6G8G | pdb_00006g8g

Flavonoid-responsive Regulator FrrA in complex with Genistein

PDB DOI: https://doi.org/10.2210/pdb6G8G/pdb

Classification: TRANSCRIPTION
Organism(s): Bradyrhizobium diazoefficiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2018-04-08 Released: 2019-04-17
Deposition Author(s): Werner, N., Hoppen, J., Palm, G., Werten, S., Goettfert, M., Hinrichs, W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.216 (Depositor), 0.224 (DCC)
R-Value Work:
0.188 (Depositor), 0.196 (DCC)
R-Value Observed:
0.190 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

The induction mechanism of the flavonoid-responsive regulator FrrA.

Werner, N., Werten, S., Hoppen, J., Palm, G.J., Gottfert, M., Hinrichs, W.

(2021) FEBS J

PubMed: 34314575 Search on PubMed
DOI: https://doi.org/10.1111/febs.16141
Primary Citation Related Structures:
6G87, 6G8G, 6G8H

PubMed Abstract:
Bradyrhizobium diazoefficiens, a bacterial symbiont of soybean and other leguminous plants, enters a nodulation-promoting genetic programme in the presence of host-produced flavonoids and related signalling compounds. Here, we describe the crystal structure of an isoflavonoid-responsive regulator (FrrA) from Bradyrhizobium, as well as cocrystal structures with inducing and noninducing ligands (genistein and naringenin, respectively). The structures reveal a TetR-like fold whose DNA-binding domain is capable of adopting a range of orientations. A single molecule of either genistein or naringenin is asymmetrically bound in a central cavity of the FrrA homodimer, mainly via C-H contacts to the π-system of the ligands. Strikingly, however, the interaction does not provoke any conformational changes in the repressor. Both the flexible positioning of the DNA-binding domain and the absence of structural change upon ligand binding are corroborated by small-angle X-ray scattering (SAXS) experiments in solution. Together with a model of the promoter-bound state of FrrA our results suggest that inducers act as a wedge, preventing the DNA-binding domains from moving close enough together to interact with successive positions of the major groove of the palindromic operator.

Organizational Affiliation

Institute for Biochemistry, Department Molecular Structural Biology, University of Greifswald, Germany.

Macromolecule Content

Total Structure Weight: 97.96 kDa
Atom Count: 6,246
Modeled Residue Count: 779
Deposited Residue Count: 856
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TetR/AcrR family transcriptional regulator	A, B, C, D	214	Bradyrhizobium diazoefficiens	Mutation(s): 0 Gene Names: CO678_15510

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GEN Query on GEN Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain L [auth D] MOL2 format, chain G [auth B] MOL2 format, chain L [auth D] mmCIF format, chain G [auth B] mmCIF format, chain L [auth D]	G [auth B], L [auth D]	GENISTEIN C₁₅ H₁₀ O₅ TZBJGXHYKVUXJN-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Focus chain L [auth D] Interactions & Density Focus chain G [auth B] Focus chain L [auth D]
NHE Query on NHE Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth C] SDF format, chain M [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth C] MOL2 format, chain M [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth C] mmCIF format, chain M [auth D]	E [auth A] F [auth A] H [auth B] I [auth B] J [auth B] E [auth A], F [auth A], H [auth B], I [auth B], J [auth B], K [auth C], M [auth D]	2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID C₈ H₁₇ N O₃ S MKWKNSIESPFAQN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth C] Focus chain M [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth C] Focus chain M [auth D]