Substitution of glutamate residue by lysine in the dimerization domain affects DNA binding ability of HapR by inducing structural deformity in the DNA binding domain

PLoS One. 2013 Oct 14;8(10):e76033. doi: 10.1371/journal.pone.0076033. eCollection 2013.

Abstract

HapR has been given the status of a high cell density master regulatory protein in Vibrio cholerae. Though many facts are known regarding its structural and functional aspects, much still can be learnt from natural variants of the wild type protein. This work aims at investigating the nature of functional inertness of a HapR natural variant harboring a substitution of a conserved glutamate residue at position 117 which participates in forming a salt bridge by lysine (HapRV2G-E(117)K). Experimental evidence presented here reveals the inability of this variant to interact with various cognate promoters by in vitro gel shift assay. Furthermore, the elution profiles of HapRV2G-E(117)K protein along with the wild type functional HapRV2G in size-exclusion chromatography as well as circular dichroism spectra did not reflect any significant differences in its structure, thereby indicating the intactness of dimer in the variant protein. To gain further insight into the global shape of the proteins, small angle X-ray scattering analysis (SAXS) was performed. Intriguingly, increased radius of gyration of HapRV2G-E(117)K of 27.5 Å in comparison to the wild type protein from SAXS data analyses implied a significant alteration in the global shape of the dimeric HapRV2G-E(117)K protein. Structure reconstruction brought forth that the DNA binding domains were substantially "parted away" in this variant. Taken together, our data illustrates that substitution of the conserved glutamate residue by lysine in the dimerization domain induces separation of the two DNA binding domains from their native-like positioning without altering the dimeric status of HapR variant.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Amino Acid Substitution*
  • Bacterial Proteins / chemistry*
  • Bacterial Proteins / metabolism*
  • Chromatography, Gel
  • Circular Dichroism
  • DNA / metabolism*
  • Electrophoresis, Polyacrylamide Gel
  • Glutamic Acid / metabolism*
  • Lysine / metabolism*
  • Molecular Sequence Data
  • Molecular Weight
  • Mutant Proteins / chemistry
  • Mutant Proteins / metabolism
  • Protein Binding
  • Protein Multimerization*
  • Protein Stability
  • Protein Structure, Secondary
  • Protein Structure, Tertiary
  • Scattering, Small Angle
  • Sequence Alignment
  • Vibrio cholerae / metabolism
  • X-Ray Diffraction

Substances

  • Bacterial Proteins
  • Mutant Proteins
  • Glutamic Acid
  • DNA
  • Lysine

Grant support

This work was partly supported by grants from the Department of Biotechnology (BT/PR3583/MED/30/659/2011-GAP/106) and CSIR network project (NWP-UNSEEN/BSC0113). RS, YSR and NSS acknowledge the University Grant Commission and Department of Biotechnology, India respectively for fellowships. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.