8YGE

pP1192R-DNA-m-AMSA complex DNA binding/cleavage domain


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.76 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.1 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 52: 11301-11316

  • 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 2
A, B
1,194African 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
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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (20-mer)20African swine fever virus pig/Kenya/KEN-50/1950
Sequence Annotations
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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (8-mer)8African swine fever virus pig/Kenya/KEN-50/1950
Sequence Annotations
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  • Reference Sequence

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Entity ID: 4
MoleculeChains LengthOrganismImage
DNA (12-mer)12African swine fever virus pig/Kenya/KEN-50/1950
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.76 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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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
  • Version 1.1: 2024-10-30
    Changes: Data collection, Database references, Structure summary