SNAP output for PDB entry 3il2 [SNAP web server]

PDB-id

3il2; SNAP-derived features in text and JSON formats; DNAproDB

Class

DNA binding protein-DNA

Method

X-ray (2.49 Å)

Summary

Crystal structure of a rex-family repressor r90d mutant-DNA complex from thermus aquaticus

Reference

McLaughlin KJ, Strain-Damerell CM, Xie K, Brekasis D, Soares AS, Paget MS, Kielkopf CL (2010): "Structural basis for NADH/NAD+ redox sensing by a Rex family repressor." Mol.Cell, 38, 563-575. doi: 10.1016/j.molcel.2010.05.006.

Abstract

Nicotinamide adenine dinucleotides have emerged as key signals of the cellular redox state. Yet the structural basis for allosteric gene regulation by the ratio of reduced NADH to oxidized NAD(+) is poorly understood. A key sensor among Gram-positive bacteria, Rex represses alternative respiratory gene expression until a limited oxygen supply elevates the intracellular NADH:NAD(+) ratio. Here we investigate the molecular mechanism for NADH/NAD(+) sensing among Rex family members by determining structures of Thermus aquaticus Rex bound to (1) NAD(+), (2) DNA operator, and (3) without ligand. Comparison with the Rex/NADH complex reveals that NADH releases Rex from the DNA site following a 40 degrees closure between the dimeric subunits. Complementary site-directed mutagenesis experiments implicate highly conserved residues in NAD-responsive DNA-binding activity. These rare views of a redox sensor in action establish a means for slight differences in the nicotinamide charge, pucker, and orientation to signal the redox state of the cell.