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Database: UniProt
Entry: Q128S1
LinkDB: Q128S1
Original site: Q128S1 
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   11-JUN-2014, entry version 58.
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 class I-like SAM-binding
CC       methyltransferase superfamily. RNA M5U methyltransferase family.
CC       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; RVIDWFC; -.
DR   OrthoDB; EOG6V4GKM; -.
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: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; IPR010280; U5_MeTrfase_fam.
DR   Pfam; PF05958; tRNA_U5-meth_tr; 2.
DR   SUPFAM; SSF50249; SSF50249; 1.
DR   SUPFAM; SSF53335; SSF53335; 2.
DR   PROSITE; PS51687; SAM_MT_RNA_M5U; 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    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
//
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