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B1XXL6

- RLMN_LEPCP

UniProt

B1XXL6 - RLMN_LEPCP

Protein

Dual-specificity RNA methyltransferase RlmN

Gene

rlmN

Organism
Leptothrix cholodnii (strain ATCC 51168 / LMG 8142 / SP-6) (Leptothrix discophora (strain SP-6))
Status
Reviewed - Annotation score: 4 out of 5- Protein inferred from homologyi
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    • History
      Entry version 45 (01 Oct 2014)
      Sequence version 1 (20 May 2008)
      Previous versions | rss
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    • Comment

    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 sitei92 – 921Proton acceptorUniRule annotation
    Metal bindingi112 – 1121Iron-sulfur (4Fe-4S-S-AdoMet)UniRule annotation
    Metal bindingi116 – 1161Iron-sulfur (4Fe-4S-S-AdoMet)UniRule annotation
    Metal bindingi119 – 1191Iron-sulfur (4Fe-4S-S-AdoMet)UniRule annotation
    Binding sitei211 – 2111S-adenosyl-L-methionineUniRule annotation
    Binding sitei316 – 3161S-adenosyl-L-methionine; via amide nitrogen and carbonyl oxygenUniRule annotation
    Active sitei359 – 3591S-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

    BioCyciLCHO395495:GHYL-2918-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:Lcho_2871
    OrganismiLeptothrix cholodnii (strain ATCC 51168 / LMG 8142 / SP-6) (Leptothrix discophora (strain SP-6))
    Taxonomic identifieri395495 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaBetaproteobacteriaBurkholderialesLeptothrix
    ProteomesiUP000001693: 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 – 393393Dual-specificity RNA methyltransferase RlmNPRO_0000350237Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Disulfide bondi105 ↔ 359(transient)UniRule annotation

    Keywords - PTMi

    Disulfide bond

    Interactioni

    Protein-protein interaction databases

    STRINGi395495.Lcho_2871.

    Structurei

    3D structure databases

    ProteinModelPortaliB1XXL6.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni179 – 1802S-adenosyl-L-methionine bindingUniRule annotation
    Regioni233 – 2353S-adenosyl-L-methionine bindingUniRule annotation

    Sequence similaritiesi

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

    Phylogenomic databases

    eggNOGiCOG0820.
    HOGENOMiHOG000217992.
    KOiK06941.
    OMAiHEGSKFE.
    OrthoDBiEOG6DJZ2N.

    Family and domain databases

    Gene3Di3.20.20.70. 1 hit.
    HAMAPiMF_01849. RNA_methyltr_RlmN.
    InterProiIPR013785. Aldolase_TIM.
    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.
    TIGRFAMsiTIGR00048. TIGR00048. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    B1XXL6-1 [UniParc]FASTAAdd to Basket

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    MTAVNLLDFD LDALAAYCEQ LGEKRFRAVQ LFRWIHQRGA ADFGQMSDLA    50
    KSLRSKLADV ACIAPLRVLS EHRSSDGTIK WLFDVGDGNA VETVYIPEDD 100
    RATLCISSQA GCAVGCRFCS TGHQGFSRNL STAEILAQLW YAEHSLRRER 150
    AEGVSVGARA ATGPASERII SNVVMMGMGE PLQNYAAVLP ALRVMLDDHG 200
    YGLSRRRVTV STSGVVPMID RLAADLPVAL AVSLHACDDA LRDVLVPLNR 250
    KYPLAELLGA CQAYLASAPR DFITFEYCML DGVNDSDEQA RALLKLVGDK 300
    GPVGRLPCKF NLIPFNPFPE SGLKRSGNER VQAFAQVLID GGLVTTVRKT 350
    RGDDIDAACG QLAGEVQDRT RVQERMTRSP IRVIRSAAQP DAA 393
    Length:393
    Mass (Da):42,738
    Last modified:May 20, 2008 - v1
    Checksum:i34A9397DB5B1FA23
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    CP001013 Genomic DNA. Translation: ACB35136.1.
    RefSeqiYP_001791901.1. NC_010524.1.

    Genome annotation databases

    EnsemblBacteriaiACB35136; ACB35136; Lcho_2871.
    GeneIDi6159746.
    KEGGilch:Lcho_2871.
    PATRICi22396153. VBILepCho83238_2902.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    CP001013 Genomic DNA. Translation: ACB35136.1 .
    RefSeqi YP_001791901.1. NC_010524.1.

    3D structure databases

    ProteinModelPortali B1XXL6.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 395495.Lcho_2871.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai ACB35136 ; ACB35136 ; Lcho_2871 .
    GeneIDi 6159746.
    KEGGi lch:Lcho_2871.
    PATRICi 22396153. VBILepCho83238_2902.

    Phylogenomic databases

    eggNOGi COG0820.
    HOGENOMi HOG000217992.
    KOi K06941.
    OMAi HEGSKFE.
    OrthoDBi EOG6DJZ2N.

    Enzyme and pathway databases

    BioCyci LCHO395495:GHYL-2918-MONOMER.

    Family and domain databases

    Gene3Di 3.20.20.70. 1 hit.
    HAMAPi MF_01849. RNA_methyltr_RlmN.
    InterProi IPR013785. Aldolase_TIM.
    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.
    TIGRFAMsi TIGR00048. TIGR00048. 1 hit.
    ProtoNeti Search...

    Publicationsi

    1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 51168 / LMG 8142 / SP-6.

    Entry informationi

    Entry nameiRLMN_LEPCP
    AccessioniPrimary (citable) accession number: B1XXL6
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: September 2, 2008
    Last sequence update: May 20, 2008
    Last modified: October 1, 2014
    This is version 45 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, Reference proteome

    Documents

    1. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3