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P75864

- RLMKL_ECOLI

UniProt

P75864 - RLMKL_ECOLI

Protein

Ribosomal RNA large subunit methyltransferase K/L

Gene

rlmL

Organism
Escherichia coli (strain K12)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 119 (01 Oct 2014)
      Sequence version 1 (01 Feb 1997)
      Previous versions | rss
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    Functioni

    Specifically methylates the guanine in position 2445 (m2G2445) and the guanine in position 2069 (m7G2069) of 23S rRNA. Methylation occurs before assembly of 23S rRNA into 50S subunits.3 Publications

    Catalytic activityi

    S-adenosyl-L-methionine + guanine(2445) in 23S rRNA = S-adenosyl-L-homocysteine + N(2)-methylguanine(2445) in 23S rRNA.
    S-adenosyl-L-methionine + guanine(2069) in 23S rRNA = S-adenosyl-L-homocysteine + N(7)-methylguanine(2069) in 23S rRNA.

    Enzyme regulationi

    The N-terminal RlmL activity is enhanced by the C-terminal RlmK activity.1 Publication

    GO - Molecular functioni

    1. 23S rRNA (guanine(2445)-N(2))-methyltransferase activity Source: UniProtKB-HAMAP
    2. protein binding Source: IntAct
    3. RNA binding Source: UniProtKB-HAMAP
    4. rRNA (guanine-N2-)-methyltransferase activity Source: UniProtKB
    5. rRNA (guanine-N7-)-methyltransferase activity Source: EcoCyc

    GO - Biological processi

    1. rRNA (guanine-N7)-methylation Source: GOC
    2. rRNA base methylation Source: EcoCyc
    3. rRNA methylation Source: UniProtKB

    Keywords - Molecular functioni

    Methyltransferase, Transferase

    Keywords - Biological processi

    rRNA processing

    Keywords - Ligandi

    RNA-binding, S-adenosyl-L-methionine

    Enzyme and pathway databases

    BioCyciEcoCyc:G6488-MONOMER.
    ECOL316407:JW0931-MONOMER.
    MetaCyc:G6488-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Ribosomal RNA large subunit methyltransferase K/L
    Including the following 2 domains:
    23S rRNA m2G2445 methyltransferase (EC:2.1.1.173)
    Alternative name(s):
    rRNA (guanine-N(2)-)-methyltransferase RlmL
    23S rRNA m7G2069 methyltransferase (EC:2.1.1.264)
    Alternative name(s):
    rRNA (guanine-N(7)-)-methyltransferase RlmK
    Gene namesi
    Name:rlmL
    Synonyms:rlmK, rlmKL, ycbY
    Ordered Locus Names:b0948, JW0931
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

    Organism-specific databases

    EcoGeneiEG13717. rlmL.

    Subcellular locationi

    Cytoplasm Curated

    GO - Cellular componenti

    1. cytoplasm Source: UniProtKB

    Keywords - Cellular componenti

    Cytoplasm

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi195 – 1951D → A: Does not affect methyltransferase activity. 1 Publication
    Mutagenesisi309 – 3091N → A: Impairs m2G2445 formation, but does not affect m7G2069 formation. 1 Publication
    Mutagenesisi397 – 3971N → A: Impairs m2G2445 formation, but does not affect m7G2069 formation. 1 Publication
    Mutagenesisi530 – 5301R → A: Does not affect methyltransferase activity. 1 Publication
    Mutagenesisi568 – 5681D → A: Impairs m7G2069 formation, but does not affect m2G2445 formation. 1 Publication
    Mutagenesisi597 – 5971D → A: Does not affect methyltransferase activity. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 702702Ribosomal RNA large subunit methyltransferase K/LPRO_0000140473Add
    BLAST

    Proteomic databases

    PaxDbiP75864.
    PRIDEiP75864.

    Expressioni

    Gene expression databases

    GenevestigatoriP75864.

    Interactioni

    Subunit structurei

    Monomer.1 Publication

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    typAP321323EBI-547718,EBI-562154

    Protein-protein interaction databases

    DIPiDIP-11486N.
    IntActiP75864. 48 interactions.
    MINTiMINT-1268879.
    STRINGi511145.b0948.

    Structurei

    Secondary structure

    1
    702
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi2 – 76
    Helixi13 – 2210
    Beta strandi26 – 316
    Beta strandi34 – 396
    Helixi41 – 5010
    Beta strandi55 – 6511
    Helixi69 – 779
    Helixi81 – 844
    Beta strandi91 – 966
    Helixi105 – 12117
    Turni122 – 1243
    Beta strandi132 – 1343
    Beta strandi136 – 1449
    Beta strandi147 – 15711
    Beta strandi163 – 1653
    Helixi175 – 18410
    Beta strandi193 – 1953
    Helixi202 – 21110
    Turni216 – 2194
    Turni224 – 2274
    Helixi233 – 25321
    Beta strandi258 – 2636
    Helixi265 – 27713
    Helixi281 – 2833
    Beta strandi284 – 2885
    Helixi291 – 2933
    Beta strandi305 – 3084
    Helixi320 – 33617
    Beta strandi341 – 3477
    Helixi349 – 3535
    Beta strandi359 – 3679
    Beta strandi370 – 3789
    Helixi393 – 41321
    Beta strandi417 – 4237
    Beta strandi430 – 4356
    Beta strandi438 – 4436
    Helixi454 – 47017
    Helixi474 – 4763
    Beta strandi477 – 4804
    Beta strandi501 – 5055
    Beta strandi508 – 5125
    Beta strandi514 – 5196
    Helixi524 – 5263
    Helixi527 – 53610
    Beta strandi541 – 5466
    Helixi551 – 5588
    Beta strandi562 – 5698
    Helixi571 – 58313
    Beta strandi591 – 5966
    Helixi598 – 6047
    Beta strandi609 – 6146
    Helixi631 – 64515
    Beta strandi646 – 65611
    Helixi665 – 6706
    Beta strandi673 – 6775
    Turni679 – 6824
    Helixi685 – 6873
    Beta strandi695 – 7017

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    3V8VX-ray2.60A/B1-702[»]
    3V97X-ray2.20A/B1-702[»]
    ProteinModelPortaliP75864.
    SMRiP75864. Positions 1-702.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini43 – 154112THUMPAdd
    BLAST

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni1 – 397397RlmLAdd
    BLAST
    Regioni398 – 702305RlmKAdd
    BLAST

    Domaini

    Consists of a N-terminal RlmL domain and a C-terminal RlmK domain, linked by a highly flexible loop.2 Publications

    Sequence similaritiesi

    Contains 1 THUMP domain.Curated

    Phylogenomic databases

    eggNOGiCOG0116.
    HOGENOMiHOG000218371.
    KOiK12297.
    OMAiNKRGFKM.
    OrthoDBiEOG6HJ238.
    PhylomeDBiP75864.

    Family and domain databases

    Gene3Di3.40.50.150. 3 hits.
    HAMAPiMF_01858. 23SrRNA_methyltr_KL.
    InterProiIPR017244. 23SrRNA_methyltr_KL.
    IPR002052. DNA_methylase_N6_adenine_CS.
    IPR002296. N12N6_MeTrfase.
    IPR000241. RNA_methylase_dom.
    IPR019614. SAM-dep_methyl-trfase.
    IPR029063. SAM-dependent_MTases-like.
    IPR004114. THUMP.
    [Graphical view]
    PfamiPF10672. Methyltrans_SAM. 1 hit.
    PF02926. THUMP. 1 hit.
    PF01170. UPF0020. 1 hit.
    [Graphical view]
    PIRSFiPIRSF037618. RNA_Mtase_bacteria_prd. 1 hit.
    PRINTSiPR00507. N12N6MTFRASE.
    SMARTiSM00981. THUMP. 1 hit.
    [Graphical view]
    SUPFAMiSSF53335. SSF53335. 3 hits.
    PROSITEiPS51165. THUMP. 1 hit.
    PS01261. UPF0020. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P75864-1 [UniParc]FASTAAdd to Basket

    « Hide

    MNSLFASTAR GLEELLKTEL ENLGAVECQV VQGGVHFKGD TRLVYQSLMW    50
    SRLASRIMLP LGECKVYSDL DLYLGVQAIN WTEMFNPGAT FAVHFSGLND 100
    TIRNSQYGAM KVKDAIVDAF TRKNLPRPNV DRDAPDIRVN VWLHKETASI 150
    ALDLSGDGLH LRGYRDRAGI APIKETLAAA IVMRSGWQPG TPLLDPMCGS 200
    GTLLIEAAML ATDRAPGLHR GRWGFSGWAQ HDEAIWQEVK AEAQTRARKG 250
    LAEYSSHFYG SDSDARVIQR ARTNARLAGI GELITFEVKD VAQLTNPLPK 300
    GPYGTVLSNP PYGERLDSEP ALIALHSLLG RIMKNQFGGW NLSLFSASPD 350
    LLSCLQLRAD KQYKAKNGPL DCVQKNYHVA ESTPDSKPAM VAEDYTNRLR 400
    KNLKKFEKWA RQEGIECYRL YDADLPEYNV AVDRYADWVV VQEYAPPKTI 450
    DAHKARQRLF DIIAATISVL GIAPNKLVLK TRERQKGKNQ YQKLGEKGEF 500
    LEVTEYNAHL WVNLTDYLDT GLFLDHRIAR RMLGQMSKGK DFLNLFSYTG 550
    SATVHAGLGG ARSTTTVDMS RTYLEWAERN LRLNGLTGRA HRLIQADCLA 600
    WLREANEQFD LIFIDPPTFS NSKRMEDAFD VQRDHLALMK DLKRLLRAGG 650
    TIMFSNNKRG FRMDLDGLAK LGLKAQEITQ KTLSQDFARN RQIHNCWLIT 700
    AA 702
    Length:702
    Mass (Da):78,854
    Last modified:February 1, 1997 - v1
    Checksum:i9EF24AD7A32AC429
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U00096 Genomic DNA. Translation: AAC74034.1.
    AP009048 Genomic DNA. Translation: BAA35703.1.
    PIRiC64835.
    RefSeqiNP_415468.1. NC_000913.3.
    YP_489220.1. NC_007779.1.

    Genome annotation databases

    EnsemblBacteriaiAAC74034; AAC74034; b0948.
    BAA35703; BAA35703; BAA35703.
    GeneIDi12931031.
    945564.
    KEGGiecj:Y75_p0920.
    eco:b0948.
    PATRICi32117115. VBIEscCol129921_0982.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U00096 Genomic DNA. Translation: AAC74034.1 .
    AP009048 Genomic DNA. Translation: BAA35703.1 .
    PIRi C64835.
    RefSeqi NP_415468.1. NC_000913.3.
    YP_489220.1. NC_007779.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    3V8V X-ray 2.60 A/B 1-702 [» ]
    3V97 X-ray 2.20 A/B 1-702 [» ]
    ProteinModelPortali P75864.
    SMRi P75864. Positions 1-702.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    DIPi DIP-11486N.
    IntActi P75864. 48 interactions.
    MINTi MINT-1268879.
    STRINGi 511145.b0948.

    Proteomic databases

    PaxDbi P75864.
    PRIDEi P75864.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAC74034 ; AAC74034 ; b0948 .
    BAA35703 ; BAA35703 ; BAA35703 .
    GeneIDi 12931031.
    945564.
    KEGGi ecj:Y75_p0920.
    eco:b0948.
    PATRICi 32117115. VBIEscCol129921_0982.

    Organism-specific databases

    EchoBASEi EB3481.
    EcoGenei EG13717. rlmL.

    Phylogenomic databases

    eggNOGi COG0116.
    HOGENOMi HOG000218371.
    KOi K12297.
    OMAi NKRGFKM.
    OrthoDBi EOG6HJ238.
    PhylomeDBi P75864.

    Enzyme and pathway databases

    BioCyci EcoCyc:G6488-MONOMER.
    ECOL316407:JW0931-MONOMER.
    MetaCyc:G6488-MONOMER.

    Miscellaneous databases

    PROi P75864.

    Gene expression databases

    Genevestigatori P75864.

    Family and domain databases

    Gene3Di 3.40.50.150. 3 hits.
    HAMAPi MF_01858. 23SrRNA_methyltr_KL.
    InterProi IPR017244. 23SrRNA_methyltr_KL.
    IPR002052. DNA_methylase_N6_adenine_CS.
    IPR002296. N12N6_MeTrfase.
    IPR000241. RNA_methylase_dom.
    IPR019614. SAM-dep_methyl-trfase.
    IPR029063. SAM-dependent_MTases-like.
    IPR004114. THUMP.
    [Graphical view ]
    Pfami PF10672. Methyltrans_SAM. 1 hit.
    PF02926. THUMP. 1 hit.
    PF01170. UPF0020. 1 hit.
    [Graphical view ]
    PIRSFi PIRSF037618. RNA_Mtase_bacteria_prd. 1 hit.
    PRINTSi PR00507. N12N6MTFRASE.
    SMARTi SM00981. THUMP. 1 hit.
    [Graphical view ]
    SUPFAMi SSF53335. SSF53335. 3 hits.
    PROSITEi PS51165. THUMP. 1 hit.
    PS01261. UPF0020. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / MG1655 / ATCC 47076.
    3. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
      Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
      Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    4. "Identification of Escherichia coli m2G methyltransferases: I. the ycbY gene encodes a methyltransferase specific for G2445 of the 23 S rRNA."
      Lesnyak D.V., Sergiev P.V., Bogdanov A.A., Dontsova O.A.
      J. Mol. Biol. 364:20-25(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, CATALYTIC ACTIVITY.
    5. "Purification, crystallization and preliminary X-ray crystallographic analysis of 23S RNA m(2)G2445 methyltransferase RlmL from Escherichia coli."
      Wang K.T., Ma L., Nan J., Su X.D., Li L.
      Acta Crystallogr. F 66:1484-1486(2010) [PubMed] [Europe PMC] [Abstract]
      Cited for: CRYSTALLIZATION.
    6. "Base methylations in the double-stranded RNA by a fused methyltransferase bearing unwinding activity."
      Kimura S., Ikeuchi Y., Kitahara K., Sakaguchi Y., Suzuki T., Suzuki T.
      Nucleic Acids Res. 40:4071-4085(2012) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, CATALYTIC ACTIVITY, ENZYME REGULATION, DOMAIN, MUTAGENESIS OF ASP-195; ASN-309; ASN-397; ARG-530; ASP-568 AND ASP-597.
    7. "Structure of the bifunctional methyltransferase YcbY (RlmKL) that adds the m7G2069 and m2G2445 modifications in Escherichia coli 23S rRNA."
      Wang K.T., Desmolaize B., Nan J., Zhang X.W., Li L.F., Douthwaite S., Su X.D.
      Nucleic Acids Res. 40:5138-5148(2012) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.20 ANGSTROMS), FUNCTION, CATALYTIC ACTIVITY, SUBUNIT, DOMAIN.

    Entry informationi

    Entry nameiRLMKL_ECOLI
    AccessioniPrimary (citable) accession number: P75864
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: November 1, 1997
    Last sequence update: February 1, 1997
    Last modified: October 1, 2014
    This is version 119 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

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. Escherichia coli
      Escherichia coli (strain K12): entries and cross-references to EcoGene
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3