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A5F5I8

- RLMD_VIBC3

UniProt

A5F5I8 - RLMD_VIBC3

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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: 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 bindingi82 – 821Iron-sulfur (4Fe-4S)UniRule annotation
Metal bindingi88 – 881Iron-sulfur (4Fe-4S)UniRule annotation
Metal bindingi91 – 911Iron-sulfur (4Fe-4S)UniRule annotation
Metal bindingi169 – 1691Iron-sulfur (4Fe-4S)UniRule annotation
Binding sitei272 – 2721S-adenosyl-L-methionineUniRule annotation
Binding sitei301 – 3011S-adenosyl-L-methionine; via carbonyl oxygenUniRule annotation
Binding sitei306 – 3061S-adenosyl-L-methionineUniRule annotation
Binding sitei322 – 3221S-adenosyl-L-methionineUniRule annotation
Binding sitei349 – 3491S-adenosyl-L-methionineUniRule annotation
Binding sitei370 – 3701S-adenosyl-L-methionineUniRule annotation
Active sitei396 – 3961NucleophileUniRule annotation

GO - Molecular functioni

  1. 4 iron, 4 sulfur cluster binding Source: UniProtKB-KW
  2. iron ion binding Source: UniProtKB-HAMAP
  3. RNA binding Source: InterPro
  4. rRNA (uridine-C5-)-methyltransferase activity Source: UniProtKB-HAMAP
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
ProteomesiUP000000249: Chromosome 2, UP000001630: Chromosome I

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 44044023S rRNA (uracil(1939)-C(5))-methyltransferase RlmDPRO_1000200859Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi345073.VC0395_A2030.

Structurei

3D structure databases

ProteinModelPortaliA5F5I8.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini11 – 6959TRAMUniRule 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

eggNOGiCOG2265.
HOGENOMiHOG000029868.
KOiK03215.
OMAiDFIQVND.

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.
IPR012340. NA-bd_OB-fold.
IPR029063. SAM-dependent_MTases-like.
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:
EMBL
GenBank
DDBJ
Links Updated
CP000627 Genomic DNA. Translation: ABQ21286.1.
CP001235 Genomic DNA. Translation: ACP10554.1.
RefSeqiYP_001217954.1. NC_009457.1.
YP_002820790.1. NC_012582.1.

Genome annotation databases

EnsemblBacteriaiABQ21286; ABQ21286; VC0395_A2030.
ACP10554; ACP10554; VC395_2567.
GeneIDi5136111.
7776319.
KEGGivco:VC0395_A2030.
vcr:VC395_2567.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
CP000627 Genomic DNA. Translation: ABQ21286.1 .
CP001235 Genomic DNA. Translation: ACP10554.1 .
RefSeqi YP_001217954.1. NC_009457.1.
YP_002820790.1. NC_012582.1.

3D structure databases

ProteinModelPortali A5F5I8.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 345073.VC0395_A2030.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai ABQ21286 ; ABQ21286 ; VC0395_A2030 .
ACP10554 ; ACP10554 ; VC395_2567 .
GeneIDi 5136111.
7776319.
KEGGi vco:VC0395_A2030.
vcr:VC395_2567.

Phylogenomic databases

eggNOGi COG2265.
HOGENOMi HOG000029868.
KOi K03215.
OMAi DFIQVND.

Family and domain databases

Gene3Di 2.40.50.140. 1 hit.
3.40.50.150. 1 hit.
HAMAPi MF_01010. 23SrRNA_methyltr_RlmD.
InterProi IPR001566. 23S_rRNA_MeTrfase_RlmD.
IPR012340. NA-bd_OB-fold.
IPR029063. SAM-dependent_MTases-like.
IPR002792. TRAM_dom.
IPR010280. U5_MeTrfase_fam.
[Graphical view ]
Pfami PF01938. TRAM. 1 hit.
PF05958. tRNA_U5-meth_tr. 1 hit.
[Graphical view ]
SUPFAMi SSF50249. SSF50249. 1 hit.
SSF53335. SSF53335. 1 hit.
TIGRFAMsi TIGR00479. rumA. 1 hit.
PROSITEi PS51687. SAM_MT_RNA_M5U. 1 hit.
PS50926. TRAM. 1 hit.
PS01230. TRMA_1. 1 hit.
PS01231. TRMA_2. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

  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.

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: October 1, 2014
This is version 51 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

External Data

Dasty 3