A structural model of anti-anti-σ inhibition by a two-component receiver domain: the PhyR stress response regulator

P>PhyR is a hybrid stress regulator conserved in alpha-proteobacteria that contains an N-terminal sigma-like (SL) domain and a C-terminal receiver domain. Phosphorylation of the receiver domain is known to promote binding of the SL domain to an anti-sigma factor. PhyR thus functions as an anti-anti-sigma factor in its phosphorylated state. We present genetic evidence that Caulobacter crescentus PhyR is a phosphorylation-dependent stress regulator that functions in the same pathway as sigma T and its anti-sigma factor, NepR. Additionally, we report the X-ray crystal structure of PhyR at 1.25 A resolution, which provides insight into the mechanism of anti-anti-sigma regulation. Direct intramolecular contact between the PhyR receiver and SL domains spans regions sigma(2) and sigma(4), likely serving to stabilize the SL domain in a closed conformation. The molecular surface of the receiver domain contacting the SL domain is the structural equivalent of alpha 4-beta 5-alpha 5, which is known to undergo dynamic conformational change upon phosphorylation in a diverse range of receiver proteins. We propose a structural model of PhyR regulation in which receiver phosphorylation destabilizes the intramolecular interaction between SL and receiver domains, thereby permitting regions sigma(2) and sigma(4) in the SL domain to open about a flexible connector loop and bind anti-sigma factor.