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Protein

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

Gene

rlmD

Organism
Azoarcus sp. (strain BH72)
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 bindingi66 – 661Iron-sulfur (4Fe-4S)UniRule annotation
Metal bindingi72 – 721Iron-sulfur (4Fe-4S)UniRule annotation
Metal bindingi75 – 751Iron-sulfur (4Fe-4S)UniRule annotation
Metal bindingi154 – 1541Iron-sulfur (4Fe-4S)UniRule annotation
Binding sitei263 – 2631S-adenosyl-L-methionineUniRule annotation
Binding sitei292 – 2921S-adenosyl-L-methionine; via carbonyl oxygenUniRule annotation
Binding sitei297 – 2971S-adenosyl-L-methionineUniRule annotation
Binding sitei313 – 3131S-adenosyl-L-methionineUniRule annotation
Binding sitei341 – 3411S-adenosyl-L-methionineUniRule annotation
Binding sitei362 – 3621S-adenosyl-L-methionineUniRule annotation
Active sitei389 – 3891NucleophileUniRule 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

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 lineageiBacteriaProteobacteriaBetaproteobacteriaRhodocyclalesRhodocyclaceaeAzoarcus
Proteomesi
  • UP000002588 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 43343323S rRNA (uracil(1939)-C(5))-methyltransferase RlmDPRO_0000282029Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi62928.azo1100.

Structurei

3D structure databases

ProteinModelPortaliA1K4G2.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini1 – 5353TRAMUniRule 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

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

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.
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.
[Graphical view]

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.
PATRICi21010530. VBIAzoSp26047_1120.

Cross-referencesi

Sequence databases

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

3D structure databases

ProteinModelPortaliA1K4G2.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi62928.azo1100.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAL93717; CAL93717; azo1100.
KEGGiazo:azo1100.
PATRICi21010530. VBIAzoSp26047_1120.

Phylogenomic databases

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

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.
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.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiRLMD_AZOSB
AccessioniPrimary (citable) accession number: A1K4G2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 3, 2007
Last sequence update: February 6, 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, 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.