7V39

Crystal structure of NP exonuclease-PCMB complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Targeted Covalent Inhibitors Allosterically Deactivate the DEDDh Lassa Fever Virus NP Exonuclease from Alternative Distal Sites.

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.

(2021) JACS Au 1: 2315-2327

  • DOI: https://doi.org/10.1021/jacsau.1c00420
  • Primary Citation of Related Structures:  
    7V37, 7V38, 7V39, 7V3A, 7V3B, 7V3C

  • PubMed Abstract: 

    For using targeted covalent inhibitors (TCIs) as anticancer and antiviral drugs, we establish that the model compounds PCMPS ( p -chloromercuriphenyl sulfate) and PCMB ( p -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.


  • Organizational Affiliation

    Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu 30010, Taiwan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleoprotein
A, B
249Lassa virus JosiahMutation(s): 0 
EC: 3.1.13
UniProt
Find proteins for P13699 (Lassa virus (strain Mouse/Sierra Leone/Josiah/1976))
Explore P13699 
Go to UniProtKB:  P13699
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13699
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.185α = 90
b = 76.292β = 90
c = 140.784γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, Taiwan)TaiwanMOST103-2311-B-009-001-MY3
Ministry of Science and Technology (MoST, Taiwan)TaiwanMOST108-2636-B-009-004

Revision History  (Full details and data files)

  • Version 1.0: 2021-12-15
    Type: Initial release
  • Version 1.1: 2022-02-16
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description