Crystal structure of the antibiotic-resistance methyltransferase Kmr

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 

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30S Subunit-Dependent Activation of the Sorangium cellulosum So ce56 Aminoglycoside Resistance-Conferring 16S rRNA Methyltransferase Kmr.

Savic, M.Sunita, S.Zelinskaya, N.Desai, P.M.Macmaster, R.Vinal, K.Conn, G.L.

(2015) Antimicrob Agents Chemother 59: 2807-2816

  • DOI: https://doi.org/10.1128/AAC.00056-15
  • Primary Citation of Related Structures:  
    4RWZ, 4RX1

  • PubMed Abstract: 

    Methylation of bacterial 16S rRNA within the ribosomal decoding center confers exceptionally high resistance to aminoglycoside antibiotics. This resistance mechanism is exploited by aminoglycoside producers for self-protection while functionally equivalent methyltransferases have been acquired by human and animal pathogenic bacteria. Here, we report structural and functional analyses of the Sorangium cellulosum So ce56 aminoglycoside resistance-conferring methyltransferase Kmr. Our results demonstrate that Kmr is a 16S rRNA methyltransferase acting at residue A1408 to confer a canonical aminoglycoside resistance spectrum in Escherichia coli. Kmr possesses a class I methyltransferase core fold but with dramatic differences in the regions which augment this structure to confer substrate specificity in functionally related enzymes. Most strikingly, the region linking core β-strands 6 and 7, which forms part of the S-adenosyl-l-methionine (SAM) binding pocket and contributes to base flipping by the m(1)A1408 methyltransferase NpmA, is disordered in Kmr, correlating with an exceptionally weak affinity for SAM. Kmr is unexpectedly insensitive to substitutions of residues critical for activity of other 16S rRNA (A1408) methyltransferases and also to the effects of by-product inhibition by S-adenosylhomocysteine (SAH). Collectively, our results indicate that adoption of a catalytically competent Kmr conformation and binding of the obligatory cosubstrate SAM must be induced by interaction with the 30S subunit substrate.

  • Organizational Affiliation

    Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative rRNA methyltransferase
A, B
223Sorangium cellulosumMutation(s): 0 
Gene Names: kmr
Find proteins for B2L3G9 (Sorangium cellulosum)
Explore B2L3G9 
Go to UniProtKB:  B2L3G9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB2L3G9
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.643α = 90
b = 89.643β = 90
c = 126.211γ = 120
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

  • Released Date: 2015-03-11 
  • Deposition Author(s): Savic, M.

Revision History  (Full details and data files)

  • Version 1.0: 2015-03-11
    Type: Initial release
  • Version 1.1: 2015-04-29
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references