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Protein

23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD

Gene

rlmD

Organism
Pseudomonas fluorescens (strain Pf-5 / ATCC BAA-477)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Protein inferred from homologyi

Functioni

Catalyzes the formation of 5-methyl-uridine at position 1939 (m5U1939) in 23S rRNA.UniRule annotation

Catalytic activityi

S-adenosyl-L-methionine + uracil(1939) in 23S rRNA = S-adenosyl-L-homocysteine + 5-methyluracil(1939) in 23S rRNA.UniRule annotation

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi91 – 911Iron-sulfur (4Fe-4S)UniRule annotation
Metal bindingi97 – 971Iron-sulfur (4Fe-4S)UniRule annotation
Metal bindingi100 – 1001Iron-sulfur (4Fe-4S)UniRule annotation
Metal bindingi179 – 1791Iron-sulfur (4Fe-4S)UniRule annotation
Binding sitei283 – 2831S-adenosyl-L-methionineUniRule annotation
Binding sitei312 – 3121S-adenosyl-L-methionine; via carbonyl oxygenUniRule annotation
Binding sitei317 – 3171S-adenosyl-L-methionineUniRule annotation
Binding sitei333 – 3331S-adenosyl-L-methionineUniRule annotation
Binding sitei360 – 3601S-adenosyl-L-methionineUniRule annotation
Binding sitei381 – 3811S-adenosyl-L-methionineUniRule annotation
Active sitei407 – 4071NucleophileUniRule annotation

GO - Molecular functioni

  1. 4 iron, 4 sulfur cluster binding Source: UniProtKB-KW
  2. iron ion binding Source: UniProtKB-HAMAP
  3. RNA binding Source: InterPro
  4. rRNA (uridine-C5-)-methyltransferase activity Source: UniProtKB-HAMAP
Complete GO annotation...

Keywords - Molecular functioni

Methyltransferase, Transferase

Keywords - Biological processi

rRNA processing

Keywords - Ligandi

4Fe-4S, Iron, Iron-sulfur, Metal-binding, S-adenosyl-L-methionine

Enzyme and pathway databases

BioCyciPFLU220664:GIX8-4482-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
23S rRNA (uracil(1939)-C(5))-methyltransferase RlmDUniRule annotation (EC:2.1.1.190UniRule annotation)
Alternative name(s):
23S rRNA(m5U1939)-methyltransferaseUniRule annotation
Gene namesi
Name:rlmDUniRule annotation
Synonyms:rumA
Ordered Locus Names:PFL_4447
OrganismiPseudomonas fluorescens (strain Pf-5 / ATCC BAA-477)
Taxonomic identifieri220664 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaPseudomonadalesPseudomonadaceaePseudomonas
ProteomesiUP000008540: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 45045023S rRNA (uracil(1939)-C(5))-methyltransferase RlmDPRO_0000229876Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi220664.PFL_4447.

Structurei

3D structure databases

ProteinModelPortaliQ4K898.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini20 – 7859TRAMUniRule annotationAdd
BLAST

Sequence similaritiesi

Belongs to the class I-like SAM-binding methyltransferase superfamily. RNA M5U methyltransferase family. RlmD subfamily.UniRule annotation
Contains 1 TRAM domain.UniRule annotation

Phylogenomic databases

eggNOGiCOG2265.
HOGENOMiHOG000029868.
KOiK03215.
OMAiQFYSPNR.
OrthoDBiEOG6V4GKM.

Family and domain databases

Gene3Di2.40.50.140. 1 hit.
3.40.50.150. 1 hit.
HAMAPiMF_01010. 23SrRNA_methyltr_RlmD.
InterProiIPR001566. 23S_rRNA_MeTrfase_RlmD.
IPR030390. MeTrfase_TrmA_AS.
IPR030391. MeTrfase_TrmA_CS.
IPR012340. NA-bd_OB-fold.
IPR029063. SAM-dependent_MTases.
IPR002792. TRAM_dom.
IPR010280. U5_MeTrfase_fam.
[Graphical view]
PfamiPF01938. TRAM. 1 hit.
PF05958. tRNA_U5-meth_tr. 1 hit.
[Graphical view]
SUPFAMiSSF50249. SSF50249. 1 hit.
SSF53335. SSF53335. 1 hit.
TIGRFAMsiTIGR00479. rumA. 1 hit.
PROSITEiPS51687. SAM_MT_RNA_M5U. 1 hit.
PS50926. TRAM. 1 hit.
PS01230. TRMA_1. 1 hit.
PS01231. TRMA_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q4K898-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAKHDRGLRF QPAGGSRAPQ IPVGKKQRLT IQRLANDGRG IAFVEGRTWF
60 70 80 90 100
VSGALAGEEV EARVLGSHGK VVEARAERIF NASDLRRPAA CAHAGRCGGC
110 120 130 140 150
SVQHLPHDEQ LALKQRMLAE QLSKVAGVEP EAWAAPLSGP EFGYRRRARV
160 170 180 190 200
AVRWDAKGKQ LEVGFRAAGS QDIVAIDDCP VLVQALQPVM NRLPAMLRRL
210 220 230 240 250
SKPQALGHVE LFSGSALAVL LRHMAPLSDS DLTILKDFCD FHQAQLWLHG
260 270 280 290 300
EGEPQPFDPS QALGYRLETW DLHLAYRPGD FVQVNAGVNE AMVAQALEWL
310 320 330 340 350
APQADERVLD LFCGLGNFAL PLARQVREVV AVEGVATMVA RAAENAASNN
360 370 380 390 400
LHNTRFFQAD LSQPLSAAEW ADEGFSAVLL DPPRDGAFEV VRQLATLGAK
410 420 430 440 450
RLVYVSCNPA TLARDTVELI KQGYRLKRAG ILDMFPQTAH VEAMALFEAS
Length:450
Mass (Da):49,118
Last modified:August 2, 2005 - v1
Checksum:iFE3C683D8B209F3E
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000076 Genomic DNA. Translation: AAY93698.1.
RefSeqiYP_261535.1. NC_004129.6.

Genome annotation databases

EnsemblBacteriaiAAY93698; AAY93698; PFL_4447.
GeneIDi3478566.
KEGGipfl:PFL_4447.
PATRICi19878326. VBIPseFlu72549_4552.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000076 Genomic DNA. Translation: AAY93698.1.
RefSeqiYP_261535.1. NC_004129.6.

3D structure databases

ProteinModelPortaliQ4K898.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi220664.PFL_4447.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAY93698; AAY93698; PFL_4447.
GeneIDi3478566.
KEGGipfl:PFL_4447.
PATRICi19878326. VBIPseFlu72549_4552.

Phylogenomic databases

eggNOGiCOG2265.
HOGENOMiHOG000029868.
KOiK03215.
OMAiQFYSPNR.
OrthoDBiEOG6V4GKM.

Enzyme and pathway databases

BioCyciPFLU220664:GIX8-4482-MONOMER.

Family and domain databases

Gene3Di2.40.50.140. 1 hit.
3.40.50.150. 1 hit.
HAMAPiMF_01010. 23SrRNA_methyltr_RlmD.
InterProiIPR001566. 23S_rRNA_MeTrfase_RlmD.
IPR030390. MeTrfase_TrmA_AS.
IPR030391. MeTrfase_TrmA_CS.
IPR012340. NA-bd_OB-fold.
IPR029063. SAM-dependent_MTases.
IPR002792. TRAM_dom.
IPR010280. U5_MeTrfase_fam.
[Graphical view]
PfamiPF01938. TRAM. 1 hit.
PF05958. tRNA_U5-meth_tr. 1 hit.
[Graphical view]
SUPFAMiSSF50249. SSF50249. 1 hit.
SSF53335. SSF53335. 1 hit.
TIGRFAMsiTIGR00479. rumA. 1 hit.
PROSITEiPS51687. SAM_MT_RNA_M5U. 1 hit.
PS50926. TRAM. 1 hit.
PS01230. TRMA_1. 1 hit.
PS01231. TRMA_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: Pf-5 / ATCC BAA-477.

Entry informationi

Entry nameiRLMD_PSEF5
AccessioniPrimary (citable) accession number: Q4K898
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 4, 2006
Last sequence update: August 2, 2005
Last modified: January 7, 2015
This is version 60 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.