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A5F5I8 (RLMD_VIBC3) Reviewed, UniProtKB/Swiss-Prot

Last modified June 11, 2014. Version 50. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (1) | 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

EC=2.1.1.190
Alternative name(s):
23S rRNA(m5U1939)-methyltransferase
Gene names
Name:rlmD
Synonyms:rumA
Ordered Locus Names:VC0395_A2030, VC395_2567
OrganismVibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395) [Complete proteome] [HAMAP]
Taxonomic identifier345073 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaVibrionalesVibrionaceaeVibrio

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 class I-like SAM-binding methyltransferase superfamily. RNA M5U methyltransferase family. RlmD subfamily.

Contains 1 TRAM domain.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 44044023S rRNA (uracil(1939)-C(5))-methyltransferase RlmD HAMAP-Rule MF_01010
PRO_1000200859

Regions

Domain11 – 6959TRAM

Sites

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

Sequences

Sequence LengthMass (Da)Tools
A5F5I8 [UniParc].

Last modified June 12, 2007. Version 1.
Checksum: FEB85661F2C4210D

FASTA44048,939
        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 KAIVNVTDCP VLEPSLNALL 

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

       250        260        270        280        290        300 
LEAGELQHVQ GEAPYCEETG SRLSFLPSHF IQVNRAVNQH MVAQALNWLE VSPQEHVLDL 

       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]Heidelberg J.
Submitted (MAR-2007) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 39541 / Classical Ogawa 395 / O395.
[2]"A recalibrated molecular clock and independent origins for the cholera pandemic clones."
Feng L., Reeves P.R., Lan R., Ren Y., Gao C., Zhou Z., Ren Y., Cheng J., Wang W., Wang J., Qian W., Li D., Wang L.
PLoS ONE 3:E4053-E4053(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 39541 / Classical Ogawa 395 / O395.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
CP000627 Genomic DNA. Translation: ABQ21286.1.
CP001235 Genomic DNA. Translation: ACP10554.1.
RefSeqYP_001217954.1. NC_009457.1.
YP_002820790.1. NC_012582.1.

3D structure databases

ProteinModelPortalA5F5I8.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING345073.VC0395_A2030.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaABQ21286; ABQ21286; VC0395_A2030.
ACP10554; ACP10554; VC395_2567.
GeneID5136111.
7776319.
KEGGvco:VC0395_A2030.
vcr:VC395_2567.

Organism-specific databases

CMRSearch...

Phylogenomic databases

eggNOGCOG2265.
HOGENOMHOG000029868.
KOK03215.
OMADFIQVND.

Family and domain databases

Gene3D2.40.50.140. 1 hit.
3.40.50.150. 1 hit.
HAMAPMF_01010. 23SrRNA_methyltr_RlmD.
InterProIPR001566. 23S_rRNA_MeTrfase_RlmD.
IPR012340. NA-bd_OB-fold.
IPR029063. SAM-dependent_MTases-like.
IPR002792. TRAM_dom.
IPR010280. U5_MeTrfase_fam.
[Graphical view]
PfamPF01938. TRAM. 1 hit.
PF05958. tRNA_U5-meth_tr. 1 hit.
[Graphical view]
SUPFAMSSF50249. SSF50249. 1 hit.
SSF53335. SSF53335. 1 hit.
TIGRFAMsTIGR00479. rumA. 1 hit.
PROSITEPS51687. SAM_MT_RNA_M5U. 1 hit.
PS50926. TRAM. 1 hit.
PS01230. TRMA_1. 1 hit.
PS01231. TRMA_2. 1 hit.
[Graphical view]
ProtoNetSearch...

Entry information

Entry nameRLMD_VIBC3
AccessionPrimary (citable) accession number: A5F5I8
Secondary accession number(s): C3M4U3
Entry history
Integrated into UniProtKB/Swiss-Prot: April 14, 2009
Last sequence update: June 12, 2007
Last modified: June 11, 2014
This is version 50 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families