Intersubunit ionic interactions stabilize the nucleoside diphosphate kinase of Mycobacterium tuberculosis

PLoS One. 2013;8(3):e57867. doi: 10.1371/journal.pone.0057867. Epub 2013 Mar 5.

Abstract

Most nucleoside diphosphate kinases (NDPKs) are hexamers. The C-terminal tail interacting with the neighboring subunits is crucial for hexamer stability. In the NDPK from Mycobacterium tuberculosis (Mt) this tail is missing. The quaternary structure of Mt-NDPK is essential for full enzymatic activity and for protein stability to thermal and chemical denaturation. We identified the intersubunit salt bridge Arg(80)-Asp(93) as essential for hexamer stability, compensating for the decreased intersubunit contact area. Breaking the salt bridge by the mutation D93N dramatically decreased protein thermal stability. The mutation also decreased stability to denaturation by urea and guanidinium. The D93N mutant was still hexameric and retained full activity. When exposed to low concentrations of urea it dissociated into folded monomers followed by unfolding while dissociation and unfolding of the wild type simultaneously occur at higher urea concentrations. The dissociation step was not observed in guanidine hydrochloride, suggesting that low concentration of salt may stabilize the hexamer. Indeed, guanidinium and many other salts stabilized the hexamer with a half maximum effect of about 0.1 M, increasing protein thermostability. The crystal structure of the D93N mutant has been solved.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Bacterial Proteins / chemistry*
  • Bacterial Proteins / genetics
  • Bacterial Proteins / metabolism
  • Crystallography, X-Ray
  • Enzyme Stability
  • Models, Molecular
  • Molecular Sequence Data
  • Mutagenesis, Site-Directed
  • Mycobacterium tuberculosis / enzymology*
  • Mycobacterium tuberculosis / genetics
  • Nucleoside-Diphosphate Kinase / chemistry*
  • Nucleoside-Diphosphate Kinase / genetics
  • Nucleoside-Diphosphate Kinase / metabolism
  • Protein Structure, Quaternary
  • Protein Subunits
  • Salts
  • Sequence Homology, Amino Acid
  • Thermodynamics

Substances

  • Bacterial Proteins
  • Protein Subunits
  • Salts
  • Nucleoside-Diphosphate Kinase

Grants and funding

This work was supported by grants from the Centre National de la Recherche scientifique (http://www.cnrs.fr/), the Région Aquitaine (http://aquitaine.fr/) and the University Bordeaux Segalen (http://www.univ-bordeauxsegalen.fr/fr/index.html). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.