7V3B

Crystal structure of NP exonuclease C409A-PCMPS complex

Summary for 7V3B

• Entry DOI: 10.2210/pdb7v3b/pdb
• Related: 7V37 7V38 7V39 7V3A
• Descriptor: Nucleoprotein, MAGNESIUM ION, PARA-MERCURY-BENZENESULFONIC ACID, ... (5 entities in total)
• Functional Keywords: deddh exonuclease, np exonuclease, anti-viral drug, pcmps, pcmb, viral protein
• Biological source: Lassa virus (strain Mouse/Sierra Leone/Josiah/1976) (LASV)
• Total number of polymer chains: 2
• Total formula weight: 55860.33

Authors

Hsiao, Y.Y.,Huang, K.W. (deposition date: 2021-08-10, release date: 2021-12-15, Last modification date: 2023-11-29)

Primary citation

Huang, K.W.,Chen, J.W.,Hua, T.Y.,Chu, Y.Y.,Chiu, T.Y.,Liu, J.Y.,Tu, C.I.,Hsu, K.C.,Kao, Y.T.,Chu, J.W.,Hsiao, Y.Y.
Targeted Covalent Inhibitors Allosterically Deactivate the DEDDh Lassa Fever Virus NP Exonuclease from Alternative Distal Sites.
Jacs Au, 1:2315-2327, 2021

PubMed Abstract: For using targeted covalent inhibitors (TCIs) as anticancer and antiviral drugs, we establish that the model compounds PCMPS (-chloromercuriphenyl sulfate) and PCMB (-chloromercuribenzoate) are inhibitors of the DEDDh family of exonucleases. The underlying mechanism is analyzed by X-ray crystallography, activity/nucleic acid-binding assays, and all-atom molecular dynamics (MD) simulations. The first TCI-complexed structures of a DEDDh enzyme, the Lassa fever virus NP exonuclease (NPexo), are resolved to elucidate that the Cys409 binding site is away from the active site and the RNA-binding lid. The NPexo C409A structures indicate Cys461 as the alternative distal site for obstructing the equally active mutant. All-atom MD simulations of the wild type and mutant NPexos in explicit solvent uncover an allosteric inhibition mechanism that the local perturbation induced by PCMPS sulfonate propagates to impact the RNA-binding lid conformation. Binding assay studies confirm that PCMPS does affect the RNA binding of NPexo. The predicted relative potency between PCMPS and PCMB is also in line with experiments. The structural data and inhibition mechanism established in this work provide an important molecular basis for the drug development of TCIs.

PubMed: 34977900
DOI: 10.1021/jacsau.1c00420

Experimental method

X-RAY DIFFRACTION (1.8 Å)