Structural Basis for the Methylation of G1405 in 16S rRNA by Aminoglycoside Resistance Methyltransferase Sgm From an Antibiotic Producer: A Diversity of Active Sites in m7G Methyltransferases

Nucleic Acids Res. 2010 Jul;38(12):4120-32. doi: 10.1093/nar/gkq122. Epub 2010 Mar 1.

Abstract

Sgm (Sisomicin-gentamicin methyltransferase) from antibiotic-producing bacterium Micromonospora zionensis is an enzyme that confers resistance to aminoglycosides like gentamicin and sisomicin by specifically methylating G1405 in bacterial 16S rRNA. Sgm belongs to the aminoglycoside resistance methyltransferase (Arm) family of enzymes that have been recently found to spread by horizontal gene transfer among disease-causing bacteria. Structural characterization of Arm enzymes is the key to understand their mechanism of action and to develop inhibitors that would block their activity. Here we report the structure of Sgm in complex with cofactors S-adenosylmethionine (AdoMet) and S-adenosylhomocysteine (AdoHcy) at 2.0 and 2.1 A resolution, respectively, and results of mutagenesis and rRNA footprinting, and protein-substrate docking. We propose the mechanism of methylation of G1405 by Sgm and compare it with other m(7)G methyltransferases, revealing a surprising diversity of active sites and binding modes for the same basic reaction of RNA modification. This analysis can serve as a stepping stone towards developing drugs that would specifically block the activity of Arm methyltransferases and thereby re-sensitize pathogenic bacteria to aminoglycoside antibiotics.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Aminoglycosides / pharmacology
  • Anti-Bacterial Agents / biosynthesis
  • Anti-Bacterial Agents / pharmacology
  • Bacterial Proteins / chemistry*
  • Base Sequence
  • Calorimetry
  • Catalytic Domain
  • Conserved Sequence
  • Drug Resistance, Bacterial
  • Methylation
  • Methyltransferases / chemistry*
  • Micromonospora / enzymology
  • Models, Molecular
  • Molecular Sequence Data
  • RNA, Ribosomal, 16S / chemistry*
  • RNA, Ribosomal, 16S / metabolism
  • Ribosome Subunits, Small, Bacterial / chemistry
  • S-Adenosylhomocysteine / chemistry
  • S-Adenosylmethionine / chemistry
  • Sequence Homology, Amino Acid

Substances

  • Aminoglycosides
  • Anti-Bacterial Agents
  • Bacterial Proteins
  • RNA, Ribosomal, 16S
  • S-Adenosylmethionine
  • S-Adenosylhomocysteine
  • 16S rRNA - m7G methyltransferase
  • Methyltransferases