8YIK

pP1192R-ATPase-domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.200 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Structural basis for difunctional mechanism of m-AMSA against African swine fever virus pP1192R.

Liu, R.Sun, J.Li, L.F.Cheng, Y.Li, M.Fu, L.Li, S.Peng, G.Wang, Y.Liu, S.Qu, X.Ran, J.Li, X.Pang, E.Qiu, H.J.Wang, Y.Qi, J.Wang, H.Gao, G.F.

(2024) Nucleic Acids Res 

  • DOI: https://doi.org/10.1093/nar/gkae703
  • Primary Citation of Related Structures:  
    8YGE, 8YGG, 8YGH, 8YIK

  • PubMed Abstract: 

    The African swine fever virus (ASFV) type II topoisomerase (Topo II), pP1192R, is the only known Topo II expressed by mammalian viruses and is essential for ASFV replication in the host cytoplasm. Herein, we report the structures of pP1192R in various enzymatic stages using both X-ray crystallography and single-particle cryo-electron microscopy. Our data structurally define the pP1192R-modulated DNA topology changes. By presenting the A2+-like metal ion at the pre-cleavage site, the pP1192R-DNA-m-AMSA complex structure provides support for the classical two-metal mechanism in Topo II-mediated DNA cleavage and a better explanation for nucleophile formation. The unique inhibitor selectivity of pP1192R and the difunctional mechanism of pP1192R inhibition by m-AMSA highlight the specificity of viral Topo II in the poison binding site. Altogether, this study provides the information applicable to the development of a pP1192R-targeting anti-ASFV strategy.


  • Organizational Affiliation

    College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan Province 450046, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA topoisomerase 2403African swine fever virus pig/Kenya/KEN-50/1950Mutation(s): 0 
Gene Names: BA71V-P1192R (i7R)P1192R
EC: 5.6.2.2
UniProt
Find proteins for A0A0C5B080 (African swine fever virus)
Explore A0A0C5B080 
Go to UniProtKB:  A0A0C5B080
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0C5B080
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP (Subject of Investigation/LOI)
Query on ATP

Download Ideal Coordinates CCD File 
B [auth A]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.200 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.753α = 90
b = 85.753β = 90
c = 211.483γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32270157

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-18
    Type: Initial release