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Database: UniProt
Entry: A1VQF1
LinkDB: A1VQF1
Original site: A1VQF1 
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-OCT-2014, entry version 55.
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=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. {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; 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; RVIDWFC; -.
DR   OrthoDB; EOG6V4GKM; -.
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: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   TIGRFAMs; TIGR00479; rumA; 1.
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; Reference proteome; rRNA processing;
KW   S-adenosyl-L-methionine; Transferase.
FT   CHAIN         1    490       23S rRNA (uracil(1939)-C(5))-
FT                                methyltransferase RlmD.
FT                                /FTId=PRO_1000148880.
FT   DOMAIN       14     75       TRAM. {ECO:0000255|HAMAP-Rule:MF_01010}.
FT   ACT_SITE    446    446       Nucleophile. {ECO:0000255|HAMAP-
FT                                Rule:MF_01010}.
FT   METAL        88     88       Iron-sulfur (4Fe-4S). {ECO:0000255|HAMAP-
FT                                Rule:MF_01010}.
FT   METAL        98     98       Iron-sulfur (4Fe-4S). {ECO:0000255|HAMAP-
FT                                Rule:MF_01010}.
FT   METAL       101    101       Iron-sulfur (4Fe-4S). {ECO:0000255|HAMAP-
FT                                Rule:MF_01010}.
FT   METAL       180    180       Iron-sulfur (4Fe-4S). {ECO:0000255|HAMAP-
FT                                Rule:MF_01010}.
FT   BINDING     289    289       S-adenosyl-L-methionine.
FT                                {ECO:0000255|HAMAP-Rule:MF_01010}.
FT   BINDING     318    318       S-adenosyl-L-methionine; via carbonyl
FT                                oxygen. {ECO:0000255|HAMAP-
FT                                Rule:MF_01010}.
FT   BINDING     323    323       S-adenosyl-L-methionine.
FT                                {ECO:0000255|HAMAP-Rule:MF_01010}.
FT   BINDING     339    339       S-adenosyl-L-methionine.
FT                                {ECO:0000255|HAMAP-Rule:MF_01010}.
FT   BINDING     374    374       S-adenosyl-L-methionine.
FT                                {ECO:0000255|HAMAP-Rule:MF_01010}.
FT   BINDING     395    395       S-adenosyl-L-methionine.
FT                                {ECO:0000255|HAMAP-Rule:MF_01010}.
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
//
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