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Protein

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

Gene

rlmD

Organism
Pseudomonas fluorescens (strain ATCC BAA-477 / NRRL B-23932 / Pf-5)
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)DescriptionActionsGraphical viewLength
Metal bindingi91Iron-sulfur (4Fe-4S)UniRule annotation1
Metal bindingi97Iron-sulfur (4Fe-4S)UniRule annotation1
Metal bindingi100Iron-sulfur (4Fe-4S)UniRule annotation1
Metal bindingi179Iron-sulfur (4Fe-4S)UniRule annotation1
Binding sitei283S-adenosyl-L-methionineUniRule annotation1
Binding sitei312S-adenosyl-L-methionine; via carbonyl oxygenUniRule annotation1
Binding sitei317S-adenosyl-L-methionineUniRule annotation1
Binding sitei333S-adenosyl-L-methionineUniRule annotation1
Binding sitei360S-adenosyl-L-methionineUniRule annotation1
Binding sitei381S-adenosyl-L-methionineUniRule annotation1
Active sitei407NucleophileUniRule annotation1

GO - Molecular functioni

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

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 ATCC BAA-477 / NRRL B-23932 / Pf-5)
Taxonomic identifieri220664 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaPseudomonadalesPseudomonadaceaePseudomonas
Proteomesi
  • UP000008540 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002298761 – 45023S rRNA (uracil(1939)-C(5))-methyltransferase RlmDAdd BLAST450

Proteomic databases

PRIDEiQ4K898.

Interactioni

Protein-protein interaction databases

STRINGi220664.PFL_4447.

Structurei

3D structure databases

ProteinModelPortaliQ4K898.
SMRiQ4K898.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini20 – 78TRAMUniRule annotationAdd BLAST59

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

eggNOGiENOG4105BZT. Bacteria.
COG2265. LUCA.
HOGENOMiHOG000029868.
KOiK03215.
OMAiDLDPFGQ.
OrthoDBiPOG091H00VG.

Family and domain databases

Gene3Di3.40.50.150. 1 hit.
HAMAPiMF_01010. 23SrRNA_methyltr_RlmD. 1 hit.
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.
RefSeqiWP_011062710.1. 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.
RefSeqiWP_011062710.1. NC_004129.6.

3D structure databases

ProteinModelPortaliQ4K898.
SMRiQ4K898.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi220664.PFL_4447.

Proteomic databases

PRIDEiQ4K898.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Phylogenomic databases

eggNOGiENOG4105BZT. Bacteria.
COG2265. LUCA.
HOGENOMiHOG000029868.
KOiK03215.
OMAiDLDPFGQ.
OrthoDBiPOG091H00VG.

Family and domain databases

Gene3Di3.40.50.150. 1 hit.
HAMAPiMF_01010. 23SrRNA_methyltr_RlmD. 1 hit.
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...

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: November 2, 2016
This is version 68 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

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 one 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.