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Protein

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

Gene

rlmD

Organism
Azoarcus sp. (strain BH72)
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 bindingi66Iron-sulfur (4Fe-4S)UniRule annotation1
Metal bindingi72Iron-sulfur (4Fe-4S)UniRule annotation1
Metal bindingi75Iron-sulfur (4Fe-4S)UniRule annotation1
Metal bindingi154Iron-sulfur (4Fe-4S)UniRule annotation1
Binding sitei263S-adenosyl-L-methionineUniRule annotation1
Binding sitei292S-adenosyl-L-methionine; via carbonyl oxygenUniRule annotation1
Binding sitei297S-adenosyl-L-methionineUniRule annotation1
Binding sitei313S-adenosyl-L-methionineUniRule annotation1
Binding sitei341S-adenosyl-L-methionineUniRule annotation1
Binding sitei362S-adenosyl-L-methionineUniRule annotation1
Active sitei389NucleophileUniRule 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

BioCyciASP62928:AZO_RS05585-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:azo1100
OrganismiAzoarcus sp. (strain BH72)
Taxonomic identifieri62928 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaBetaproteobacteriaRhodocyclalesZoogloeaceaeAzoarcus
Proteomesi
  • UP000002588 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002820291 – 43323S rRNA (uracil(1939)-C(5))-methyltransferase RlmDAdd BLAST433

Interactioni

Protein-protein interaction databases

STRINGi62928.azo1100

Structurei

3D structure databases

ProteinModelPortaliA1K4G2
SMRiA1K4G2
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini1 – 53TRAMUniRule annotationAdd BLAST53

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiENOG4105BZT Bacteria
COG2265 LUCA
HOGENOMiHOG000029868
KOiK03215
OMAiACGGCKM
OrthoDBiPOG091H00VG

Family and domain databases

HAMAPiMF_01010 23SrRNA_methyltr_RlmD, 1 hit
InterProiView protein in InterPro
IPR001566 23S_rRNA_MeTrfase_RlmD
IPR030390 MeTrfase_TrmA_AS
IPR012340 NA-bd_OB-fold
IPR029063 SAM-dependent_MTases
IPR002792 TRAM_dom
IPR010280 U5_MeTrfase_fam
PANTHERiPTHR11061 PTHR11061, 1 hit
PfamiView protein in Pfam
PF01938 TRAM, 1 hit
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

Sequencei

Sequence statusi: Complete.

A1K4G2-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MPTAVIESLD HEGRGIARVE GKAVFIEGGL PGETVEYRVL RSKPNYEQAE
60 70 80 90 100
ATRIVRRSAL RVAPRCPHFG VCGGCSMQHL DTLAQAATKQ RVLEDALWRI
110 120 130 140 150
GKVKPGIIYS AIQGPAWGYR YRARLGVRLV PAKGGVLIGF HERRSSYIAD
160 170 180 190 200
LGVCPVLPAH VSALLPALKV LVASLSIADR LPQIEVAVSE ATTVLVFRNL
210 220 230 240 250
LALKKADEAQ LRSFAETHGV QVWLQPEGPD SIVPLHPRSG PGLTYTLPEF
260 270 280 290 300
DVALDFRATD FTQVNVHINR LLIRRAMQLL QPAPGERIAD LFCGLGNFSL
310 320 330 340 350
PIARRGATVV GVEGSEALVA RALENARRNG LDSRTEFHAA NLFDATEDSL
360 370 380 390 400
AALGPLDKLL IDPPREGAIA VVKAVGPAQQ PARIVYVSCN PATLARDAAV
410 420 430
LVHEKGYVLR GAGIANMFPQ TSHVESIALF ERP
Length:433
Mass (Da):46,820
Last modified:February 6, 2007 - v1
Checksum:i800C50DE7E044281
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AM406670 Genomic DNA Translation: CAL93717.1
RefSeqiWP_011764834.1, NC_008702.1

Genome annotation databases

EnsemblBacteriaiCAL93717; CAL93717; azo1100
KEGGiazo:azo1100

Similar proteinsi

Entry informationi

Entry nameiRLMD_AZOSB
AccessioniPrimary (citable) accession number: A1K4G2
Entry historyiIntegrated into UniProtKB/Swiss-Prot: April 3, 2007
Last sequence update: February 6, 2007
Last modified: June 20, 2018
This is version 65 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, Reference proteome

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