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Protein

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

Gene

rlmD

Organism
Francisella tularensis subsp. novicida (strain U112)
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 bindingi79 – 791Iron-sulfur (4Fe-4S)UniRule annotation
Metal bindingi85 – 851Iron-sulfur (4Fe-4S)UniRule annotation
Metal bindingi88 – 881Iron-sulfur (4Fe-4S)UniRule annotation
Metal bindingi169 – 1691Iron-sulfur (4Fe-4S)UniRule annotation
Binding sitei280 – 2801S-adenosyl-L-methionineUniRule annotation
Binding sitei309 – 3091S-adenosyl-L-methionine; via carbonyl oxygenUniRule annotation
Binding sitei314 – 3141S-adenosyl-L-methionineUniRule annotation
Binding sitei330 – 3301S-adenosyl-L-methionineUniRule annotation
Binding sitei357 – 3571S-adenosyl-L-methionineUniRule annotation
Binding sitei379 – 3791S-adenosyl-L-methionineUniRule annotation
Active sitei405 – 4051NucleophileUniRule annotation

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

Enzyme and pathway databases

BioCyciFNOV401614:GC4M-615-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:FTN_0616
OrganismiFrancisella tularensis subsp. novicida (strain U112)
Taxonomic identifieri401614 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaThiotrichalesFrancisellaceaeFrancisella
Proteomesi
  • UP000000762 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 44944923S rRNA (uracil(1939)-C(5))-methyltransferase RlmDPRO_0000282043Add
BLAST

Structurei

3D structure databases

ProteinModelPortaliA0Q5J5.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini1 – 6666TRAMUniRule 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

HOGENOMiHOG000029868.
KOiK03215.
OMAiWGEEYIY.

Family and domain databases

Gene3Di2.40.50.140. 1 hit.
3.40.50.150. 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]
PfamiPF05958. 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.

A0Q5J5-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MGRSRHHNKL KEGIFEAEIT ALSHDGRGIA KVDGKTTFIP FTLPGEVVKF
60 70 80 90 100
EYTFTKAKFD EAKVVEYVKK SSNRVNPPCE HFQICGGCSL QHMSTDAQIE
110 120 130 140 150
HKQQTLINQL KYIGNGVEPE NILPPLRTSN TEGYRNKARL GVRYVSKKGK
160 170 180 190 200
ILVGFRERNG RFLADIDKCI VLNPLVGDKI TEISSFIETL SIYQHIAQLE
210 220 230 240 250
IAIDDTRPAM IVRHLEPFTN EDLEKLRSFA QQNNYWIYLQ SKGPDTIFRL
260 270 280 290 300
YPQGDVEPKK LSYQPAAGID IGFEPNDFTQ VNNDINKKMI KRAIELLDIS
310 320 330 340 350
ENDSIIDLFC GLGNFTLPIS QHAKTVIGVE GEPTMVKRAK ETADNNNITN
360 370 380 390 400
VNFYAANLFE SFEDKEWFNN FEYNKMLLDP PRAGAQEVCN NIEKFNVKRI
410 420 430 440
VYVSCDTATL ARDAGILVNN KDYKLISAGV MDMFPHTMHV ESIAVFEKI
Length:449
Mass (Da):50,925
Last modified:January 9, 2007 - v1
Checksum:i8BCEC382E373877C
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000439 Genomic DNA. Translation: ABK89510.1.
RefSeqiWP_003038679.1. NZ_CP009633.1.

Genome annotation databases

EnsemblBacteriaiABK89510; ABK89510; FTN_0616.
KEGGiftn:FTN_0616.
ftx:AW25_1411.
PATRICi17934327. VBIFraNov128299_0634.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000439 Genomic DNA. Translation: ABK89510.1.
RefSeqiWP_003038679.1. NZ_CP009633.1.

3D structure databases

ProteinModelPortaliA0Q5J5.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABK89510; ABK89510; FTN_0616.
KEGGiftn:FTN_0616.
ftx:AW25_1411.
PATRICi17934327. VBIFraNov128299_0634.

Phylogenomic databases

HOGENOMiHOG000029868.
KOiK03215.
OMAiWGEEYIY.

Enzyme and pathway databases

BioCyciFNOV401614:GC4M-615-MONOMER.

Family and domain databases

Gene3Di2.40.50.140. 1 hit.
3.40.50.150. 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]
PfamiPF05958. 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_FRATN
AccessioniPrimary (citable) accession number: A0Q5J5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 3, 2007
Last sequence update: January 9, 2007
Last modified: September 7, 2016
This is version 57 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.