ID RLMD_POLSJ Reviewed; 486 AA.
AC Q128S1;
DT 03-APR-2007, integrated into UniProtKB/Swiss-Prot.
DT 22-AUG-2006, sequence version 1.
DT 01-MAY-2013, entry version 52.
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=Bpro_3057;
OS Polaromonas sp. (strain JS666 / ATCC BAA-500).
OC Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales;
OC Comamonadaceae; Polaromonas.
OX NCBI_TaxID=296591;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=JS666 / ATCC BAA-500;
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., Brettin T., Bruce D., Han C., Tapia R., Munk A.C.,
RA Gilna P., Schmutz J., Larimer F., Land M., Hauser L., Kyrpides N.,
RA Anderson I., Richardson P.;
RT "Complete sequence of chromosome of Polaromonas sp. JS666.";
RL Submitted (APR-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; CP000316; ABE44971.1; -; Genomic_DNA.
DR RefSeq; YP_549869.1; NC_007948.1.
DR ProteinModelPortal; Q128S1; -.
DR STRING; 296591.Bpro_3057; -.
DR EnsemblBacteria; ABE44971; ABE44971; Bpro_3057.
DR GeneID; 4014287; -.
DR KEGG; pol:Bpro_3057; -.
DR PATRIC; 22959306; VBIPolSp102244_3110.
DR eggNOG; COG2265; -.
DR HOGENOM; HOG000029868; -.
DR KO; K03215; -.
DR OMA; YSIANSE; -.
DR ProtClustDB; PRK13168; -.
DR BioCyc; PSP296591:GHI4-3778-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 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 1 486 23S rRNA (uracil(1939)-C(5))-
FT methyltransferase RlmD.
FT /FTId=PRO_0000282050.
FT DOMAIN 10 71 TRAM.
FT ACT_SITE 442 442 Nucleophile (By similarity).
FT METAL 84 84 Iron-sulfur (4Fe-4S) (By similarity).
FT METAL 94 94 Iron-sulfur (4Fe-4S) (By similarity).
FT METAL 97 97 Iron-sulfur (4Fe-4S) (By similarity).
FT METAL 176 176 Iron-sulfur (4Fe-4S) (By similarity).
FT BINDING 285 285 S-adenosyl-L-methionine (By similarity).
FT BINDING 314 314 S-adenosyl-L-methionine; via carbonyl
FT oxygen (By similarity).
FT BINDING 319 319 S-adenosyl-L-methionine (By similarity).
FT BINDING 335 335 S-adenosyl-L-methionine (By similarity).
FT BINDING 370 370 S-adenosyl-L-methionine (By similarity).
FT BINDING 391 391 S-adenosyl-L-methionine (By similarity).
SQ SEQUENCE 486 AA; 53838 MW; 3D7E043438169856 CRC64;
MTDEKLNDHT VKAPEYLPDI LTVESLDMEA QGIAHRADGK VVFIEGALPF ERVTANVYRK
KSSFEKAVVM AIHRESSQRV RPACPHFGLH TGACGGCKMQ HLHVGAQVAV KQRVLEDNLW
HIGKVKADNL LRPIEGPAWG YRYRARLSVR YVRKKNAVLV GFHERKSSYV ADMTECHVVP
RHVSDMLVPL RELIAGMDAR ETLPQIELAC GDTVTAMVLR HMEPLSSGDL ARLRAFAVSH
PGLQWWLQPG GLDSVKLLDE GVPELSYDLP EFGITMPFKP TDFTQVNPHI NQVLVSRALR
LLAVQPHERV IDWFCGLGNF TLPLATCARE VLGIEGSEAL VARSCQNFKK NQPASQSRSA
LSATEFVARN LFEMTPAMLV KDGMADKWLV DPPREGAFEL FKSLAALHQQ MVTGVPCDDG
EQQQSLVLGD WTPPQRIVYV SCNPATLARD AGVLVESGAY RCTLAGVVNM FPHTAHVESI
AVFERG
//
