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Published on: April 26, 2013
Iron(II) triggered conformational changes in Escherichia coli fur upon DNA binding: a study using molecular modeling
Mazen Y Hamed1, Salih Al-Jabour
1Computational Science Program, Chemistry Department, Birzeit University, PO Box 14, Birzeit, Palestine. mhamed@birzeit.edu
Journal of Molecular Graphics & Modelling
|January 31, 2006
Summary
The ferric uptake regulation protein (Fur EC) dimer structure reveals key residues for DNA binding and dimerization. Iron (Fe2+) enhances Fur EC binding to DNA, inducing conformational changes in both proteins and DNA.
Area of Science:
- Structural biology
- Molecular biology
- Biochemistry
Background:
- The ferric uptake regulation protein (Fur) controls iron homeostasis in bacteria.
- Understanding Fur's structure is crucial for elucidating its regulatory mechanisms.
- The dimerization domain and DNA-binding interface of Fur EC were not fully characterized.
Purpose of the Study:
- To determine the three-dimensional structure of the Fur dimer from Escherichia coli (Fur EC).
- To identify key residues involved in Fur EC dimerization and DNA binding.
- To investigate the role of iron (Fe2+) in modulating Fur EC-DNA interactions.
Main Methods:
- Homology modeling and energy minimization were employed to predict the Fur EC structure.
- Molecular docking was used to simulate Fur EC dimer binding to DNA.
- Analysis of residue interactions and distances was performed to identify key binding sites.
Main Results:
- The Fur EC monomer comprises distinct N-terminal and C-terminal domains with helical and beta-strand motifs.
- Residues 45-70, rich in hydrophobic amino acids, are critical for Fur EC dimer formation.
- Iron (Fe2+) enhances Fur EC dimer binding to the AT-rich 'iron box' on DNA, inducing conformational changes in both the protein and DNA.
Conclusions:
- The study elucidates the structural basis of Fur EC dimerization and DNA binding.
- Iron (Fe2+) acts as a crucial allosteric regulator, mediating Fur EC-DNA interactions.
- The identified structural features provide insights into the regulation of iron uptake in Escherichia coli.
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