Rifampin phosphotransferase is an unusual antibiotic resistance kinase

Nat Commun. 2016 Apr 22;7:11343. doi: 10.1038/ncomms11343.

Abstract

Rifampin (RIF) phosphotransferase (RPH) confers antibiotic resistance by conversion of RIF and ATP, to inactive phospho-RIF, AMP and Pi. Here we present the crystal structure of RPH from Listeria monocytogenes (RPH-Lm), which reveals that the enzyme is comprised of three domains: two substrate-binding domains (ATP-grasp and RIF-binding domains); and a smaller phosphate-carrying His swivel domain. Using solution small-angle X-ray scattering and mutagenesis, we reveal a mechanism where the swivel domain transits between the spatially distinct substrate-binding sites during catalysis. RPHs are previously uncharacterized dikinases that are widespread in environmental and pathogenic bacteria. These enzymes are members of a large unexplored group of bacterial enzymes with substrate affinities that have yet to be fully explored. Such an enzymatically complex mechanism of antibiotic resistance augments the spectrum of strategies used by bacteria to evade antimicrobial compounds.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Adenosine Triphosphate / chemistry
  • Adenosine Triphosphate / metabolism
  • Amino Acid Sequence
  • Anti-Bacterial Agents / metabolism*
  • Anti-Bacterial Agents / pharmacology
  • Bacterial Proteins / chemistry*
  • Bacterial Proteins / genetics
  • Bacterial Proteins / metabolism
  • Binding Sites
  • Biotransformation
  • Crystallography, X-Ray
  • Drug Resistance, Bacterial
  • Escherichia coli / genetics
  • Escherichia coli / metabolism
  • Gene Expression
  • Listeria monocytogenes / classification
  • Listeria monocytogenes / drug effects
  • Listeria monocytogenes / enzymology*
  • Listeria monocytogenes / genetics
  • Models, Molecular
  • Molecular Sequence Data
  • Phosphotransferases / chemistry*
  • Phosphotransferases / genetics
  • Phosphotransferases / metabolism
  • Phylogeny
  • Protein Binding
  • Protein Structure, Secondary
  • Protein Structure, Tertiary
  • Recombinant Proteins / chemistry
  • Recombinant Proteins / genetics
  • Recombinant Proteins / metabolism
  • Rifampin / metabolism*
  • Rifampin / pharmacology
  • Sequence Alignment

Substances

  • Anti-Bacterial Agents
  • Bacterial Proteins
  • Recombinant Proteins
  • Adenosine Triphosphate
  • Phosphotransferases
  • Rifampin