Q4K898 (RLMD_PSEF5) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD
EC=2.1.1.190

Alternative name(s):
23S rRNA(m5U1939)-methyltransferase

Gene names

Name:	rlmD
Synonyms:	rumA
Ordered Locus Names:	PFL_4447

Organism

Pseudomonas fluorescens (strain Pf-5 / ATCC BAA-477) [Complete proteome] [HAMAP]

Taxonomic identifier

220664 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › Gammaproteobacteria › Pseudomonadales › Pseudomonadaceae › Pseudomonas › Pseudomonas fluorescens group › Pseudomonas protegens

Protein attributes

Sequence length	450 AA.
Sequence status	Complete.
Protein existence	Inferred from homology

General annotation (Comments)

Function	Catalyzes the formation of 5-methyl-uridine at position 1939 (m5U1939) in 23S rRNA By similarity. HAMAP-Rule MF_01010
Catalytic activity	S-adenosyl-L-methionine + uracil(1939) in 23S rRNA = S-adenosyl-L-homocysteine + 5-methyluracil(1939) in 23S rRNA. HAMAP-Rule MF_01010
Sequence similarities	Belongs to the methyltransferase superfamily. RNA M5U methyltransferase family. RlmD subfamily. Contains 1 TRAM domain.

Ontologies

Keywords
Biological process	rRNA processing
Ligand	4Fe-4S Iron Iron-sulfur Metal-binding S-adenosyl-L-methionine
Molecular function	Methyltransferase Transferase
Technical term	Complete proteome
Gene Ontology (GO)
Molecular_function	4 iron, 4 sulfur cluster binding Inferred from electronic annotation. Source: UniProtKB-KW RNA binding Inferred from electronic annotation. Source: InterPro iron ion binding Inferred from electronic annotation. Source: HAMAP rRNA (uridine-C5-)-methyltransferase activity Inferred from electronic annotation. Source: HAMAP
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 450	450	23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD HAMAP-Rule MF_01010		PRO_0000229876
Regions
	Domain	20 – 78	59	TRAM
Sites
	Active site	407	1	Nucleophile By similarity
	Metal binding	91	1	Iron-sulfur (4Fe-4S) By similarity
	Metal binding	97	1	Iron-sulfur (4Fe-4S) By similarity
	Metal binding	100	1	Iron-sulfur (4Fe-4S) By similarity
	Metal binding	179	1	Iron-sulfur (4Fe-4S) By similarity
	Binding site	283	1	S-adenosyl-L-methionine By similarity
	Binding site	312	1	S-adenosyl-L-methionine; via carbonyl oxygen By similarity
	Binding site	317	1	S-adenosyl-L-methionine By similarity
	Binding site	333	1	S-adenosyl-L-methionine By similarity
	Binding site	360	1	S-adenosyl-L-methionine By similarity
	Binding site	381	1	S-adenosyl-L-methionine By similarity

Sequences

	Sequence		Length	Mass (Da)
	Q4K898 [UniParc]. Last modified August 2, 2005. Version 1. Checksum: FE3C683D8B209F3E	FASTA	450	49,118
	10 20 30 40 50 60 MAKHDRGLRF QPAGGSRAPQ IPVGKKQRLT IQRLANDGRG IAFVEGRTWF VSGALAGEEV 70 80 90 100 110 120 EARVLGSHGK VVEARAERIF NASDLRRPAA CAHAGRCGGC SVQHLPHDEQ LALKQRMLAE 130 140 150 160 170 180 QLSKVAGVEP EAWAAPLSGP EFGYRRRARV AVRWDAKGKQ LEVGFRAAGS QDIVAIDDCP 190 200 210 220 230 240 VLVQALQPVM NRLPAMLRRL SKPQALGHVE LFSGSALAVL LRHMAPLSDS DLTILKDFCD 250 260 270 280 290 300 FHQAQLWLHG EGEPQPFDPS QALGYRLETW DLHLAYRPGD FVQVNAGVNE AMVAQALEWL 310 320 330 340 350 360 APQADERVLD LFCGLGNFAL PLARQVREVV AVEGVATMVA RAAENAASNN LHNTRFFQAD 370 380 390 400 410 420 LSQPLSAAEW ADEGFSAVLL DPPRDGAFEV VRQLATLGAK RLVYVSCNPA TLARDTVELI 430 440 450 KQGYRLKRAG ILDMFPQTAH VEAMALFEAS

References

[1]

"Complete genome sequence of the plant commensal Pseudomonas fluorescens Pf-5." Paulsen I.T., Press C.M., Ravel J., Kobayashi D.Y., Myers G.S.A., Mavrodi D.V., DeBoy R.T., Seshadri R., Ren Q., Madupu R., Dodson R.J., Durkin A.S., Brinkac L.M., Daugherty S.C., Sullivan S.A., Rosovitz M.J., Gwinn M.L., Zhou L. , Schneider D.J., Cartinhour S.W., Nelson W.C., Weidman J., Watkins K., Tran K., Khouri H., Pierson E.A., Pierson L.S. III, Thomashow L.S., Loper J.E. Nat. Biotechnol. 23:873-878(2005) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: Pf-5 / ATCC BAA-477.

Cross-references

Sequence databases
EMBL GenBank DDBJ	CP000076 Genomic DNA. Translation: AAY93698.1.
RefSeq	YP_261535.1. NC_004129.6.
3D structure databases
ProteinModelPortal	Q4K898.
ModBase	Search...
Protein-protein interaction databases
STRING	220664.PFL_4447.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblBacteria	AAY93698; AAY93698; PFL_4447.
GeneID	3478566.
KEGG	pfl:PFL_4447.
PATRIC	19878326. VBIPseFlu72549_4552.
Organism-specific databases
CMR	Search...
Phylogenomic databases
eggNOG	COG2265.
HOGENOM	HOG000029868.
KO	K03215.
OMA	ALTIRHM.
ProtClustDB	PRK13168.
Enzyme and pathway databases
BioCyc	PFLU220664:GIX8-4482-MONOMER.
Family and domain databases
Gene3D	2.40.50.140. 1 hit.
HAMAP	MF_01010. 23SrRNA_methyltr_RlmD.
InterPro	IPR001566. 23S_rRNA_MeTrfase_RlmD. IPR012340. NA-bd_OB-fold. IPR002792. TRAM_dom. IPR010280. U5_MeTrfase. [Graphical view]
Pfam	PF01938. TRAM. 1 hit. PF05958. tRNA_U5-meth_tr. 1 hit. [Graphical view]
SUPFAM	SSF50249. Nucleic_acid_OB. 1 hit.
TIGRFAMs	TIGR00479. rumA. 1 hit.
PROSITE	PS50926. TRAM. 1 hit. PS01230. TRMA_1. 1 hit. PS01231. TRMA_2. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

RLMD_PSEF5

Accession

Primary (citable) accession number: Q4K898

Entry history

Integrated into UniProtKB/Swiss-Prot:	April 4, 2006
Last sequence update:	August 2, 2005
Last modified:	May 1, 2013
This is version 52 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program