAGVLVE GGGYRCTAAG VVNMFPHTAH
VESMAVFERL
//
