3L4K

Topoisomerase II-DNA cleavage complex, metal-bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.98 Å
  • R-Value Free: 
    0.273 (Depositor), 0.270 (DCC) 
  • R-Value Work: 
    0.239 (Depositor), 0.250 (DCC) 
  • R-Value Observed: 
    0.241 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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This is version 1.6 of the entry. See complete history


Literature

A novel and unified two-metal mechanism for DNA cleavage by type II and IA topoisomerases.

Schmidt, B.H.Burgin, A.B.Deweese, J.E.Osheroff, N.Berger, J.M.

(2010) Nature 465: 641-644

  • DOI: https://doi.org/10.1038/nature08974
  • Primary Citation of Related Structures:  
    3L4J, 3L4K

  • PubMed Abstract: 

    Type II topoisomerases are required for the management of DNA tangles and supercoils, and are targets of clinical antibiotics and anti-cancer agents. These enzymes catalyse the ATP-dependent passage of one DNA duplex (the transport or T-segment) through a transient, double-stranded break in another (the gate or G-segment), navigating DNA through the protein using a set of dissociable internal interfaces, or 'gates'. For more than 20 years, it has been established that a pair of dimer-related tyrosines, together with divalent cations, catalyse G-segment cleavage. Recent efforts have proposed that strand scission relies on a 'two-metal mechanism', a ubiquitous biochemical strategy that supports vital cellular processes ranging from DNA synthesis to RNA self-splicing. Here we present the structure of the DNA-binding and cleavage core of Saccharomyces cerevisiae topoisomerase II covalently linked to DNA through its active-site tyrosine at 2.5A resolution, revealing for the first time the organization of a cleavage-competent type II topoisomerase configuration. Unexpectedly, metal-soaking experiments indicate that cleavage is catalysed by a novel variation of the classic two-metal approach. Comparative analyses extend this scheme to explain how distantly-related type IA topoisomerases cleave single-stranded DNA, unifying the cleavage mechanisms for these two essential enzyme families. The structure also highlights a hitherto undiscovered allosteric relay that actuates a molecular 'trapdoor' to prevent subunit dissociation during cleavage. This connection illustrates how an indispensable chromosome-disentangling machine auto-regulates DNA breakage to prevent the aberrant formation of mutagenic and cytotoxic genomic lesions.


  • Organizational Affiliation

    Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA topoisomerase 2757Saccharomyces cerevisiaeMutation(s): 1 
Gene Names: N2244TOP2TOR3YNL088W
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 Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06786
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TSP
Query on TSP

Download Ideal Coordinates CCD File 
M [auth D]3'-THIO-THYMIDINE-5'-PHOSPHATE
C10 H15 N2 O7 P S
BORVFKJZAOEGOO-GJMOJQLCSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth A]
I [auth A]
J [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PTR
Query on PTR
A
L-PEPTIDE LINKINGC9 H12 N O6 PTYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.98 Å
  • R-Value Free:  0.273 (Depositor), 0.270 (DCC) 
  • R-Value Work:  0.239 (Depositor), 0.250 (DCC) 
  • R-Value Observed: 0.241 (Depositor) 
Space Group: P 21 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.064α = 90
b = 91.851β = 90
c = 115.939γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted TSPClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-05-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-09-13
    Changes: Derived calculations
  • Version 1.3: 2019-07-31
    Changes: Data collection, Derived calculations
  • Version 1.4: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.5: 2023-11-22
    Changes: Data collection
  • Version 1.6: 2024-10-16
    Changes: Structure summary