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<StructureSection load='4omz' size='350' side='right' caption='Crystal Structure of NolR from Sinorhizobium fredii (PDB entry [[4omz]])' scene=''>
<StructureSection load='4omz' size='350' side='right' caption='Crystal Structure of NolR from Sinorhizobium fredii (PDB entry [[4omz]])' scene=''>
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==Structural and Biological Significance==
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===Abstract===
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===Global Regulation of Nitrogen Fixation Symbiosis===
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The symbiosis between rhizobial bacteria and leguminous plants is a critical ecological process leading to nitrogen fixation. This process is tightly regulated by a series of ''nod'' genes. '''NolR''' is a global regulatory protein (transcription factor) conserved across ''Sinorhizobium'' and ''Rhizobium'' species that represses these nodulation genes to optimize symbiosis. This paper presents the crystal structures of NolR in both unliganded and DNA-bound forms, revealing an asymmetric binding mechanism and a specific conformational switch that allows the protein to recognize variable DNA sequences.
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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.
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=== Structural Architecture and DNA-Binding Mechanism===
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===Overall Structure of NolR===
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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.
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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.
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===The Gln56 Conformational Switch: A Novel Regulatory Innovation===
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* '''Dimerization:''' Two alpha-helices (alpha-1 and alpha-5) from each monomer form a coiled-coil dimerization interface.
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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.
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* '''DNA Binding Domain:''' A triangular set of helices (alpha-2 to alpha-4) positions the recognition helix (alpha-3 and alpha-4) for interaction with the DNA major groove.
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* '''The Wing:''' A two-stranded antiparallel beta-sheet extends outward to interact with the minor groove.
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===DNA Binding and Recognition===
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The co-crystal structure of NolR with a 22-base pair operator sequence (Oligo AT) reveals how the repressor recognizes its target. The NolR dimer binds to an asymmetric operator site.
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* '''Major Groove:''' The alpha-4 helix of each monomer inserts deep into the major groove of the DNA.
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* '''Minor Groove:''' The beta-wing residues contact the minor groove.
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* '''Electrostatics:''' The DNA-binding surface of NolR is positively charged, facilitating interaction with the phosphate backbone, while the opposite face is negatively charged.
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* '''DNA Bending:''' Upon binding, the DNA duplex bends approximately 16.8 degrees from an ideal B-form.
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===The Gln56 Conformational Switch===
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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).
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* '''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'.
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* '''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.
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===References===
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* Lee SG, Krishnan HB, Jez JM. Structural basis for regulation of rhizobial nodulation and symbiosis gene expression by the regulatory protein NolR. ''Proc Natl Acad Sci U S A.'' 2014 Apr 29;111(17):6509-14. doi: 10.1073/pnas.1402243111.
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===About this Page===
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This page was created by '''[[User:Your_Username|Your Name Here]]'''.<br>
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</StructureSection>
</StructureSection>

Revision as of 07:15, 28 November 2025

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

Crystal Structure of NolR from Sinorhizobium fredii (PDB entry 4omz)

Drag the structure with the mouse to rotate
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