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Protein

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

Gene

rlmD

Organism
Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395)
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)DescriptionActionsGraphical viewLength
Metal bindingi82Iron-sulfur (4Fe-4S)UniRule annotation1
Metal bindingi88Iron-sulfur (4Fe-4S)UniRule annotation1
Metal bindingi91Iron-sulfur (4Fe-4S)UniRule annotation1
Metal bindingi169Iron-sulfur (4Fe-4S)UniRule annotation1
Binding sitei272S-adenosyl-L-methionineUniRule annotation1
Binding sitei301S-adenosyl-L-methionine; via carbonyl oxygenUniRule annotation1
Binding sitei306S-adenosyl-L-methionineUniRule annotation1
Binding sitei322S-adenosyl-L-methionineUniRule annotation1
Binding sitei349S-adenosyl-L-methionineUniRule annotation1
Binding sitei370S-adenosyl-L-methionineUniRule annotation1
Active sitei396NucleophileUniRule annotation1

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:VC0395_A2030, VC395_2567
OrganismiVibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395)
Taxonomic identifieri345073 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaVibrionalesVibrionaceaeVibrio
Proteomesi
  • UP000000249 Componenti: Chromosome 2

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_10002008591 – 44023S rRNA (uracil(1939)-C(5))-methyltransferase RlmDAdd BLAST440

Interactioni

Protein-protein interaction databases

STRINGi345073.VC0395_A2030.

Structurei

3D structure databases

ProteinModelPortaliA5F5I8.
SMRiA5F5I8.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini11 – 69TRAMUniRule annotationAdd BLAST59

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

Gene3Di3.40.50.150. 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]
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.

A5F5I8-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MARFFQPKKH STLDTKHQPV TIERLDHQGS GLAFLHKKPL FVDGALPGEE
60 70 80 90 100
VLIQLTENKS KYARGQLIKV LKPSAERVAP FCAHYAQCGG CDLQHLDRAG
110 120 130 140 150
QIHHKQQALS QLMVKFAGQS LALSAPVCSD DQGYRRRARL SLMWDKKTQQ
160 170 180 190 200
LQLGFRRKQS KAIVNVTDCP VLEPSLNALL PDLNALLSEW SQPERLGHVE
210 220 230 240 250
LVKGDNTRVL VLRHLGALIE QDQQRLTDFA SQNQLTLYLM LEAGELQHVQ
260 270 280 290 300
GEAPYCEETG SRLSFLPSHF IQVNRAVNQH MVAQALNWLE VSPQEHVLDL
310 320 330 340 350
FCGLGNFTLP LAKQAQAVVG VEGVDEMVQH ATHNAKLNQI NNVAFYQANL
360 370 380 390 400
EQDMTSASWA QQKFAKVLLD PARAGAEGIV DQLSALGAKR VVYVSCNPAT
410 420 430 440
LARDSQSLLS QGFRLEKLGM LDMFPHTSHL ESMALFVKKG
Length:440
Mass (Da):48,939
Last modified:June 12, 2007 - v1
Checksum:iFEB85661F2C4210D
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000627 Genomic DNA. Translation: ABQ21286.1.
CP001235 Genomic DNA. Translation: ACP10554.1.
RefSeqiWP_000090453.1. NC_012582.1.

Genome annotation databases

EnsemblBacteriaiABQ21286; ABQ21286; VC0395_A2030.
ACP10554; ACP10554; VC395_2567.
KEGGivco:VC0395_A2030.
vcr:VC395_2567.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000627 Genomic DNA. Translation: ABQ21286.1.
CP001235 Genomic DNA. Translation: ACP10554.1.
RefSeqiWP_000090453.1. NC_012582.1.

3D structure databases

ProteinModelPortaliA5F5I8.
SMRiA5F5I8.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi345073.VC0395_A2030.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABQ21286; ABQ21286; VC0395_A2030.
ACP10554; ACP10554; VC395_2567.
KEGGivco:VC0395_A2030.
vcr:VC395_2567.

Phylogenomic databases

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

Family and domain databases

Gene3Di3.40.50.150. 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]
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...

Entry informationi

Entry nameiRLMD_VIBC3
AccessioniPrimary (citable) accession number: A5F5I8
Secondary accession number(s): C3M4U3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 14, 2009
Last sequence update: June 12, 2007
Last modified: November 2, 2016
This is version 61 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.