Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.222 

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This is version 1.3 of the entry. See complete history


A 26 kDa yeast DNA topoisomerase I fragment: crystallographic structure and mechanistic implications.

Lue, N.Sharma, A.Mondragon, A.Wang, J.C.

(1995) Structure 3: 1315-1322

  • DOI: https://doi.org/10.1016/s0969-2126(01)00269-6
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Type I DNA topoisomerases, divided mechanistically into two subfamilies, are ubiquitous enzymes that participate in replication and transcription. In addition to its role in these fundamental processes, the biological importance of eukaryotic DNA topoisomerase I is underscored by its identification as the target of the antitumor alkaloid camptothecin. An understanding of the mechanism of catalysis and interactions with camptothecin and other drugs has been hampered by a lack of detailed structural information. The three-dimensional structure of a 26 kDA fragment (residues 135 to about 363) of Saccharomyces cerevisiae DNA topoisomerase I has been determined at 1.9 A resolution. The fragment has a novel architecture comprising a concave platform and a pair of outlying V-shaped helices. Photocrosslinking and protein footprinting experiments show that the positively charged concave surface and the junction region of the V-shaped pair of helices contact DNA in the enzyme-DNA complex. Crystallographic, biochemical and genetic data indicate that this 26 kDa fragment of yeast DNA topoisomerase I is involved in complex formation between the enzyme and DNA, and probably also in camptothecin-enzyme-DNA ternary complex formation. A molecular model for protein-DNA interaction based on these data is proposed. The bipartite DNA-binding regions of the 26 kDa fragment may enable eukaryotic DNA topoisomerase I to adapt to sequence-dependent structural variations in its DNA substrates.

  • Organizational Affiliation

    Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA TOPOISOMERASE I223Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: TOP1
Find proteins for P04786 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P04786 
Go to UniProtKB:  P04786
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04786
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.222 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.2α = 90
b = 53.07β = 90
c = 116.89γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
DENZOdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1997-03-12
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references, Other, Structure summary