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P13956

- ERM_BACIU

UniProt

P13956 - ERM_BACIU

Protein

rRNA adenine N-6-methyltransferase

Gene

ermC'

Organism
Bacillus subtilis
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 87 (01 Oct 2014)
      Sequence version 1 (01 Jan 1990)
      Previous versions | rss
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    Functioni

    This protein produces a dimethylation of the adenine residue at position 2085 in 23S rRNA, resulting in reduced affinity between ribosomes and macrolide-lincosamide-streptogramin B antibiotics.2 Publications

    Catalytic activityi

    2 S-adenosyl-L-methionine + adenine(2085) in 23S rRNA = 2 S-adenosyl-L-homocysteine + N(6)-dimethyladenine(2085) in 23S rRNA.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei11 – 111S-adenosyl-L-methionine; via carbonyl oxygen
    Binding sitei13 – 131S-adenosyl-L-methionine; via amide nitrogen
    Binding sitei38 – 381S-adenosyl-L-methionine; via carbonyl oxygen
    Binding sitei59 – 591S-adenosyl-L-methionine
    Binding sitei84 – 841S-adenosyl-L-methionine
    Binding sitei101 – 1011S-adenosyl-L-methionine

    GO - Molecular functioni

    1. 23S rRNA (adenine(2085)-N(6))-dimethyltransferase activity Source: UniProtKB-EC
    2. RNA binding Source: UniProtKB-KW
    3. rRNA (adenine-N6,N6-)-dimethyltransferase activity Source: InterPro

    GO - Biological processi

    1. response to antibiotic Source: UniProtKB-KW

    Keywords - Molecular functioni

    Methyltransferase, Transferase

    Keywords - Biological processi

    Antibiotic resistance

    Keywords - Ligandi

    RNA-binding, S-adenosyl-L-methionine

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    rRNA adenine N-6-methyltransferase (EC:2.1.1.184)
    Alternative name(s):
    Erythromycin resistance protein
    Macrolide-lincosamide-streptogramin B resistance protein
    Gene namesi
    Name:ermC'
    Encoded oniPlasmid pIM130 Publication
    OrganismiBacillus subtilis
    Taxonomic identifieri1423 [NCBI]
    Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi11 – 111N → A: Reduces activity about 3-fold.
    Mutagenesisi101 – 1011N → A: Decreases affinity for S-adenosyl-L-methionine 4-fold. Reduces activity by 90%. 1 Publication
    Mutagenesisi104 – 1041Y → A: Loss of activity. 1 Publication
    Mutagenesisi108 – 1081T → A: Decreases affinity for S-adenosyl-L-methionine 8-fold. Reduces activity by 99%. 1 Publication
    Mutagenesisi112 – 1121R → A: Reduces activity by 90%. 1 Publication
    Mutagenesisi112 – 1121R → D: Decreases affinity for S-adenosyl-L-methionine 5-fold. Decreases affinity for RNA 6-fold. Reduces activity by 99%. 1 Publication
    Mutagenesisi133 – 1331K → A: Reduces activity by about 80%. 1 Publication
    Mutagenesisi134 – 1341R → A: Decreases affinity for S-adenosyl-L-methionine 7-fold. Decreases affinity for RNA about 4-fold. Reduces activity by over 99%. May severely impair protein folding. 1 Publication
    Mutagenesisi140 – 1401R → A: Decreases affinity for S-adenosyl-L-methionine 7-fold. Reduces activity by about 85%. 1 Publication
    Mutagenesisi165 – 1651P → A: Decreases affinity for S-adenosyl-L-methionine 6-fold. Reduces activity by about 96%. 1 Publication
    Mutagenesisi166 – 1661K → A: Decreases affinity for RNA about 6-fold. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 244244rRNA adenine N-6-methyltransferasePRO_0000101674Add
    BLAST

    Interactioni

    Structurei

    Secondary structure

    1
    244
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi16 – 238
    Beta strandi33 – 375
    Helixi43 – 519
    Beta strandi52 – 587
    Helixi62 – 7110
    Turni72 – 743
    Beta strandi77 – 815
    Helixi85 – 873
    Beta strandi92 – 943
    Beta strandi97 – 1015
    Helixi104 – 1063
    Helixi107 – 11610
    Beta strandi121 – 1288
    Helixi129 – 1357
    Beta strandi138 – 1403
    Helixi141 – 1466
    Turni147 – 1493
    Beta strandi150 – 1589
    Helixi160 – 1623
    Beta strandi163 – 1653
    Beta strandi171 – 1788
    Helixi185 – 1873
    Helixi188 – 19912
    Helixi203 – 2053
    Helixi209 – 21911
    Helixi229 – 24214

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1QAMX-ray2.20A1-244[»]
    1QANX-ray2.40A1-244[»]
    1QAOX-ray2.70A1-244[»]
    1QAQX-ray2.80A1-244[»]
    2ERCX-ray3.03A/B1-244[»]
    ProteinModelPortaliP13956.
    SMRiP13956. Positions 9-244.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP13956.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the class I-like SAM-binding methyltransferase superfamily. rRNA adenine N(6)-methyltransferase family.PROSITE-ProRule annotation

    Family and domain databases

    Gene3Di1.10.8.100. 1 hit.
    3.40.50.150. 1 hit.
    InterProiIPR023165. rRNA_Ade_diMease-like.
    IPR020596. rRNA_Ade_Mease_Trfase_CS.
    IPR001737. rRNA_Ade_methylase_transferase.
    IPR020598. rRNA_Ade_methylase_Trfase_N.
    IPR029063. SAM-dependent_MTases-like.
    [Graphical view]
    PANTHERiPTHR11727. PTHR11727. 1 hit.
    PfamiPF00398. RrnaAD. 1 hit.
    [Graphical view]
    SMARTiSM00650. rADc. 1 hit.
    [Graphical view]
    SUPFAMiSSF53335. SSF53335. 1 hit.
    PROSITEiPS01131. RRNA_A_DIMETH. 1 hit.
    PS51689. SAM_RNA_A_N6_MT. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P13956-1 [UniParc]FASTAAdd to Basket

    « Hide

    MNEKNIKHSQ NFITSKHNID KIMTNIRLNE HDNIFEIGSG KGHFTLELVQ    50
    RCNFVTAIEI DHKLCKTTEN KLVDHDNFQV LNKDILQFKF PKNQSYKIFG 100
    NIPYNISTDI IRKIVFDSIA DEIYLIVEYG FAKRLLNTKR SLALFLMAEV 150
    DISILSMVPR EYFHPKPKVN SSLIRLNRKK SRISHKDKQK YNYFVMKWVN 200
    KEYKKIFTKN QFNNSLKHAG IDDLNNISFE QFLSLFNSYK LFNK 244
    Length:244
    Mass (Da):28,907
    Last modified:January 1, 1990 - v1
    Checksum:iFC7CA6524034D820
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    M13761 Genomic DNA. Translation: AAA98136.1.
    PIRiB25233.
    RefSeqiNP_040407.1. NC_001376.1.

    Genome annotation databases

    GeneIDi1263203.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    M13761 Genomic DNA. Translation: AAA98136.1 .
    PIRi B25233.
    RefSeqi NP_040407.1. NC_001376.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1QAM X-ray 2.20 A 1-244 [» ]
    1QAN X-ray 2.40 A 1-244 [» ]
    1QAO X-ray 2.70 A 1-244 [» ]
    1QAQ X-ray 2.80 A 1-244 [» ]
    2ERC X-ray 3.03 A/B 1-244 [» ]
    ProteinModelPortali P13956.
    SMRi P13956. Positions 9-244.
    ModBasei Search...
    MobiDBi Search...

    Chemistry

    BindingDBi P13956.
    ChEMBLi CHEMBL4251.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    GeneIDi 1263203.

    Miscellaneous databases

    EvolutionaryTracei P13956.

    Family and domain databases

    Gene3Di 1.10.8.100. 1 hit.
    3.40.50.150. 1 hit.
    InterProi IPR023165. rRNA_Ade_diMease-like.
    IPR020596. rRNA_Ade_Mease_Trfase_CS.
    IPR001737. rRNA_Ade_methylase_transferase.
    IPR020598. rRNA_Ade_methylase_Trfase_N.
    IPR029063. SAM-dependent_MTases-like.
    [Graphical view ]
    PANTHERi PTHR11727. PTHR11727. 1 hit.
    Pfami PF00398. RrnaAD. 1 hit.
    [Graphical view ]
    SMARTi SM00650. rADc. 1 hit.
    [Graphical view ]
    SUPFAMi SSF53335. SSF53335. 1 hit.
    PROSITEi PS01131. RRNA_A_DIMETH. 1 hit.
    PS51689. SAM_RNA_A_N6_MT. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Sequence and properties of pIM13, a macrolide-lincosamide-streptogramin B resistance plasmid from Bacillus subtilis."
      Monod M., Denoya C., Dubnau D.
      J. Bacteriol. 167:138-147(1986) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    2. "Substrate requirements for ErmC' methyltransferase activity."
      Zhong P., Pratt S.D., Edalji R.P., Walter K.A., Holzman T.F., Shivakumar A.G., Katz L.
      J. Bacteriol. 177:4327-4332(1995) [PubMed] [Europe PMC] [Abstract]
      Cited for: CHARACTERIZATION.
    3. "Mutational analysis defines the roles of conserved amino acid residues in the predicted catalytic pocket of the rRNA:m6A methyltransferase ErmC'."
      Maravic G., Feder M., Pongor S., Floegel M., Bujnicki J.M.
      J. Mol. Biol. 332:99-109(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: MUTAGENESIS OF ASN-101; TYR-104; PRO-165 AND LYS-166, RNA-BINDING, FUNCTION.
    4. "Alanine-scanning mutagenesis of the predicted rRNA-binding domain of ErmC' redefines the substrate-binding site and suggests a model for protein-RNA interactions."
      Maravic G., Bujnicki J.M., Feder M., Pongor S., Floegel M.
      Nucleic Acids Res. 31:4941-4949(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: MUTAGENESIS OF THR-108; ARG-112; LYS-133; ARG-134 AND ARG-140, RNA-BINDING, FUNCTION.
    5. "Crystal structure of ErmC', an rRNA methyltransferase which mediates antibiotic resistance in bacteria."
      Bussiere D.E., Muchmore S.W., Dealwis C.G., Schluckebier G., Nienaber V.L., Edalji R.P., Walter K.A., Ladror U.S., Holzman T.F., Abad-Zapatero C.
      Biochemistry 37:7103-7112(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS) OF 10-244.
      Strain: BD1109.
    6. "The 2.2-A structure of the rRNA methyltransferase ErmC' and its complexes with cofactor and cofactor analogs: implications for the reaction mechanism."
      Schluckebier G., Zhong P., Stewart K.D., Kavanaugh T.J., Abad-Zapatero C.
      J. Mol. Biol. 289:277-291(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS) IN COMPLEXES WITH S-ADENOSYL-L-METHIONINE AND SUBSTRATE ANALOGS.

    Entry informationi

    Entry nameiERM_BACIU
    AccessioniPrimary (citable) accession number: P13956
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: January 1, 1990
    Last sequence update: January 1, 1990
    Last modified: October 1, 2014
    This is version 87 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Caution

    In the genome of Neisseria meningitidis (serogroup B), the gene for this protein is present (NMB0066). It was introduced as part of a construct built to neutralize the virulence of the bacterium.Curated

    Keywords - Technical termi

    3D-structure, Plasmid

    Documents

    1. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3