8H5A

Crystal structure of YhaJ effector binding domain (ligand-bound)

Summary for 8H5A

• Entry DOI: 10.2210/pdb8h5a/pdb
• Descriptor: HTH-type transcriptional regulator YhaJ, 2-methylbenzene-1,4-diol, SODIUM ION, ... (4 entities in total)
• Functional Keywords: transcription
• Biological source: Escherichia coli K-12
• Total number of polymer chains: 16
• Total formula weight: 376554.19

Authors

Kim, M.,Ryu, S.E. (deposition date: 2022-10-12, release date: 2023-10-25, Last modification date: 2024-03-06)

Primary citation

Kim, M.,Kang, R.,Jeon, T.J.,Ryu, S.E.
Structural basis of transcription factor YhaJ for DNT detection.
Iscience, 26:107984-107984, 2023

PubMed Abstract: Detection of landmines without harming personnel is a global issue. The bacterial transcription factor YhaJ selectively detects metabolites of explosives, and it can be used as a key component of DNT biosensors. However, the wild-type YhaJ has a binding affinity that is not sufficient for the detection of trace amounts of explosives leaked from landmines buried in the soil. Here, we report crystal structures of the effector-binding domain of YhaJ in both the apo- and effector-bound forms. A structural comparison of the two forms revealed that the loop above the primary effector-binding site significantly switches its conformation upon effector binding. The primary effector-binding site involves hydrophobic and polar interactions, having specificity to hydroxyl-substituted benzene compounds. The structures explain the mechanism of activity-enhancing mutations and provide information for the rational engineering of YhaJ biosensors for the sensitive detection of explosives.

PubMed: 37822509
DOI: 10.1016/j.isci.2023.107984

Experimental method

X-RAY DIFFRACTION (2.803 Å)