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Database: UniProt
Entry: Q4K898
LinkDB: Q4K898
Original site: Q4K898 
ID   RLMD_PSEF5              Reviewed;         450 AA.
AC   Q4K898;
DT   04-APR-2006, integrated into UniProtKB/Swiss-Prot.
DT   02-AUG-2005, sequence version 1.
DT   01-OCT-2014, entry version 59.
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=PFL_4447;
OS   Pseudomonas fluorescens (strain Pf-5 / ATCC BAA-477).
OC   Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales;
OC   Pseudomonadaceae; Pseudomonas.
OX   NCBI_TaxID=220664;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=Pf-5 / ATCC BAA-477;
RX   PubMed=15980861; DOI=10.1038/nbt1110;
RA   Paulsen I.T., Press C.M., Ravel J., Kobayashi D.Y., Myers G.S.A.,
RA   Mavrodi D.V., DeBoy R.T., Seshadri R., Ren Q., Madupu R., Dodson R.J.,
RA   Durkin A.S., Brinkac L.M., Daugherty S.C., Sullivan S.A.,
RA   Rosovitz M.J., Gwinn M.L., Zhou L., Schneider D.J., Cartinhour S.W.,
RA   Nelson W.C., Weidman J., Watkins K., Tran K., Khouri H., Pierson E.A.,
RA   Pierson L.S. III, Thomashow L.S., Loper J.E.;
RT   "Complete genome sequence of the plant commensal Pseudomonas
RT   fluorescens Pf-5.";
RL   Nat. Biotechnol. 23:873-878(2005).
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; CP000076; AAY93698.1; -; Genomic_DNA.
DR   RefSeq; YP_261535.1; NC_004129.6.
DR   ProteinModelPortal; Q4K898; -.
DR   STRING; 220664.PFL_4447; -.
DR   EnsemblBacteria; AAY93698; AAY93698; PFL_4447.
DR   GeneID; 3478566; -.
DR   KEGG; pfl:PFL_4447; -.
DR   PATRIC; 19878326; VBIPseFlu72549_4552.
DR   eggNOG; COG2265; -.
DR   HOGENOM; HOG000029868; -.
DR   KO; K03215; -.
DR   OMA; DFIQVND; -.
DR   OrthoDB; EOG6V4GKM; -.
DR   BioCyc; PFLU220664:GIX8-4482-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; IPR002792; TRAM_dom.
DR   InterPro; IPR010280; U5_MeTrfase_fam.
DR   Pfam; PF01938; TRAM; 1.
DR   Pfam; PF05958; tRNA_U5-meth_tr; 1.
DR   SUPFAM; SSF50249; SSF50249; 1.
DR   SUPFAM; SSF53335; SSF53335; 1.
DR   TIGRFAMs; TIGR00479; rumA; 1.
DR   PROSITE; PS51687; SAM_MT_RNA_M5U; 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; Reference proteome; rRNA processing;
KW   S-adenosyl-L-methionine; Transferase.
FT   CHAIN         1    450       23S rRNA (uracil(1939)-C(5))-
FT                                methyltransferase RlmD.
FT                                /FTId=PRO_0000229876.
FT   DOMAIN       20     78       TRAM. {ECO:0000255|HAMAP-Rule:MF_01010}.
FT   ACT_SITE    407    407       Nucleophile. {ECO:0000255|HAMAP-
FT                                Rule:MF_01010}.
FT   METAL        91     91       Iron-sulfur (4Fe-4S). {ECO:0000255|HAMAP-
FT                                Rule:MF_01010}.
FT   METAL        97     97       Iron-sulfur (4Fe-4S). {ECO:0000255|HAMAP-
FT                                Rule:MF_01010}.
FT   METAL       100    100       Iron-sulfur (4Fe-4S). {ECO:0000255|HAMAP-
FT                                Rule:MF_01010}.
FT   METAL       179    179       Iron-sulfur (4Fe-4S). {ECO:0000255|HAMAP-
FT                                Rule:MF_01010}.
FT   BINDING     283    283       S-adenosyl-L-methionine.
FT                                {ECO:0000255|HAMAP-Rule:MF_01010}.
FT   BINDING     312    312       S-adenosyl-L-methionine; via carbonyl
FT                                oxygen. {ECO:0000255|HAMAP-
FT                                Rule:MF_01010}.
FT   BINDING     317    317       S-adenosyl-L-methionine.
FT                                {ECO:0000255|HAMAP-Rule:MF_01010}.
FT   BINDING     333    333       S-adenosyl-L-methionine.
FT                                {ECO:0000255|HAMAP-Rule:MF_01010}.
FT   BINDING     360    360       S-adenosyl-L-methionine.
FT                                {ECO:0000255|HAMAP-Rule:MF_01010}.
FT   BINDING     381    381       S-adenosyl-L-methionine.
FT                                {ECO:0000255|HAMAP-Rule:MF_01010}.
SQ   SEQUENCE   450 AA;  49118 MW;  FE3C683D8B209F3E CRC64;
     MAKHDRGLRF QPAGGSRAPQ IPVGKKQRLT IQRLANDGRG IAFVEGRTWF VSGALAGEEV
     EARVLGSHGK VVEARAERIF NASDLRRPAA CAHAGRCGGC SVQHLPHDEQ LALKQRMLAE
     QLSKVAGVEP EAWAAPLSGP EFGYRRRARV AVRWDAKGKQ LEVGFRAAGS QDIVAIDDCP
     VLVQALQPVM NRLPAMLRRL SKPQALGHVE LFSGSALAVL LRHMAPLSDS DLTILKDFCD
     FHQAQLWLHG EGEPQPFDPS QALGYRLETW DLHLAYRPGD FVQVNAGVNE AMVAQALEWL
     APQADERVLD LFCGLGNFAL PLARQVREVV AVEGVATMVA RAAENAASNN LHNTRFFQAD
     LSQPLSAAEW ADEGFSAVLL DPPRDGAFEV VRQLATLGAK RLVYVSCNPA TLARDTVELI
     KQGYRLKRAG ILDMFPQTAH VEAMALFEAS
//
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