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C3NVE8 (C3NVE8_VIBCJ) Unreviewed, UniProtKB/TrEMBL

Last modified May 1, 2013. Version 32. Feed History...

Clusters with 100%, 90%, 50% identity | Third-party data text xml rdf/xml gff fasta
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Names and origin

Protein namesRecommended name:
23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD HAMAP-Rule MF_01010
EC=2.1.1.190 HAMAP-Rule MF_01010
Alternative name(s):
23S rRNA(m5U1939)-methyltransferase HAMAP-Rule MF_01010
Gene names
Name:rlmD HAMAP-Rule MF_01010
Ordered Locus Names:VCD_001902
OrganismVibrio cholerae serotype O1 (strain MJ-1236) [Complete proteome] [HAMAP] EMBL ACQ60071.1
Taxonomic identifier593588 [NCBI]
Taxonomic lineageBacteria › Proteobacteria › Gammaproteobacteria › Vibrionales › Vibrionaceae › Vibrio ›

Protein attributes

Sequence length440 AA.
Sequence statusComplete.
Protein existenceInferred from homology

General annotation (Comments)

Function

Catalyzes the formation of 5-methyl-uridine at position 1939 (m5U1939) in 23S rRNA By similarity. HAMAP-Rule MF_01010

Catalytic activity

S-adenosyl-L-methionine + uracil(1939) in 23S rRNA = S-adenosyl-L-homocysteine + 5-methyluracil(1939) in 23S rRNA. HAMAP-Rule MF_01010

Sequence similarities

Belongs to the methyltransferase superfamily. RNA M5U methyltransferase family. RlmD subfamily. HAMAP-Rule MF_01010

Contains 1 TRAM domain. SAAS SAAS010280 HAMAP-Rule MF_01010

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Regions

Domain11 – 6959TRAM By similarity HAMAP-Rule MF_01010

Sites

Active site3961Nucleophile By similarity HAMAP-Rule MF_01010
Metal binding821Iron-sulfur (4Fe-4S) By similarity HAMAP-Rule MF_01010
Metal binding881Iron-sulfur (4Fe-4S) By similarity HAMAP-Rule MF_01010
Metal binding911Iron-sulfur (4Fe-4S) By similarity HAMAP-Rule MF_01010
Metal binding1691Iron-sulfur (4Fe-4S) By similarity HAMAP-Rule MF_01010
Binding site2721S-adenosyl-L-methionine By similarity HAMAP-Rule MF_01010
Binding site3011S-adenosyl-L-methionine; via carbonyl oxygen By similarity HAMAP-Rule MF_01010
Binding site3061S-adenosyl-L-methionine By similarity HAMAP-Rule MF_01010
Binding site3221S-adenosyl-L-methionine By similarity HAMAP-Rule MF_01010
Binding site3491S-adenosyl-L-methionine By similarity HAMAP-Rule MF_01010
Binding site3701S-adenosyl-L-methionine By similarity HAMAP-Rule MF_01010

Sequences

Sequence LengthMass (Da)Tools
C3NVE8 [UniParc].

Last modified June 16, 2009. Version 1.
Checksum: F66F73E577543C48

FASTA44049,008
        10         20         30         40         50         60 
MARFFQPKKH STLDTKHQPV TIERLDHQGS GLAFLHKKPL FVDGALPGEE VLIQLTENKS 

        70         80         90        100        110        120 
KYARGQLIKV LKPSAERVAP FCAHYAQCGG CDLQHLDRAG QIHHKQQALS QLMVKFAGQS 

       130        140        150        160        170        180 
LALSAPVCSD DQGYRRRARL SLMWDKKTQQ LQLGFRRKQS KAIVNVTHCP VLEPSLNALL 

       190        200        210        220        230        240 
PDLNALLSEW SQPERLGHVE LVKGDNTRVL VLRHLGALIE QDQQRLTDFA SQNQLTLYLM 

       250        260        270        280        290        300 
LEAGELQHVQ GEAPYCEETG SRLSFLPSHF IQVNRAVNQH MVVQALNWLE VSPQERVLDL 

       310        320        330        340        350        360 
FCGLGNFTLP LAKQAQAVVG VEGVDEMVQH ATHNAKLNQI NNVAFYQANL EQDMTSASWA 

       370        380        390        400        410        420 
QQKFAKVLLD PARAGAEGIV DQLSALGAKR VVYVSCNPAT LARDSQSLLS QGFRLEKLGM 

       430        440 
LDMFPHTSHL ESMALFVKKG

« Hide

References

[1]"Comparative genomics reveals mechanism for short-term and long-term clonal transitions in pandemic Vibrio cholerae."
Chun J., Grim C.J., Hasan N.A., Lee J.H., Choi S.Y., Haley B.J., Taviani E., Jeon Y.-S., Kim D.W., Lee J.-H., Brettin T.S., Bruce D.C., Challacombe J.F., Detter J.C., Han C.S., Munk A.C., Chertkov O., Meincke L. expand/collapse author list , Saunders E., Walters R.A., Huq A., Nair G.B., Colwell R.R.
Proc. Natl. Acad. Sci. U.S.A. 106:15442-15447(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: MJ-1236.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ		CP001485 Genomic DNA. Translation: ACQ60071.1.
RefSeqYP_002877641.1. NC_012668.1.

3D structure databases

ProteinModelPortalC3NVE8.
ModBaseSearch...

Protein-protein interaction databases

STRING593588.VCD_001902.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaACQ60071; ACQ60071; VCD_001902.
GeneID7855925.
KEGGvcj:VCD_001902.
PATRIC20075160. VBIVibCho20143_1922.

Organism-specific databases

CMRSearch...

Phylogenomic databases

eggNOGCOG2265.
HOGENOMHOG000029868.
KOK03215.
OMAFCPHFGV.
ProtClustDBPRK13168.

Family and domain databases

Gene3D2.40.50.140. 1 hit.
HAMAPMF_01010. 23SrRNA_methyltr_RlmD.
InterProIPR001566. 23S_rRNA_MeTrfase_RlmD.
IPR012340. NA-bd_OB-fold.
IPR002792. TRAM_dom.
IPR010280. U5_MeTrfase.
[Graphical view]
PfamPF01938. TRAM. 1 hit.
PF05958. tRNA_U5-meth_tr. 1 hit.
[Graphical view]
SUPFAMSSF50249. Nucleic_acid_OB. 1 hit.
TIGRFAMsTIGR00479. rumA. 1 hit.
PROSITEPS50926. TRAM. 1 hit.
PS01230. TRMA_1. 1 hit.
PS01231. TRMA_2. 1 hit.
[Graphical view]
ProtoNetSearch...

Entry information

Entry nameC3NVE8_VIBCJ
AccessionPrimary (citable) accession number: C3NVE8
Entry history
Integrated into UniProtKB/TrEMBL: June 16, 2009
Last sequence update: June 16, 2009
Last modified: May 1, 2013
This is version 32 of the entry and version 1 of the sequence. [Complete history]
Entry statusUnreviewed (UniProtKB/TrEMBL)
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info