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Protein

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

Gene

rlmD

Organism
Shewanella sp. (strain ANA-3)
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 bindingi83 – 831Iron-sulfur (4Fe-4S)UniRule annotation
Metal bindingi89 – 891Iron-sulfur (4Fe-4S)UniRule annotation
Metal bindingi92 – 921Iron-sulfur (4Fe-4S)UniRule annotation
Metal bindingi170 – 1701Iron-sulfur (4Fe-4S)UniRule annotation
Binding sitei282 – 2821S-adenosyl-L-methionineUniRule annotation
Binding sitei311 – 3111S-adenosyl-L-methionine; via carbonyl oxygenUniRule annotation
Binding sitei316 – 3161S-adenosyl-L-methionineUniRule annotation
Binding sitei332 – 3321S-adenosyl-L-methionineUniRule annotation
Binding sitei359 – 3591S-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

BioCyciSSP94122:GJ9K-1146-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:Shewana3_1110
OrganismiShewanella sp. (strain ANA-3)
Taxonomic identifieri94122 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaAlteromonadalesShewanellaceaeShewanella
Proteomesi
  • UP000002589 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 44944923S rRNA (uracil(1939)-C(5))-methyltransferase RlmDPRO_0000282063Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi94122.Shewana3_1110.

Structurei

3D structure databases

ProteinModelPortaliA0KU76.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini12 – 7059TRAMUniRule 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.
OrthoDBiEOG6V4GKM.

Family and domain databases

Gene3Di2.40.50.140. 1 hit.
3.40.50.150. 1 hit.
HAMAPiMF_01010. 23SrRNA_methyltr_RlmD.
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.

A0KU76-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAQFFKAKPN SSKQLSAKQS FSVHQLDHLG AGIAQHQGKV VFIPGALPNE
60 70 80 90 100
TVQAQLTEQK KNYARAKLIK VETPSAERVT PLCPHYQSCG GCDLQHMSLA
110 120 130 140 150
GQREHKSAAL VDIMAKFAGA EGNSVPALTG EGWHYRRRAR LATLFDKNTK
160 170 180 190 200
QLSLGFRASS SNQVVPIDSC LVLAKPLADL IAPFAKLLNQ LAAKSSLGHV
210 220 230 240 250
ELIDADNGHF AVIRITKPLN DKDMAKLAQF AEQHQIHICL QDNNGEFHGV
260 270 280 290 300
NGTLLLPVYQ LLDDNADATP VSLTFTPGNF VQVNAQINKT MVAQALEWLA
310 320 330 340 350
PQPGERILDL FCGMGNFSLP LAKLGAEVIG VEGVPEMVSQ ARENAAANGL
360 370 380 390 400
SNLTFYHGDL SADLSCEPWM GKIDKLLLDP ARAGAFESLQ WLKKMKPRQV
410 420 430 440
VYVSCNPASL ARDSAVLLER GYKLQKLGLI DMFPQTHHIE AMALFELAK
Length:449
Mass (Da):48,957
Last modified:December 12, 2006 - v1
Checksum:i0C6A65D1B5727FB2
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000469 Genomic DNA. Translation: ABK47345.1.
RefSeqiWP_011716212.1. NC_008577.1.

Genome annotation databases

EnsemblBacteriaiABK47345; ABK47345; Shewana3_1110.
KEGGishn:Shewana3_1110.
PATRICi23569874. VBISheSp134792_1382.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000469 Genomic DNA. Translation: ABK47345.1.
RefSeqiWP_011716212.1. NC_008577.1.

3D structure databases

ProteinModelPortaliA0KU76.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi94122.Shewana3_1110.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABK47345; ABK47345; Shewana3_1110.
KEGGishn:Shewana3_1110.
PATRICi23569874. VBISheSp134792_1382.

Phylogenomic databases

eggNOGiENOG4105BZT. Bacteria.
COG2265. LUCA.
HOGENOMiHOG000029868.
KOiK03215.
OMAiDLDPFGQ.
OrthoDBiEOG6V4GKM.

Enzyme and pathway databases

BioCyciSSP94122:GJ9K-1146-MONOMER.

Family and domain databases

Gene3Di2.40.50.140. 1 hit.
3.40.50.150. 1 hit.
HAMAPiMF_01010. 23SrRNA_methyltr_RlmD.
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...

Publicationsi

  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ANA-3.

Entry informationi

Entry nameiRLMD_SHESA
AccessioniPrimary (citable) accession number: A0KU76
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 3, 2007
Last sequence update: December 12, 2006
Last modified: November 11, 2015
This is version 59 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.