2RGR

Topoisomerase IIA bound to G-segment DNA

• PDB DOI:  https://doi.org/10.2210/pdb2RGR/pdb
• NAKB: 2RGR

• Classification: Isomerase/DNA
• Organism(s): Saccharomyces cerevisiae
• Expression System: Saccharomyces cerevisiae
• Mutation(s): No 


• Deposited: 2007-10-04 Released: 2007-12-25 
• Deposition Author(s): Dong, K.C., Berger, J.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.278 
• R-Value Work: 0.229 
• R-Value Observed: 0.231 

Literature

Structural basis for gate-DNA recognition and bending by type IIA topoisomerases.

Dong, K.C., Berger, J.M.

(2007) Nature 450: 1201-1205

• PubMed: 18097402 
• DOI: https://doi.org/10.1038/nature06396
• Primary Citation of Related Structures:  
  2RGR


• PubMed Abstract: 
  

Type II topoisomerases disentangle DNA to facilitate chromosome segregation, and represent a major class of therapeutic targets. Although these enzymes have been studied extensively, a molecular understanding of DNA binding has been lacking. Here we present the structure of a complex between the DNA-binding and cleavage core of Saccharomyces cerevisiae Topo II (also known as Top2) and a gate-DNA segment. The structure reveals that the enzyme enforces a 150 degrees DNA bend through a mechanism similar to that of remodelling proteins such as integration host factor. Large protein conformational changes accompany DNA deformation, creating a bipartite catalytic site that positions the DNA backbone near a reactive tyrosine and a coordinated magnesium ion. This configuration closely resembles the catalytic site of type IA topoisomerases, reinforcing an evolutionary link between these structurally and functionally distinct enzymes. Binding of DNA facilitates opening of an enzyme dimerization interface, providing visual evidence for a key step in DNA transport.

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Organizational Affiliation: 

Chemical Biology Graduate Program, Department of Chemistry, College of Chemistry, University of California, Berkeley, California 94720-3220, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 98.69 kDa 
• Atom Count: 6,668 
• Modelled Residue Count: 755 
• Deposited Residue Count: 793 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA topoisomerase 2	C [auth A]	759	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: TOP2, TOR3 EC: 5.99.1.3 (PDB Primary Data), 5.6.2.2 (UniProt)
UniProt
Find proteins for P06786 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P06786  Go to UniProtKB:  P06786

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA	A [auth C]	15	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA	B [auth D]	19	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.278 
• R-Value Work: 0.229 
• R-Value Observed: 0.231 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.435	α = 90
b = 126.801	β = 90
c = 223.492	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-12-25 
Deposition Author(s): Dong, K.C., Berger, J.M.

Revision History  

• Version 1.0: 2007-12-25
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description