1ZXN

Human DNA topoisomerase IIa ATPase/ADP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.235 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Nucleotide-dependent Domain Movement in the ATPase Domain of a Human Type IIA DNA Topoisomerase.

Wei, H.Ruthenburg, A.J.Bechis, S.K.Verdine, G.L.

(2005) J.Biol.Chem. 280: 37041-37047

  • DOI: 10.1074/jbc.M506520200
  • Primary Citation of Related Structures:  
  • Also Cited By: 4R1F

  • PubMed Abstract: 
  • Type IIA DNA topoisomerases play multiple essential roles in the management of higher-order DNA structure, including modulation of topological state, chromosome segregation, and chromatin condensation. These diverse physiologic functions are all acco ...

    Type IIA DNA topoisomerases play multiple essential roles in the management of higher-order DNA structure, including modulation of topological state, chromosome segregation, and chromatin condensation. These diverse physiologic functions are all accomplished through a common molecular mechanism, wherein the protein catalyzes transient cleavage of a DNA duplex (the G-segment) to yield a double-stranded gap through which another duplex (the T-segment) is passed. The overall process is orchestrated by the opening and closing of molecular "gates" in the topoisomerase structure, which is regulated by ATP binding, hydrolysis, and release of ADP and inorganic phosphate. Here we present two crystal structures of the ATPase domain of human DNA topoisomerase IIalpha in different nucleotide-bound states. Comparison of these structures revealed rigid-body movement of the structural modules within the ATPase domain, suggestive of the motions of a molecular gate.


    Organizational Affiliation

    Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA topoisomerase II, alpha isozyme
A, B, C, D
400Homo sapiensMutation(s): 0 
Gene Names: TOP2A (TOP2)
EC: 5.99.1.3
Find proteins for P11388 (Homo sapiens)
Go to Gene View: TOP2A
Go to UniProtKB:  P11388
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
B, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ADP
Query on ADP

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Download CCD File 
A, B, C, D
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A, B, C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.235 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 71.015α = 90.00
b = 90.492β = 89.97
c = 148.293γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
AMoREphasing
SCALEPACKdata scaling
CNSrefinement
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-08-23
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance