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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: -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 bindingi79Iron-sulfur (4Fe-4S)UniRule annotation1
Metal bindingi85Iron-sulfur (4Fe-4S)UniRule annotation1
Metal bindingi88Iron-sulfur (4Fe-4S)UniRule annotation1
Metal bindingi169Iron-sulfur (4Fe-4S)UniRule annotation1
Binding sitei280S-adenosyl-L-methionineUniRule annotation1
Binding sitei309S-adenosyl-L-methionine; via carbonyl oxygenUniRule annotation1
Binding sitei314S-adenosyl-L-methionineUniRule annotation1
Binding sitei330S-adenosyl-L-methionineUniRule annotation1
Binding sitei357S-adenosyl-L-methionineUniRule annotation1
Binding sitei379S-adenosyl-L-methionineUniRule annotation1
Active sitei405NucleophileUniRule annotation1

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionMethyltransferase, Transferase
Biological processrRNA processing
Ligand4Fe-4S, Iron, Iron-sulfur, Metal-binding, S-adenosyl-L-methionine

Enzyme and pathway databases

BioCyciFTUL401614:G1G75-641-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)DescriptionActionsGraphical viewLength
ChainiPRO_00002820431 – 44923S rRNA (uracil(1939)-C(5))-methyltransferase RlmDAdd BLAST449

Proteomic databases

PRIDEiA0Q5J5

Structurei

3D structure databases

ProteinModelPortaliA0Q5J5
SMRiA0Q5J5
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini1 – 66TRAMUniRule annotationAdd BLAST66

Sequence similaritiesi

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

Phylogenomic databases

HOGENOMiHOG000029868
KOiK03215
OMAiACGGCKM

Family and domain databases

HAMAPiMF_01010 23SrRNA_methyltr_RlmD, 1 hit
InterProiView protein in InterPro
IPR001566 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
PANTHERiPTHR11061 PTHR11061, 1 hit
PfamiView protein in Pfam
PF05958 tRNA_U5-meth_tr, 1 hit
SUPFAMiSSF50249 SSF50249, 1 hit
SSF53335 SSF53335, 1 hit
TIGRFAMsiTIGR00479 rumA, 1 hit
PROSITEiView protein in PROSITE
PS51687 SAM_MT_RNA_M5U, 1 hit
PS50926 TRAM, 1 hit
PS01230 TRMA_1, 1 hit
PS01231 TRMA_2, 1 hit

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

Similar proteinsi

Entry informationi

Entry nameiRLMD_FRATN
AccessioniPrimary (citable) accession number: A0Q5J5
Entry historyiIntegrated into UniProtKB/Swiss-Prot: April 3, 2007
Last sequence update: January 9, 2007
Last modified: May 23, 2018
This is version 64 of the entry and version 1 of the sequence. See 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

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