Iron(II) triggered conformational changes in Escherichia coli fur upon DNA binding: a study using molecular modeling.

In order to identify the Fur dimerization domain, a three-dimensional structure of the ferric uptake regulation protein from Escherichia coli (Fur EC) was determined using homology modeling and energy minimization. The Fur monomer consists of turn- helix -turn motif on the N-terminal domain, followed by another helix-turn-helix-turn motif, and two beta-strands separated by a turn which forms the wing. The C-terminal domain, separated by a long coil from the N-terminal, and consisting of two anti parallel beta strands, and a turn-helix-turn-helix-turn motif. Residues in central domain were found to aid the dimer formation, residues 45-70 as evident in the calculated distances; this region is rich in hydrophobic residues. Most interactions occur between residues Val55, Leu53, Gln52, Glu49 and Tyr56 with closest contacts occurring at residues 49-56. These residues are part of an alpha-helix (alpha(4)) near the N-terminal. Upon raising the Fe(2+) concentration the binding of Fur dimer to DNA was enhanced, this was evident when, the Fur EC dimer was docked onto DNA "iron box" (it was found to bind the AT-rich region) and upon addition of Fe(2+) the helices near the N-terminal bound to the major groove of the DNA. Addition of high Fe(2+) concentration triggered further conformational changes in the Fur dimer as was measured by distances between the two subunits, Fe(2+) mediated the Fur binding to DNA by attaching itself to the DNA. At the same time DNA changed conformation as was evident in the distortion in the backbone and the shrinking of major groove distance from 11.4 to 9.3A. Two major Fe(2+) sites were observed on the C-terminal domain: site 1, the traditional Zn site, the cavity contains the residues Cys92, Cys95, Asp137, Asp141, Arg139, Glu 140, His 145 and His 143 at distances range from 1.3 to 2.2A. Site 2 enclave consists of His71, Ile50, Asn72, Gly97, Asp105 and Ala109 at very close proximity to Fe(2+). The closest contacts between Fur dimer and DNA at the AT-rich region were at residues Ala11, Gly12, Leu13, Pro18 and Arg19 mostly hydrophobic residues near the N-terminal domain. Close contacts repeated at His87, His88 and Arg112, and a third region near the C-terminal at Asn137, Arg 139, Glu140, Asn141, His143, Asn141 and His145. Fur dimer has three major contact regions with DNA, the first on the N-terminal domain, a second smaller region at His87, His88 and Arg112 mediated by Fe(2+) ions, and a third region on the C-terminal domain consisting mainly of hydrophobic contacts and mediated by Fe(2+) ions at high concentration.