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A5F5I8

- RLMD_VIBC3

UniProt

A5F5I8 - RLMD_VIBC3

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
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    • History
      Entry version 51 (01 Oct 2014)
      Sequence version 1 (12 Jun 2007)
      Previous versions | rss
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    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

    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

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    MARFFQPKKH STLDTKHQPV TIERLDHQGS GLAFLHKKPL FVDGALPGEE    50
    VLIQLTENKS KYARGQLIKV LKPSAERVAP FCAHYAQCGG CDLQHLDRAG 100
    QIHHKQQALS QLMVKFAGQS LALSAPVCSD DQGYRRRARL SLMWDKKTQQ 150
    LQLGFRRKQS KAIVNVTDCP VLEPSLNALL PDLNALLSEW SQPERLGHVE 200
    LVKGDNTRVL VLRHLGALIE QDQQRLTDFA SQNQLTLYLM LEAGELQHVQ 250
    GEAPYCEETG SRLSFLPSHF IQVNRAVNQH MVAQALNWLE VSPQEHVLDL 300
    FCGLGNFTLP LAKQAQAVVG VEGVDEMVQH ATHNAKLNQI NNVAFYQANL 350
    EQDMTSASWA QQKFAKVLLD PARAGAEGIV DQLSALGAKR VVYVSCNPAT 400
    LARDSQSLLS QGFRLEKLGM LDMFPHTSHL ESMALFVKKG 440
    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