Regulation of transcription initiation is the primary strategy used by bacteria to reprogram gene expression to adjust to changing internal and environmental conditions. Alpha-Proteobacteria uniquely integrate features of two-component signal transduction (TCS) and alternative sigma factor regulation to control transcription in response to general stress. PhyR is a key component of this regulatory system, as it comprises an ECF (extracytoplasmic function) sigma-like (SL) domain and a TCS receiver domain.

This superfamily entry consists of ECF SL domains, such as the one found in PhyR. It is made up from seven helices arranged in a seven-helix bundle. In terms of tertiary structure, the first six helices of PhyR present a high degree of similarity to proteins possessing a cyclin fold. These structural homologues include viral cyclins, cyclin A, retinoblastoma B domain, and TFIIB. The amino acid sequence is conserved across two regions which are similar to the classical sigma factors sigma-2 and sigma-4, although they do not interact with the DNA. PhyR is thought not to interact with RNAP, since it lacks the residues required for core polymerase binding and promoter recognition. The SL domain has sequence similarity to the EcfG-family of alternative sigma factors.

The largest and most diverse group of alternative sigma factors comprises the ECF (group IV) sigma factors of the sigma-70 superfamily. In contrast to other sigma factors, ECF sigma factors consist only of the two core domains, sigma-2 and sigma-4, which are required for recognition of the -10 and -35 region in the DNA, and are responsible for the RNA polymerase binding. ECF sigma factors are often regulated through sequestration by cognate anti-sigma factors, such as NepR, which interfere with their ability to bind the RNA polymerase core enzyme or promoter regions by occluding their respective molecular determinants or by altering their conformations.

Aspartyl phosphorylation of the PhyR receiver in response to stress signals promotes its dissociation from the PhyR-SL domain, exposing the binding site to the anti-sigma factor, NepR. NepR and the receiver domain of PhyR bind the same surface of PhyR-SL. Unphosphorylated PhyR receiver domain can be described as an anti-anti-anti-sigma factor. The SL domain contains hydrophobic determinants for the binding of NepR PFAM:PF04542, PFAM:PF04545, [PfamClan:CL0123], INTERPRO:IPR013325, INTERPRO:IPR007630,PMID:20735776,PMID:22550171,PMID:22550172