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P13956

- ERM_BACIU

UniProt

P13956 - ERM_BACIU

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Protein

rRNA adenine N-6-methyltransferase

Gene
ermC'
Organism
Bacillus subtilis
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

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
Complete GO annotation...

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.

Miscellaneous databases

EvolutionaryTraceiP13956.

Family & Domainsi

Sequence similaritiesi

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: June 11, 2014
This is version 86 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.

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

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