Crystal structure of a cobalt-activated diphtheria toxin repressor-DNA complex reveals a metal-binding SH3-like domain

The diphtheria toxin repressor (DtxR) is the prototype of a family of iron- dependent regulator (IdeR) proteins, which are activated by divalent iron a nd bind DNA to prevent the transcription of downstream genes. In Corynebact erium diphtheriae, DtxR regulates not only the expression of diphtheria tox in encoded by a corynebacteriophage, but also of components of the sideroph ore-mediated iron-transport system. Here we report the crystal structure of wild-type DtxR, a 226 residue three-domain dimeric protein, activated by c obalt and bound to a 21 bp DNA duplex based on the consensus operator seque nce. Two DtxR dimers surround the DNA duplex which is distorted compared to canonical B-DNA. The SH3-like third domain interacts with the metal at sit e 1 via the side-chains of Glu170 and Gln173, revealing for the first time a metal-binding function for this class of domains. The SH3-like domain is also in contact with the DNA-binding first domain and with the second, or d imerization, domain. The DNA-binding helices in the first domain are shifte d by 3 to 5 Angstrom when compared to the ape-repressor, and fit into the m ajor groove of the duplex bound. These shifts are due to a hinge-binding mo tion of the DNA-binding domain with respect to the dimerization domains of DtxR. The third domain might play a role in regulating this hinge motion. ( C) 1999 Academic Press.