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-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=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 (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; 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; ALTIRHM; -.
DR ProtClustDB; PRK13168; -.
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: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; IPR002792; TRAM_dom.
DR InterPro; IPR010280; U5_MeTrfase.
DR Pfam; PF01938; TRAM; 1.
DR Pfam; PF05958; tRNA_U5-meth_tr; 1.
DR SUPFAM; SSF50249; Nucleic_acid_OB; 1.
DR TIGRFAMs; TIGR00479; rumA; 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; rRNA processing; S-adenosyl-L-methionine;
KW Transferase.
FT CHAIN 1 450 23S rRNA (uracil(1939)-C(5))-
FT methyltransferase RlmD.
FT /FTId=PRO_0000229876.
FT DOMAIN 20 78 TRAM.
FT ACT_SITE 407 407 Nucleophile (By similarity).
FT METAL 91 91 Iron-sulfur (4Fe-4S) (By similarity).
FT METAL 97 97 Iron-sulfur (4Fe-4S) (By similarity).
FT METAL 100 100 Iron-sulfur (4Fe-4S) (By similarity).
FT METAL 179 179 Iron-sulfur (4Fe-4S) (By similarity).
FT BINDING 283 283 S-adenosyl-L-methionine (By similarity).
FT BINDING 312 312 S-adenosyl-L-methionine; via carbonyl
FT oxygen (By similarity).
FT BINDING 317 317 S-adenosyl-L-methionine (By similarity).
FT BINDING 333 333 S-adenosyl-L-methionine (By similarity).
FT BINDING 360 360 S-adenosyl-L-methionine (By similarity).
FT BINDING 381 381 S-adenosyl-L-methionine (By similarity).
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
//
