4GFH

Topoisomerase II-DNA-AMPPNP complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.41 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.241 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of a topoisomerase II-DNA-nucleotide complex reveals a new control mechanism for ATPase activity.

Schmidt, B.H.Osheroff, N.Berger, J.M.

(2012) Nat Struct Mol Biol 19: 1147-1154

  • DOI: 10.1038/nsmb.2388
  • Primary Citation of Related Structures:  
    4GFH

  • PubMed Abstract: 
  • Type IIA topoisomerases control DNA supercoiling and disentangle chromosomes through a complex ATP-dependent strand-passage mechanism. Although a general framework exists for type IIA topoisomerase function, the architecture of the full-length enzyme has remained undefined ...

    Type IIA topoisomerases control DNA supercoiling and disentangle chromosomes through a complex ATP-dependent strand-passage mechanism. Although a general framework exists for type IIA topoisomerase function, the architecture of the full-length enzyme has remained undefined. Here we present the structure of a fully catalytic Saccharomyces cerevisiae topoisomerase II homodimer complexed with DNA and a nonhydrolyzable ATP analog. The enzyme adopts a domain-swapped configuration wherein the ATPase domain of one protomer sits atop the nucleolytic region of its partner subunit. This organization produces an unexpected interaction between bound DNA and a conformational transducing element in the ATPase domain, which we show is critical for both DNA-stimulated ATP hydrolysis and global topoisomerase activity. Our data indicate that the ATPase domains pivot about each other to ensure unidirectional strand passage and that this state senses bound DNA to promote ATP turnover and enzyme reset.


    Organizational Affiliation

    Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA topoisomerase 2A, F1177Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TOP2TOR3YNL088WN2244
EC: 5.99.1.3 (PDB Primary Data), 5.6.2.2 (UniProt)
Find proteins for P06786 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P06786 
Go to UniProtKB:  P06786
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(P*CP*CP*TP*AP*CP*TP*GP*CP*TP*AP*C)-3')B, G11N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*CP*GP*CP*GP*GP*TP*AP*GP*CP*AP*GP*TP*AP*GP*G)-3')C, H15N/A
      • Find similar nucleic acids by:  Sequence   |   Structure
      • Entity ID: 4
        MoleculeChainsLengthOrganismImage
        DNA (5'-D(P*GP*GP*AP*TP*GP*AP*CP*GP*AP*TP*(TSP))-3')D, I11N/A
        • Find similar nucleic acids by:  Sequence   |   Structure
        • Entity ID: 5
          MoleculeChainsLengthOrganismImage
          DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*CP*GP*TP*CP*AP*TP*CP*C)-3')E, J15N/A
          Small Molecules
          Ligands 2 Unique
          IDChainsName / Formula / InChI Key2D Diagram3D Interactions
          ANP
          Query on ANP

          Download Ideal Coordinates CCD File 
          L [auth A], N [auth F]PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
          C10 H17 N6 O12 P3
          PVKSNHVPLWYQGJ-KQYNXXCUSA-N
           Ligand Interaction
          MG
          Query on MG

          Download Ideal Coordinates CCD File 
          K [auth A], M [auth F]MAGNESIUM ION
          Mg
          JLVVSXFLKOJNIY-UHFFFAOYSA-N
           Ligand Interaction
          Modified Residues  1 Unique
          IDChainsTypeFormula2D DiagramParent
          PTR
          Query on PTR
          A, FL-PEPTIDE LINKINGC9 H12 N O6 PTYR
          Experimental Data & Validation

          Experimental Data

          • Method: X-RAY DIFFRACTION
          • Resolution: 4.41 Å
          • R-Value Free: 0.275 
          • R-Value Work: 0.239 
          • R-Value Observed: 0.241 
          • Space Group: P 21 21 21
          Unit Cell:
          Length ( Å )Angle ( ˚ )
          a = 169.135α = 90
          b = 169.884β = 90
          c = 169.212γ = 90
          Software Package:
          Software NamePurpose
          ADSCdata collection
          PHASERphasing
          PHENIXrefinement
          HKL-2000data reduction
          HKL-2000data scaling

          Structure Validation

          View Full Validation Report



          Entry History 

          Deposition Data

          Revision History  (Full details and data files)

          • Version 1.0: 2012-10-03
            Type: Initial release
          • Version 1.1: 2012-12-12
            Changes: Database references
          • Version 1.2: 2019-07-31
            Changes: Data collection, Derived calculations