Iron‐Dependent Regulators

Crystal Structure of an IdeR–DNA Complex Reveals a Conformational Change in Activated IdeR for Base-specific Interactions

“…These residues are part of the HTH motif and are invariant throughout the iron-dependent repressor protein family in many Gram-positive bacteria. 19 The distance between two conserved thymine bases at the C2 and C7 consensus positions on different DNA strands determines to a significant degree how far apart the two HTH motifs of IdeR dimer should be to fit to the DNA. This underlines the importance of thymine at positions C2 and C7 in both strands, particularly the methyl group where most contacts with Ser37 and Pro39 occur, for IdeR-DNA recognition through base specificity, as was also observed for DtxR by Chen et al 22 The function of Gln43 in the iron-dependent repressor protein family is interesting.…”

“…These residues are highly conserved in the iron-dependent repressor protein family from Gram-positive bacteria despite a low level of sequence homology in this domain. 19 The present IdeR-DNA complex structure contains all third domain residues 151-230 in each of the monomers. The electron density of this domain is excellent except for two loop regions (residues 158-161 and residues 200-206) that have lower quality electron density in essentially all eight subunits reflecting its flexibility.…”

“…Most of the interactions involve residues 27-50 in the HTH motif of IdeR, which are highly conserved in the iron-dependent repressor protein family, 19 and the interactions are similar in both double-dimer complexes of IdeR in the asymmetric unit. These contacts are dominated by hydrogen bonds and van der Waals interactions between IdeR and the deoxyribose phosphate backbone, but a limited number of contacts between nucleotide bases and the regulator occur as well.…”

“…Gln43 interacts variably with the N7 atom of guanine, the C5 and/or N4 atoms of cytosine, and the C5 atom, and the methyl group of thymine (Table 4). The Gln43-base interactions are non-specific because Gln43 in different subunits contact different bases, C, G, and T. Yet, Gln43 is completely conserved in all members of the irondependent repressor family 19 .…”

“…19 In addition to activation by Fe 2C , IdeR can be activated by Co 2C , Ni 2C , Mn 2C , Cd 2C , and Zn 2C in vitro. 13 The initial zincactivated IdeR structure described by Pohl et al 7 and the subsequent high-resolution crystal structure of cobalt-activated IdeR by Feese et al 8 revealed a structural similarity to DtxR in that it forms a dimer, with three domains and two metalbinding sites per monomer.…”