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Q87B36

- RLMN_XYLFT

UniProt

Q87B36 - RLMN_XYLFT

Protein

Dual-specificity RNA methyltransferase RlmN

Gene

rlmN

Organism
Xylella fastidiosa (strain Temecula1 / ATCC 700964)
Status
Reviewed - Annotation score: 4 out of 5- Protein inferred from homologyi
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    • History
      Entry version 80 (01 Oct 2014)
      Sequence version 1 (01 Jun 2003)
      Previous versions | rss
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    Functioni

    Specifically methylates position 2 of adenine 2503 in 23S rRNA and position 2 of adenine 37 in tRNAs. m2A2503 modification seems to play a crucial role in the proofreading step occurring at the peptidyl transferase center and thus would serve to optimize ribosomal fidelity.UniRule annotation

    Catalytic activityi

    2 S-adenosyl-L-methionine + adenine(2503) in 23S rRNA = S-adenosyl-L-homocysteine + L-methionine + 5'-deoxyadenosine + 2-methyladenine(2503) in 23S rRNA.UniRule annotation
    2 S-adenosyl-L-methionine + adenine(37) in tRNA = S-adenosyl-L-homocysteine + L-methionine + 5'-deoxyadenosine + 2-methyladenine(37) in tRNA.UniRule annotation

    Cofactori

    Binds 1 4Fe-4S cluster. The cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine.UniRule annotation

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Active sitei119 – 1191Proton acceptorUniRule annotation
    Metal bindingi139 – 1391Iron-sulfur (4Fe-4S-S-AdoMet)UniRule annotation
    Metal bindingi143 – 1431Iron-sulfur (4Fe-4S-S-AdoMet)UniRule annotation
    Metal bindingi146 – 1461Iron-sulfur (4Fe-4S-S-AdoMet)UniRule annotation
    Binding sitei224 – 2241S-adenosyl-L-methionineUniRule annotation
    Binding sitei332 – 3321S-adenosyl-L-methionine; via amide nitrogen and carbonyl oxygenUniRule annotation
    Active sitei375 – 3751S-methylcysteine intermediateUniRule annotation

    GO - Molecular functioni

    1. 4 iron, 4 sulfur cluster binding Source: UniProtKB-HAMAP
    2. metal ion binding Source: UniProtKB-KW
    3. rRNA (adenine-C2-)-methyltransferase activity Source: UniProtKB-HAMAP
    4. rRNA binding Source: UniProtKB-HAMAP
    5. tRNA (adenine-C2-)-methyltransferase activity Source: UniProtKB-HAMAP
    6. tRNA binding Source: UniProtKB-HAMAP

    GO - Biological processi

    1. rRNA base methylation Source: UniProtKB-HAMAP

    Keywords - Molecular functioni

    Methyltransferase, Transferase

    Keywords - Biological processi

    rRNA processing, tRNA processing

    Keywords - Ligandi

    4Fe-4S, Iron, Iron-sulfur, Metal-binding, S-adenosyl-L-methionine

    Enzyme and pathway databases

    BioCyciXFAS183190:GIX4-1624-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Dual-specificity RNA methyltransferase RlmNUniRule annotation (EC:2.1.1.-UniRule annotation, EC:2.1.1.192UniRule annotation)
    Alternative name(s):
    23S rRNA (adenine(2503)-C(2))-methyltransferaseUniRule annotation
    23S rRNA m2A2503 methyltransferaseUniRule annotation
    Ribosomal RNA large subunit methyltransferase NUniRule annotation
    tRNA (adenine(37)-C(2))-methyltransferaseUniRule annotation
    tRNA m2A37 methyltransferaseUniRule annotation
    Gene namesi
    Name:rlmNUniRule annotation
    Ordered Locus Names:PD_1624
    OrganismiXylella fastidiosa (strain Temecula1 / ATCC 700964)
    Taxonomic identifieri183190 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaXanthomonadalesXanthomonadaceaeXylella
    ProteomesiUP000002516: Chromosome

    Subcellular locationi

    Cytoplasm UniRule annotation

    GO - Cellular componenti

    1. cytoplasm Source: UniProtKB-SubCell

    Keywords - Cellular componenti

    Cytoplasm

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 406406Dual-specificity RNA methyltransferase RlmNPRO_0000350536Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Disulfide bondi132 ↔ 375(transient)UniRule annotation

    Keywords - PTMi

    Disulfide bond

    Interactioni

    Protein-protein interaction databases

    STRINGi183190.PD1624.

    Structurei

    3D structure databases

    ProteinModelPortaliQ87B36.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni192 – 1932S-adenosyl-L-methionine bindingUniRule annotation
    Regioni246 – 2483S-adenosyl-L-methionine bindingUniRule annotation

    Sequence similaritiesi

    Belongs to the radical SAM superfamily. RlmN family.UniRule annotation

    Phylogenomic databases

    eggNOGiCOG0820.
    KOiK06941.
    OMAiPEAPYAK.
    OrthoDBiEOG6DJZ2N.

    Family and domain databases

    Gene3Di3.20.20.70. 1 hit.
    HAMAPiMF_01849. RNA_methyltr_RlmN.
    InterProiIPR013785. Aldolase_TIM.
    IPR006638. Elp3/MiaB/NifB.
    IPR027492. RNA_MTrfase_RlmN.
    IPR004383. rRNA_lsu_MTrfase_RlmN/Cfr.
    IPR007197. rSAM.
    [Graphical view]
    PANTHERiPTHR30544. PTHR30544. 1 hit.
    PfamiPF04055. Radical_SAM. 1 hit.
    [Graphical view]
    PIRSFiPIRSF006004. CHP00048. 1 hit.
    SMARTiSM00729. Elp3. 1 hit.
    [Graphical view]
    TIGRFAMsiTIGR00048. TIGR00048. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    Q87B36-1 [UniParc]FASTAAdd to Basket

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    MNGFAVIPSV TTTTTSGEPI ASDVARKQNL LELDREGLER FFEDVLGEKR    50
    YRAHQVMKWI HHRYVADFEQ MTDVGKALRT RLQACAEVRV PRVVFDKHSA 100
    DGTHKWLLAM GTDRKNAIET VYIPDKGRGT LCVSSQIGCG LNCTFCSTAT 150
    QGFNRNLTTA EIIGQVWVAA RHLGNVPHQQ RRLTNVVMMG MGEPLMNFDN 200
    VVRAMSVMRD DLGYGLSNKR VTLSTSGLVP MIDRLSTESD VSLAVSLHAP 250
    NDKLREQLVP LNKKYPIVEL MASCERYLSV NRKRDSVTFE YTLMKGVNDK 300
    QEHAHELAKL MRQFDCAMQV KGAAKVNLIP FNPFPGTCYE RSTEVDIRAF 350
    QKILLDAQIL AMVRRTRGDD IDAACGQLKG QVVDRTRRQA EFRRTIEDRV 400
    GRDVAA 406
    Length:406
    Mass (Da):45,706
    Last modified:June 1, 2003 - v1
    Checksum:iAA90F341DC96A7C2
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AE009442 Genomic DNA. Translation: AAO29464.1.
    RefSeqiNP_779815.1. NC_004556.1.

    Genome annotation databases

    EnsemblBacteriaiAAO29464; AAO29464; PD_1624.
    GeneIDi1142966.
    KEGGixft:PD1624.
    PATRICi24151562. VBIXylFas71109_2084.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AE009442 Genomic DNA. Translation: AAO29464.1 .
    RefSeqi NP_779815.1. NC_004556.1.

    3D structure databases

    ProteinModelPortali Q87B36.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 183190.PD1624.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAO29464 ; AAO29464 ; PD_1624 .
    GeneIDi 1142966.
    KEGGi xft:PD1624.
    PATRICi 24151562. VBIXylFas71109_2084.

    Phylogenomic databases

    eggNOGi COG0820.
    KOi K06941.
    OMAi PEAPYAK.
    OrthoDBi EOG6DJZ2N.

    Enzyme and pathway databases

    BioCyci XFAS183190:GIX4-1624-MONOMER.

    Family and domain databases

    Gene3Di 3.20.20.70. 1 hit.
    HAMAPi MF_01849. RNA_methyltr_RlmN.
    InterProi IPR013785. Aldolase_TIM.
    IPR006638. Elp3/MiaB/NifB.
    IPR027492. RNA_MTrfase_RlmN.
    IPR004383. rRNA_lsu_MTrfase_RlmN/Cfr.
    IPR007197. rSAM.
    [Graphical view ]
    PANTHERi PTHR30544. PTHR30544. 1 hit.
    Pfami PF04055. Radical_SAM. 1 hit.
    [Graphical view ]
    PIRSFi PIRSF006004. CHP00048. 1 hit.
    SMARTi SM00729. Elp3. 1 hit.
    [Graphical view ]
    TIGRFAMsi TIGR00048. TIGR00048. 1 hit.
    ProtoNeti Search...

    Publicationsi

    1. "Comparative analyses of the complete genome sequences of Pierce's disease and citrus variegated chlorosis strains of Xylella fastidiosa."
      Van Sluys M.A., de Oliveira M.C., Monteiro-Vitorello C.B., Miyaki C.Y., Furlan L.R., Camargo L.E.A., da Silva A.C.R., Moon D.H., Takita M.A., Lemos E.G.M., Machado M.A., Ferro M.I.T., da Silva F.R., Goldman M.H.S., Goldman G.H., Lemos M.V.F., El-Dorry H., Tsai S.M.
      , Carrer H., Carraro D.M., de Oliveira R.C., Nunes L.R., Siqueira W.J., Coutinho L.L., Kimura E.T., Ferro E.S., Harakava R., Kuramae E.E., Marino C.L., Giglioti E., Abreu I.L., Alves L.M.C., do Amaral A.M., Baia G.S., Blanco S.R., Brito M.S., Cannavan F.S., Celestino A.V., da Cunha A.F., Fenille R.C., Ferro J.A., Formighieri E.F., Kishi L.T., Leoni S.G., Oliveira A.R., Rosa V.E. Jr., Sassaki F.T., Sena J.A.D., de Souza A.A., Truffi D., Tsukumo F., Yanai G.M., Zaros L.G., Civerolo E.L., Simpson A.J.G., Almeida N.F. Jr., Setubal J.C., Kitajima J.P.
      J. Bacteriol. 185:1018-1026(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: Temecula1 / ATCC 700964.

    Entry informationi

    Entry nameiRLMN_XYLFT
    AccessioniPrimary (citable) accession number: Q87B36
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: September 2, 2008
    Last sequence update: June 1, 2003
    Last modified: October 1, 2014
    This is version 80 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Reaction proceeds by a ping-pong mechanism involving intermediate methylation of a conserved cysteine residue.UniRule annotation

    Keywords - Technical termi

    Complete proteome

    Documents

    1. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3