4Z5V | pdb_00004z5v

Crystal Structure of MHV ns2 PDE Domain

• PDB DOI: https://doi.org/10.2210/pdb4Z5V/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Murine hepatitis virus strain A59
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-04-03 Released: 2016-02-10 
• Deposition Author(s): Sui, B.K., Huang, J.H., Peng, G.Q., Zhao, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.05 Å
• R-Value Free: 
  0.266 (Depositor), 0.261 (DCC) 
• R-Value Work: 
  0.226 (Depositor), 0.228 (DCC) 
• R-Value Observed: 
  0.230 (Depositor) 

Literature

Crystal structure of the mouse hepatitis virus ns2 phosphodiesterase domain that antagonizes RNase L activation

Sui, B.K., Huang, J.H., Jha, B.K., Yin, P., Zhou, M., Fu, Z.F., Silverman, R.H., Weiss, S.R., Peng, G.Q., Zhao, L.

(2016) J Gen Virol 97: 880-886

• PubMed: 26757803 
• DOI: https://doi.org/10.1099/jgv.0.000395
• Primary Citation Related Structures: 
  4Z5V


• PubMed Abstract: 
  

  Prior studies have demonstrated that the mouse hepatitis virus (MHV) A59 strain ns2 protein is a member of the 2H phosphoesterase family and exhibits 2',5'-phosphodiesterase (PDE) activity. During the IFN antiviral response, ns2 cleaves 2',5'-oligoadenylate (2-5A), a key mediator of RNase L activation, thereby subverting the activation of RNase L and evading host innate immunity. However, the mechanism of 2-5A cleavage by ns2 remains unclear. Here, we present the crystal structure of the MHV ns2 PDE domain and demonstrate a PDE fold similar to that of the cellular protein, a kinase anchoring protein 7 central domain (AKAP7(CD)) and rotavirus VP3 carboxy-terminal domain. The structure displays a pair of strictly conserved HxT/Sx motifs and forms a deep, positively charged catalytic groove with β-sheets and an arginine-containing loop. These findings provide insight into the structural basis for 2-5A binding of MHV ns2.

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Organizational Affiliation: 
• State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, PRChina.
Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA.
National Key Laboratory of Crop Improvement, Huazhong Agricultural University, Wuhan 430070, PRChina.
Department of Pathology, University of Georgia, Athens, GA 30602, USA.
Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 48.28 kDa 
• Atom Count: 2,511 
• Modeled Residue Count: 309 
• Deposited Residue Count: 416 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-structural protein 2a	A, B	208	Murine hepatitis virus strain A59	Mutation(s): 0  Gene Names: 2a
UniProt
Find proteins for P19738 (Murine coronavirus (strain A59)) Explore P19738  Go to UniProtKB:  P19738

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.05 Å
• R-Value Free:  0.266 (Depositor), 0.261 (DCC) 
• R-Value Work:  0.226 (Depositor), 0.228 (DCC) 
• R-Value Observed: 0.230 (Depositor) 

Space Group: P 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.042	α = 90
b = 101.042	β = 90
c = 165.806	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data processing
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-02-10 
Deposition Author(s): Sui, B.K., Huang, J.H., Peng, G.Q., Zhao, L.

Revision History  

• Version 1.0: 2016-02-10
  Type: Initial release
  
• Version 1.1: 2016-05-04
  Changes: Database references
• Version 1.2: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary