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Q4K898 (RLMD_PSEF5) Reviewed, UniProtKB/Swiss-Prot

Last modified June 11, 2014. Version 58. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (1) | Third-party data text xml rdf/xml gff fasta
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Names and origin

Protein namesRecommended 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
OrganismPseudomonas fluorescens (strain Pf-5 / ATCC BAA-477) [Complete proteome] [HAMAP]
Taxonomic identifier220664 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaPseudomonadalesPseudomonadaceaePseudomonas

Protein attributes

Sequence length450 AA.
Sequence statusComplete.
Protein existenceInferred 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 class I-like SAM-binding methyltransferase superfamily. RNA M5U methyltransferase family. RlmD subfamily.

Contains 1 TRAM domain.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 45045023S rRNA (uracil(1939)-C(5))-methyltransferase RlmD HAMAP-Rule MF_01010
PRO_0000229876

Regions

Domain20 – 7859TRAM

Sites

Active site4071Nucleophile By similarity
Metal binding911Iron-sulfur (4Fe-4S) By similarity
Metal binding971Iron-sulfur (4Fe-4S) By similarity
Metal binding1001Iron-sulfur (4Fe-4S) By similarity
Metal binding1791Iron-sulfur (4Fe-4S) By similarity
Binding site2831S-adenosyl-L-methionine By similarity
Binding site3121S-adenosyl-L-methionine; via carbonyl oxygen By similarity
Binding site3171S-adenosyl-L-methionine By similarity
Binding site3331S-adenosyl-L-methionine By similarity
Binding site3601S-adenosyl-L-methionine By similarity
Binding site3811S-adenosyl-L-methionine By similarity

Sequences

Sequence LengthMass (Da)Tools
Q4K898 [UniParc].

Last modified August 2, 2005. Version 1.
Checksum: FE3C683D8B209F3E

FASTA45049,118
        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 

« Hide

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
CP000076 Genomic DNA. Translation: AAY93698.1.
RefSeqYP_261535.1. NC_004129.6.

3D structure databases

ProteinModelPortalQ4K898.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING220664.PFL_4447.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAY93698; AAY93698; PFL_4447.
GeneID3478566.
KEGGpfl:PFL_4447.
PATRIC19878326. VBIPseFlu72549_4552.

Organism-specific databases

CMRSearch...

Phylogenomic databases

eggNOGCOG2265.
HOGENOMHOG000029868.
KOK03215.
OMADFIQVND.
OrthoDBEOG6V4GKM.

Enzyme and pathway databases

BioCycPFLU220664:GIX8-4482-MONOMER.

Family and domain databases

Gene3D2.40.50.140. 1 hit.
3.40.50.150. 1 hit.
HAMAPMF_01010. 23SrRNA_methyltr_RlmD.
InterProIPR001566. 23S_rRNA_MeTrfase_RlmD.
IPR012340. NA-bd_OB-fold.
IPR029063. SAM-dependent_MTases-like.
IPR002792. TRAM_dom.
IPR010280. U5_MeTrfase_fam.
[Graphical view]
PfamPF01938. TRAM. 1 hit.
PF05958. tRNA_U5-meth_tr. 1 hit.
[Graphical view]
SUPFAMSSF50249. SSF50249. 1 hit.
SSF53335. SSF53335. 1 hit.
TIGRFAMsTIGR00479. rumA. 1 hit.
PROSITEPS51687. SAM_MT_RNA_M5U. 1 hit.
PS50926. TRAM. 1 hit.
PS01230. TRMA_1. 1 hit.
PS01231. TRMA_2. 1 hit.
[Graphical view]
ProtoNetSearch...

Entry information

Entry nameRLMD_PSEF5
AccessionPrimary (citable) accession number: Q4K898
Entry history
Integrated into UniProtKB/Swiss-Prot: April 4, 2006
Last sequence update: August 2, 2005
Last modified: June 11, 2014
This is version 58 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families