Structure of the Nosiheptide-resistance methyltransferase S-adenosyl-L-methionine Complex

Experimental Data Snapshot

  • Resolution: 2.10 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.199 

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Crystal Structure of the Nosiheptide-Resistance Methyltransferase of Streptomyces actuosus

Yang, H.Wang, Z.Shen, Y.Wang, P.Jia, X.Zhao, L.Zhou, P.Gong, R.Li, Z.Yang, Y.Chen, D.Murchie, A.I.H.Xu, Y.

(2010) Biochemistry 49: 6440-6450

  • DOI: https://doi.org/10.1021/bi1005915
  • Primary Citation of Related Structures:  
    3NK6, 3NK7

  • PubMed Abstract: 

    Nosiheptide-resistance methyltransferase (NHR) of Streptomyces actuosus is a class IV methyltransferase of the SpoU family and methylates 23S rRNA at nucleotide adenosine corresponding to A1067 in Escherichia coli. Such methylation is essential for resistance against nosiheptide, a sulfur peptide antibiotic, which is produced by the nosiheptide-producing strain, S. actuosus. Here, we report the crystal structures of NHR and NHR in complex with SAM (S-adenosyl-l-methionine) at 2.0 and 2.1 A resolution, respectively. NHR forms a functional homodimer, and dimerization is required for methyltransferase activity. The monomeric NHR is comprised of the N-terminal RNA binding domain (NTD) and the C-terminal catalytic domain (CTD). Overall, the structure of NHR suggests that the methyltransferase activity is achieved by "reading" the RNA substrate with NTD and "adding" methyl group using CTD. Comprehensive mutagenesis and methyltransferase activity assays reveal critical regions for SAM binding in CTD and loops (L1 and L3) essential for RNA recognition in NTD. Finally, the catalytic mechanism and structural model that NHR recognizes 23S rRNA is proposed based on the structural and biochemical analyses. Thus, our systematic structural studies reveal the substrate recognition and modification by the nosiheptide-resistance methyltransferase.

  • Organizational Affiliation

    Cancer Institute, Shanghai Cancer Center, Fudan University, Shanghai, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
23S rRNA methyltransferase
A, B
277Streptomyces actuosusMutation(s): 0 
Gene Names: nsr
EC: 2.1.1
Find proteins for P52391 (Streptomyces actuosus)
Explore P52391 
Go to UniProtKB:  P52391
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP52391
Sequence Annotations
  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Resolution: 2.10 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.199 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.651α = 90
b = 69.211β = 117.56
c = 64.444γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-07-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description