8V90

TtgR variant 3A7 with naltrexone

Summary for 8V90

• Entry DOI: 10.2210/pdb8v90/pdb
• Descriptor: HTH-type transcriptional regulator TtgR, nalterxone, MAGNESIUM ION, ... (4 entities in total)
• Functional Keywords: regulatory, tetr like, transcription
• Biological source: Pseudomonas putida DOT-T1E
• Total number of polymer chains: 4
• Total formula weight: 98620.55

Authors

Acheson, J.F.,Lee, D.,Ramen, S. (deposition date: 2023-12-06, release date: 2024-12-11, Last modification date: 2025-12-24)

Primary citation

Nishikawa, K.K.,Chen, J.,Acheson, J.F.,Harbaugh, S.V.,Huss, P.,Frenkel, M.,Novy, N.,Sieren, H.R.,Lodewyk, E.C.,Lee, D.H.,Chavez, J.L.,Fox, B.G.,Raman, S.
Highly multiplexed design of an allosteric transcription factor to sense new ligands.
Nat Commun, 15:10001-10001, 2024

PubMed Abstract: Allosteric transcription factors (aTF) regulate gene expression through conformational changes induced by small molecule binding. Although widely used as biosensors, aTFs have proven challenging to design for detecting new molecules because mutation of ligand-binding residues often disrupts allostery. Here, we develop Sensor-seq, a high-throughput platform to design and identify aTF biosensors that bind to non-native ligands. We screen a library of 17,737 variants of the aTF TtgR, a regulator of a multidrug exporter, against six non-native ligands of diverse chemical structures - four derivatives of the cancer therapeutic tamoxifen, the antimalarial drug quinine, and the opiate analog naltrexone - as well as two native flavonoid ligands, naringenin and phloretin. Sensor-seq identifies biosensors for each of these ligands with high dynamic range and diverse specificity profiles. The structure of a naltrexone-bound design shows shape-complementary methionine-aromatic interactions driving ligand specificity. To demonstrate practical utility, we develop cell-free detection systems for naltrexone and quinine. Sensor-seq enables rapid and scalable design of new biosensors, overcoming constraints of natural biosensors.

PubMed: 39562775
DOI: 10.1038/s41467-024-54260-8

Experimental method

X-RAY DIFFRACTION (2.08 Å)