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Protein

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

Gene

rlmD

Organism
Pseudomonas entomophila (strain L48)
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 bindingi93Iron-sulfur (4Fe-4S)UniRule annotation1
Metal bindingi99Iron-sulfur (4Fe-4S)UniRule annotation1
Metal bindingi102Iron-sulfur (4Fe-4S)UniRule annotation1
Metal bindingi181Iron-sulfur (4Fe-4S)UniRule annotation1
Binding sitei285S-adenosyl-L-methionineUniRule annotation1
Binding sitei314S-adenosyl-L-methionine; via carbonyl oxygenUniRule annotation1
Binding sitei319S-adenosyl-L-methionineUniRule annotation1
Binding sitei335S-adenosyl-L-methionineUniRule annotation1
Binding sitei362S-adenosyl-L-methionineUniRule annotation1
Binding sitei383S-adenosyl-L-methionineUniRule annotation1
Active sitei409NucleophileUniRule 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:PSEEN1363
OrganismiPseudomonas entomophila (strain L48)
Taxonomic identifieri384676 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaPseudomonadalesPseudomonadaceaePseudomonas
Proteomesi
  • UP000000658 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002820531 – 45223S rRNA (uracil(1939)-C(5))-methyltransferase RlmDAdd BLAST452

Interactioni

Protein-protein interaction databases

STRINGi384676.PSEEN1363.

Structurei

3D structure databases

ProteinModelPortaliQ1IDL9.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini22 – 80TRAMUniRule 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.
OMAiWGEEYIY.
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.

Q1IDL9-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSRKKSNGGL RFQPAGGNRA TQIPVGKKQR LLIERVAGDG RGIAFIEGRT
60 70 80 90 100
WFVSGALGGE EVEARVLGAR GKVVEARLER VFQASPERRE APCRHYARCG
110 120 130 140 150
GCNLQHLPHD GQLALKQRLL AEQLQRVAGV QPEEWAAPLC GPEFGYRRRA
160 170 180 190 200
RVAVRWDVKQ RQLDVGFRAE ASQDIVAIDD CPVLVQPLQA IMRHLPTVLR
210 220 230 240 250
SLSKPQTLGH VELFSGTAEA VLVRHVAALP AEDLARLEAF CREAGAQLWL
260 270 280 290 300
QGEGDPAPVD AAQRLGFALE PWGMELAWRP GDFVQVNAQV NTLMIQQALA
310 320 330 340 350
WLAPQAHERV LDLFCGLGNF ALPLARQARE VVAVEGVQAM VERAEANAHG
360 370 380 390 400
NNVYNARFFQ ADLSQPLAGA EWVAEGFSAV LLDPPRDGAY EVVQGIARLG
410 420 430 440 450
AKRLVYVSCN PATLARDTQV LVGQGYRLKR AGILDMFPQT AHVEAMALFE

AG
Length:452
Mass (Da):49,420
Last modified:June 13, 2006 - v1
Checksum:i8C6F8A8F742E1CC0
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CT573326 Genomic DNA. Translation: CAK14240.1.
RefSeqiWP_011532656.1. NC_008027.1.

Genome annotation databases

EnsemblBacteriaiCAK14240; CAK14240; PSEEN1363.
KEGGipen:PSEEN1363.
PATRICi19860878. VBIPseEnt83862_1293.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CT573326 Genomic DNA. Translation: CAK14240.1.
RefSeqiWP_011532656.1. NC_008027.1.

3D structure databases

ProteinModelPortaliQ1IDL9.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi384676.PSEEN1363.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAK14240; CAK14240; PSEEN1363.
KEGGipen:PSEEN1363.
PATRICi19860878. VBIPseEnt83862_1293.

Phylogenomic databases

eggNOGiENOG4105BZT. Bacteria.
COG2265. LUCA.
HOGENOMiHOG000029868.
KOiK03215.
OMAiWGEEYIY.
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_PSEE4
AccessioniPrimary (citable) accession number: Q1IDL9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 3, 2007
Last sequence update: June 13, 2006
Last modified: November 2, 2016
This is version 66 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

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.