Small-angle X-ray scattering study of a Rex family repressor: conformational response to NADH and NAD+ binding in solution

J Mol Biol. 2011 May 13;408(4):670-83. doi: 10.1016/j.jmb.2011.02.050. Epub 2011 Mar 21.


The transcriptional repressor Rex is a sensor of the intracellular NADH/NAD(+) redox state through direct binding of NADH or NAD(+). Homodimeric Rex protein from Thermus aquaticus (T-Rex) and Bacillus subtilis (B-Rex) exists in several different conformations. In both organisms, Rex in complex with NADH has the DNA binding domains packed together at the dimer interface, whereas in the apo form of B-Rex the linkers connecting these domains to the core are flexible. The crystal structures of the apo forms of B-Rex and a mutated variant of T-Rex are radically different. We describe the solution structures of B-Rex in complex with NAD(+) or NADH and in its apo form, on the basis of small-angle X-ray scattering (SAXS) measurements. This study addresses to what extent the unusual orientation of the DNA recognition domains of the crystal structure of apo B-Rex is due to stabilization by crystal packing. Low-resolution ab initio solution structures were obtained for apo B-Rex, B-Rex:NADH and B-Rex:NAD(+). Models giving a more detailed picture of these three solution structures were obtained also by rigid body fitting of the crystallographic domains. The SAXS data confirm the elongated and flexible nature of apo-B-Rex and the existence of two distinct and more rigid conformations for the complexes with NADH and NAD(+). The models emerging from this study indicate a reaction mechanism for B-Rex in which the recognition domains are rotated upon binding to NADH.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Bacillus subtilis / metabolism
  • Bacterial Proteins / chemistry*
  • Binding Sites
  • Crystallography, X-Ray
  • NAD / chemistry
  • Protein Conformation
  • Recombinant Proteins / chemistry
  • Repressor Proteins / chemistry*
  • Scattering, Small Angle
  • Solutions / chemistry
  • Thermus / metabolism


  • Bacterial Proteins
  • Recombinant Proteins
  • Repressor Proteins
  • Solutions
  • NAD