Sandbox
From Proteopedia
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===Overall Structure of NolR=== | ===Overall Structure of NolR=== | ||
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. | 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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| + | <scene name="Overall_Structure">Show Overall Structure (PDB 4OMZ)</scene> | ||
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* '''Dimerization:''' Two alpha-helices (alpha-1 and alpha-5) from each monomer form a coiled-coil dimerization interface. | * '''Dimerization:''' Two alpha-helices (alpha-1 and alpha-5) from each monomer form a coiled-coil dimerization interface. | ||
* '''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. | * '''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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===DNA Binding and Recognition=== | ===DNA Binding and Recognition=== | ||
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. | 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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| + | <scene name="DNA_Binding">Show DNA Interactions (PDB 4OMY)</scene> | ||
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* '''Major Groove:''' The alpha-4 helix of each monomer inserts deep into the major groove of the DNA. | * '''Major Groove:''' The alpha-4 helix of each monomer inserts deep into the major groove of the DNA. | ||
* '''Minor Groove:''' The beta-wing residues contact the minor groove. | * '''Minor Groove:''' The beta-wing residues contact the minor groove. | ||
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===The Gln56 Conformational Switch=== | ===The Gln56 Conformational Switch=== | ||
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). | 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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| + | <scene name="Gln56_Switch">Focus on Gln56 Switch</scene> | ||
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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'. | * '''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'. | ||
* '''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. | * '''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. | ||
Revision as of 07:32, 28 November 2025
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Structural basis for regulation of rhizobial nodulation and symbiosis gene expression by the regulatory protein NolR | |
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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
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