Modomics - A Database of RNA Modifications

ID Card:

Full name: rRNA adenine N-6-methyltransferase
Synonym: macrolide-lincosamide-streptogramin B resistance 23S rRNA methyltransferase
GI: 127198
Orf: ermC'
COG: COG0030
UniProt: P13956
Structures: | 1QAM | 1QAN | 1QAO | 1QAQ | 2ERC |
Alpha Fold Predicted Structure: AF-P13956-F1
Enzyme type: methyltransferase
Position of modification - modification: l:2085(2058) - m6A


PDB Structures:


1QAM

Structure Description:

Title:
Classification:
Technique:

Abstract of the PDB Structure's related Publication:

The rRNA methyltransferase ErmC' transfers methyl groups from S -adenosyl-l-methionine to atom N6 of an adenine base within the peptidyltransferase loop of 23 S rRNA, thus conferring antibiotic resistance against a number of macrolide antibiotics. The crystal structures of ErmC' and of its complexes with the cofactor S -adenosyl-l-methionine, the reaction product S-adenosyl-l-homocysteine and the methyltransferase inhibitor Sinefungin, respectively, show that the enzyme undergoes small conformational changes upon ligand binding. Overall, the ligand molecules bind to the protein in a similar mode as observed for other methyltransferases. Small differences between the binding of the amino acid parts of the different ligands are correlated with differences in their chemical structure. A model for the transition-state based on the atomic details of the active site is consistent with a one-step methyl-transfer mechanism and might serve as a first step towards the design of potent Erm inhibitors.

Download RCSB-PDB Structures:

Pdb Files   1QAM.pdb   1QAN.pdb   1QAO.pdb   1QAQ.pdb   2ERC.pdb  
Pdbx/mmCIF Files   1QAM.cif   1QAN.cif   1QAO.cif   1QAQ.cif   2ERC.cif  


Protein sequence:

MNEKNIKHSQNFITSKHNIDKIMTNIRLNEHDNIFEIGSGKGHFTLELVQRCNFVTAIEIDHKLCKTTENKLVDHDNFQVLNKDILQFKFPKNQSYKIFGNIPYNISTDIIRKIVFDSIADEIYLIVEYGFAKRLLNTKRSLALFLMAEVDISILSMVPREYFHPKPKVNSSLIRLNRKKSRISHKDKQKYNYFVMKWVNKEYKKIFTKNQFNNSLKHAGIDDLNNISFEQFLSLFNSYKLFNK

Comments:

ErmC' methylates the exocyclic amine of A2058 (E. coli numbering) in helix 75 of 23S rRNA. It is responsible for the development of bacterial resistance to lincosamide/streptogramin-type of antibiotics.




Reaction Substrate SubstrateType Position (Anti)Codon Modified (Anti)Codon Amino Acid Change Transcript Name Transcript Region Cellular Localization References
A:m6A RNA rRNA 2085 LSU-23S Prokaryotic Cytosol 7543473   

Alpha Fold Predicted Structure:






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Protein sequence:

M N E K N I K H S Q N F I T S K H N I D K I M T N I R L N E H D N I F E I G S G K G H F T L E L V Q R C N F V T A I E I D H K L C K T T E N K L V D H D N F Q V L N K D I L Q F K F P K N Q S Y K I F G N I P Y N I S T D I I R K I V F D S I A D E I Y L I V E Y G F A K R L L N T K R S L A L F L M A E V D I S I L S M V P R E Y F H P K P K V N S S L I R L N R K K S R I S H K D K Q K Y N Y F V M K W V N K E Y K K I F T K N Q F N N S L K H A G I D D L N N I S F E Q F L S L F N S Y K L F N K

Secondary Structure Alphabet

  • G: 3-turn helix (310helix)
  • H: α-helix
  • I: 𝝅-helix (5 - turn helix)
  • T: Hydrogen Bonded Turn
  • B: β-sheet
  • S: Bend
  • C: Coil (residues not present in any of the above conformations)
  • N: Not assigned

Download PDB Structures & DSSP Secondary Structures:

Alpha Fold Pdb Files   AF-P13956-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-P13956-F1.cif  
DSSP Secondary Structures   P13956.dssp  





Publications:

Title Authors Journal Details PubMed Id DOI
Sequence and properties of pIM13, a macrolide-lincosamide-streptogramin B resistance plasmid from Bacillus subtilis. Monod M, Denoya C, Dubnau D J Bacteriol [details] 3087948 -
Substrate requirements for ErmC' methyltransferase activity. Zhong P, Pratt SD, Edalji RP, Walter KA, Holzman TF, Shivakumar AG, Katz L J Bacteriol [details] 7543473 -
Family background of children with Down's syndrome and of children with a similar degree of mental retardation. Gath A, Gumley D Br J Psychiatry [details] 2946350 -
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 JM, Feder M, Pongor S, Flogel M Nucleic Acids Res [details] 12907737 -
Crystal structure of ErmC', an rRNA methyltransferase which mediates antibiotic resistance in bacteria. Bussiere DE, Muchmore SW, Dealwis CG, Schluckebier G, Nienaber VL, Edalji RP, Walter KA, Ladror US, Holzman TF, Abad-Zapatero C Biochemistry [details] 9585521 -
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 KD, Kavanaugh TJ, Abad-Zapatero C J Mol Biol [details] 10366505 -

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