Crystal structure of rRNA methyltransferase Erm38 in complex with SAM

Experimental Data Snapshot

  • Resolution: 2.25 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 

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Crystal structure and functional analysis of mycobacterial erythromycin resistance methyltransferase Erm38 reveals its RNA-binding site.

Goh, B.C.Xiang, X.Lescar, J.Dedon, P.C.

(2022) J Biol Chem 298: 101571-101571

  • DOI: https://doi.org/10.1016/j.jbc.2022.101571
  • Primary Citation of Related Structures:  
    7F8A, 7F8B, 7F8C

  • PubMed Abstract: 

    Erythromycin resistance methyltransferases (Erms) confer resistance to macrolide, lincosamide, and streptogramin antibiotics in Gram-positive bacteria and mycobacteria. Although structural information for ErmAM, ErmC, and ErmE exists from Gram-positive bacteria, little is known about the Erms in mycobacteria, as there are limited biochemical data and no structures available. Here, we present crystal structures of Erm38 from Mycobacterium smegmatis in apoprotein and cofactor-bound forms. Based on structural analysis and mutagenesis, we identified several catalytically critical, positively charged residues at a putative RNA-binding site. We found that mutation of any of these sites is sufficient to abolish methylation activity, whereas the corresponding RNA-binding affinity of Erm38 remains unchanged. The methylation reaction thus appears to require a precise ensemble of amino acids to accurately position the RNA substrate, such that the target nucleotide can be methylated. In addition, we computationally constructed a model of Erm38 in complex with a 32-mer RNA substrate. This model shows the RNA substrate stably bound to Erm38 by a patch of positively charged residues. Furthermore, a π-π stacking interaction between a key aromatic residue of Erm38 and a target adenine of the RNA substrate forms a critical interaction needed for methylation. Taken together, these data provide valuable insights into Erm-RNA interactions, which will aid subsequent structure-based drug design efforts.

  • Organizational Affiliation

    Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology Centre, Singapore, Singapore; NTU Institute of Structural Biology, Experimental Medicine Building (EMB), Nanyang Technological University, Singapore, Singapore. Electronic address: boonchong@smart.mit.edu.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Erm(38)261Mycolicibacterium smegmatisMutation(s): 0 
Gene Names: erm(38)
Find proteins for Q79N53 (Mycolicibacterium smegmatis)
Explore Q79N53 
Go to UniProtKB:  Q79N53
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ79N53
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.25 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.018α = 90
b = 78.018β = 90
c = 101.536γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Research Foundation (NRF, Singapore)Singapore--

Revision History  (Full details and data files)

  • Version 1.0: 2022-01-12
    Type: Initial release
  • Version 1.1: 2022-07-27
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description