Modomics - A Database of RNA Modifications

ID Card:

Full name: rRNA adenine N-6-methyltransferase
Synonym: Erythromycin resistance protein, Macrolide-lincosamide-streptogramin B resistance protein
GI: 150421549
UniProt: P07287
Structures: | 6NVM |
Alpha Fold Predicted Structure: AF-P07287-F1
Complex: none
Enzyme type: methyltransferase


PDB Structures:


6NVM

Structure Description:

Title: Crystal structure of 23S rRNA methyltransferase ErmE
Classification: TRANSFERASE
Technique: X-Ray Diffraction
Resolution: 1.75
R value free: 0.218
R value observed: 0.194
R value work: 0.192

Abstract of the PDB Structure's related Publication:

Pathogens often receive antibiotic resistance genes through horizontal gene transfer from bacteria that produce natural antibiotics. ErmE is a methyltransferase (MTase) from Saccharopolyspora erythraea that dimethylates A2058 in 23S rRNA using S-adenosyl methionine (SAM) as methyl donor, protecting the ribosomes from macrolide binding. To gain insights into the mechanism of macrolide resistance, the crystal structure of ErmE was determined to 1.75 Å resolution. ErmE consists of an N-terminal Rossmann-like α/ß catalytic domain and a C-terminal helical domain. Comparison with ErmC' that despite only 24% sequence identity has the same function, reveals highly similar catalytic domains. Accordingly, superposition with the catalytic domain of ErmC' in complex with SAM suggests that the cofactor binding site is conserved. The two structures mainly differ in the C-terminal domain, which in ErmE contains a longer loop harboring an additional 3 10 helix that interacts with the catalytic domain to stabilize the tertiary structure. Notably, ErmE also differs from ErmC' by having long disordered extensions at its N- and C-termini. A C-terminal disordered region rich in arginine and glycine is also a present in two other MTases, PikR1 and PikR2, which share about 30% sequence identity with ErmE and methylate the same nucleotide in 23S rRNA.

Download RCSB-PDB Structures:

Pdb Files   6NVM.pdb  
Pdbx/mmCIF Files   6NVM.cif  


Protein sequence:

MSSSDEQPRPRRRNQDRQHPNQNRPVLGRTERDRNRRQFGQNFLRDRKTIARIAETAELRPDLPVLEAGPGEGLLTRELADRARQVTSYEIDPRLAKSLREKLSGHPNIEVVNADFLTAEPPPEPFAFVGAIPYGITSAIVDWCLEAPTIETATMVTQLEFARKRTGDYGRWSRLTVMTWPLFEWEFVEKVDRRLFKPVPKVDSAIMRLRRRAEPLLEGAALERYESMVELCFTGVGGNIQASLLRKYPRRRVEAALDHAGVGGGAVVAYVRPEQWLRLFERLDQKNEPRGGQPQRGRRTGGRDHGDRRTGGQDRGDRRTGGRDHRDRQASGHGDRRSSGRNRDDGRTGEREQGDQGGRRGPSGGGRTGGRPGRRGGPGQR

Comments:

The Erm methyltransferases confer resistance to macrolide, lincosamide and streptogramin B (MLS) antibiotics by methylation of a single adenosine base within bacterial 23 S ribosomal RNA. The ErmE methyltransferase, from the macrolide-producing bacterium Saccharopolyspora erythraea, recognizes a motif within domain V of the rRNA that specifically targets adenosine 2058 (A2058) for methylation.





Alpha Fold Predicted Structure:






Clear Selection and Reset Camera

Protein sequence:

M S S S D E Q P R P R R R N Q D R Q H P N Q N R P V L G R T E R D R N R R Q F G Q N F L R D R K T I A R I A E T A E L R P D L P V L E A G P G E G L L T R E L A D R A R Q V T S Y E I D P R L A K S L R E K L S G H P N I E V V N A D F L T A E P P P E P F A F V G A I P Y G I T S A I V D W C L E A P T I E T A T M V T Q L E F A R K R T G D Y G R W S R L T V M T W P L F E W E F V E K V D R R L F K P V P K V D S A I M R L R R R A E P L L E G A A L E R Y E S M V E L C F T G V G G N I Q A S L L R K Y P R R R V E A A L D H A G V G G G A V V A Y V R P E Q W L R L F E R L D Q K N E P R G G Q P Q R G R R T G G R D H G D R R T G G Q D R G D R R T G G R D H R D R Q A S G H G D R R S S G R N R D D G R T G E R E Q G D Q G G R R G P S G G G R T G G R P G R R G G P G Q R
50100150200250300350SequenceGHTSN

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-P07287-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-P07287-F1.cif  
DSSP Secondary Structures   P07287.dssp  





Publications: