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Structural basis for regulation of rhizobial nodulation and symbiosis gene expression by the regulatory protein NolR

Paul C. Rosen, Samantha M. Horwitz, Daniel J. Brooks, Erica Kim, Joseph A. Ambarian, Lidia Waidmann, Katherine M. Davis and Gary Yellen PNAS,  March 6, 2025, Vol. 122  No. 10 e2426324122, [1]

Structure Tour

spinqualitylabelsall models Crystal Structure of NolR from Sinorhizobium fredii (PDB entry 4omz) Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural and Biological Significance Global Regulation of Nitrogen Fixation Symbiosis NolR is a transcriptional regulator that fine-tunes the expression of nodulation (nod) and symbiosis genes across diverse Rhizobium species. Despite its critical ecological importance, the molecular basis of NolR's regulatory mechanism remained largely unknown until the comprehensive structural characterization presented in this paper. Structural Architecture and DNA-Binding Mechanism The crystallographic structures of NolR reveal a homodimeric winged helix-turn-helix transcription factor, comprising two α-helical regions (α1 and α5) forming the dimerization interface and a triangular configuration of helices (α2–α4) that positions the conserved helix-turn-helix motif (α3–α4) for DNA major groove binding. Notably, a distinctive "wing" composed of antiparallel β-sheets extends into the DNA minor groove. This architectural arrangement enables NolR to recognize asymmetric operator sequences—a remarkable feature that confers specificity and versatility in binding diverse target genes. The Gln56 Conformational Switch: A Novel Regulatory Innovation Perhaps the most striking discovery of this work is the identification of a **conformational switching mechanism** centered on **glutamine residue 56 (Gln56)**. This glutamine adopts different conformational states depending on the nucleotide composition of target DNA sequences. In the first half-site of the operator, Gln56 orients toward the adenine base (A2), while in the second half-site, its side-chain can flip away from thymine (T7') or reorient toward adenine (A7') depending on the sequence variation.