Three-dimensional structure of the diphtheria toxin repressor in complex with divalent cation co-repressors

AbstractBackground: When Corynebacterium diphtheriae encounters an environment with a low concentration of iron ions, it initiates the synthesis of several virulence factors, including diphtheria toxin. The diphtheria toxin repressor (DtxR) plays a key role in this iron–dependent, global regulatory system and is the prototype for a new family of iron –dependent repressor proteins in Gram-positive bacteria. This study aimed to increase understanding of the general regulatory principles of cation binding to DtxR.Results The crystal structure of dimeric DtxR holo-repressor in complex with different transition metals shows that each subunit comprises an amino-terminal DNA–binding domain, an interface domain (which contains two metal-binding sites) and a third, very flexible carboxy-terminal domain. Each DNA–binding domain contains a helix–turn–helix motif and has a topology which is very similar to catabolite gene activator protein (CAP). Molecular modeling suggests that bound DNA adopts a bent conformation with helices α3 of DtxR interacting with the major grooves. The two metal-binding sites lie ∼10 Å apart. Binding site 2 is positioned at a potential hinge region between the DNA–binding and interface domains. Residues 98–108 appear to be crucial for the functioning of the repressor; these provide four of the ligands of the two metal-binding sites and three residues at the other side of the helix which are at the heart of the dimer interface.Conclusion The crystal structure of the DtxR holo-repressor suggests that the divalent cation co–repressor controls motions of the DNA-binding domain. In this way the metal co–repressor governs the distance between operator recognition elements in the two subunits and, consequently, DNA recognition

Protein structure-based design of anti-protozoal drugs

The repertory of drugs to fight protozoal diseases such as malaria, Chagas' disease, leishmaniasis, and African trypanosomiasis is woefully inadequate. Now, genome sequencing and structural genomics projects are quickly elucidating new drug targets, providing incredible opportunities for medicinal chemists. Here, we illustrate the power of structure-based drug design in this process by our efforts to selectively block trypanosomal glycolysis