Abstract
The Ton and Tol systems are proton‑driven motor complexes that are essential for high‑affinity nutrient uptake and for maintaining outer‑membrane integrity in Gram‑negative bacteria. Their activity depends on coordinated interactions among the inner‑membrane proteins ExbB–ExbD–TonB and TolQ–TolR–TolA, but the structural basis of these interactions has been poorly understood. This paper presents near-atomic-resolution cryo-EM structures of both complexes, revealing a conserved architecture in which a pentameric ExbB or TolQ ring encloses a dimeric ExbD or TolR transmembrane segment.
Overall Structure of
NolR is a member of the ArsR/SmtB family of transcription factors. The crystal structure reveals that the protein functions as a homodimer. Each monomer folds into a winged helix-turn-helix motif.
Click on "" of "NolR".
Click on "" of "NolR".
- Dimerization: Two alpha-helices ( from each monomer form a coiled-coil dimerization interface.
- DNA Binding Domain: A triangular set of helices () positions the recognition helix () for interaction with the DNA major groove.
- The Wing: A two-stranded antiparallel beta-sheet extends outward to interact with the minor groove.
DNA Binding and Recognition
The co-crystal structure of NolR with a 22-base pair operator sequence () reveals how the repressor recognizes its target. The NolR dimer binds to an asymmetric operator site.
Select to visualize the binding of NolR on oligo AT rich DNA.
- Major Groove: The alpha-4 helix of each monomer inserts deep into the major groove of the DNA.
- Minor Groove: The beta-wing residues contact the minor groove.
- Electrostatics: The DNA-binding surface of NolR is positively charged, facilitating interaction with the phosphate backbone, while the opposite face is negatively charged.
- DNA Bending: Upon binding, the DNA duplex bends approximately 16.8 degrees from an ideal B-form.
The Gln56 Conformational Switch
A key finding of this study is the mechanism by which NolR binds to diverse operator sequences that vary at specific positions (A vs T). The authors crystallized NolR with two different DNA sequences: "Oligo AT" (consensus) and "Oligo AA" (variable).
Click to visualize the Gln56 residues that are essential for the variable binding of NolR.
- Consensus Binding (Oligo AT): In the first half-site, Gln56 hydrogen bonds with Adenine 2. However, in the second half-site, the Gln56 side chain flips away from Thymine 7'.
- Variable Binding (Oligo AA): When bound to the Oligo AA sequence (where T7' is replaced by A7'), Gln56 undergoes a conformational switch. It rotates to form a hydrogen bond with the new Adenine base.
References
About this Page
This page was created by Niranjana Vinod.
University/Institution Name (Indian Institute of Science Education and Research,Pune)
