Cryo-EM structure of Asfv topoisomerase 2 - apo conformer IIIb

Experimental Data Snapshot

  • Resolution: 2.69 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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A unified view on enzyme catalysis by cryo-EM study of a DNA topoisomerase.

Chang, C.M.Wang, S.C.Wang, C.H.Pang, A.H.Yang, C.H.Chang, Y.K.Wu, W.J.Tsai, M.D.

(2024) Commun Chem 7: 45-45

  • DOI: https://doi.org/10.1038/s42004-024-01129-y
  • Primary Citation of Related Structures:  
    8J87, 8J88, 8J89, 8J8A, 8J8B, 8J8C, 8J9V, 8J9W, 8J9X, 8JA1, 8JA2

  • PubMed Abstract: 

    The theories for substrate recognition in enzyme catalysis have evolved from lock-key to induced fit, then conformational selection, and conformational selection followed by induced fit. However, the prevalence and consensus of these theories require further examination. Here we use cryogenic electron microscopy and African swine fever virus type 2 topoisomerase (AsfvTop2) to demonstrate substrate binding theories in a joint and ordered manner: catalytic selection by the enzyme, conformational selection by the substrates, then induced fit. The apo-AsfvTop2 pre-exists in six conformers that comply with the two-gate mechanism directing DNA passage and release in the Top2 catalytic cycle. The structures of AsfvTop2-DNA-inhibitor complexes show that substantial induced-fit changes occur locally from the closed apo-conformer that however is too far-fetched for the open apo-conformer. Furthermore, the ATPase domain of AsfvTop2 in the MgAMP-PNP-bound crystal structures coexist in reduced and oxidized forms involving a disulfide bond, which can regulate the AsfvTop2 function.

  • Organizational Affiliation

    Institute of Biological Chemistry, Academia Sinica, Taipei, 115, Taiwan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA topoisomerase 2
A, B
1,197African swine fever virusMutation(s): 0 
Gene Names: P1192R
Find proteins for Q00942 (African swine fever virus (strain Badajoz 1971 Vero-adapted))
Explore Q00942 
Go to UniProtKB:  Q00942
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ00942
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.69 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Academia Sinica (Taiwan)TaiwanAS-KPQ-109-TPP2

Revision History  (Full details and data files)

  • Version 1.0: 2024-02-07
    Type: Initial release
  • Version 1.1: 2024-04-17
    Changes: Database references