Biological Assembly 1  

 3D View: Structure | Electron Density

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 79.77 kDa 
• Atom Count: 5402 
• Residue Count: 685 
• Unique protein chains: 1

1ZVU

Structure of the full-length E. coli ParC subunit

• DOI: 10.2210/pdb1ZVU/pdb

• Classification: ISOMERASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2005-06-02 Released: 2005-07-05 
• Deposition Author(s): Corbett, K.D., Schoeffler, A.J., Thomsen, N.D., Berger, J.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.296 
• R-Value Work: 0.240 
• R-Value Observed: 0.243 

Literature

The Structural Basis for Substrate Specificity in DNA Topoisomerase IV.

Corbett, K.D., Schoeffler, A.J., Thomsen, N.D., Berger, J.M.

(2005) J Mol Biol 351: 545-561

• PubMed: 16023670 
• DOI: 10.1016/j.jmb.2005.06.029
• Primary Citation of Related Structures:  
  1ZVT, 1ZVU


• PubMed Abstract: 
  

Most bacteria possess two type IIA topoisomerases, DNA gyrase and topo IV, that together help manage chromosome integrity and topology. Gyrase primarily introduces negative supercoils into DNA, an activity mediated by the C-terminal domain of its DNA binding subunit (GyrA). Although closely related to gyrase, topo IV preferentially decatenates DNA and relaxes positive supercoils. Here we report the structure of the full-length Escherichia coli ParC dimer at 3.0 A resolution. The N-terminal DNA binding region of ParC is highly similar to that of GyrA, but the ParC dimer adopts a markedly different conformation. The C-terminal domain (CTD) of ParC is revealed to be a degenerate form of the homologous GyrA CTD, and is anchored to the top of the N-terminal domains in a configuration different from that thought to occur in gyrase. Biochemical assays show that the ParC CTD controls the substrate specificity of topo IV, likely by capturing DNA segments of certain crossover geometries. This work delineates strong mechanistic parallels between topo IV and gyrase, while explaining how structural differences between the two enzyme families have led to distinct activity profiles. These findings in turn explain how the structures and functions of bacterial type IIA topoisomerases have evolved to meet specific needs of different bacterial families for the control of chromosome superstructure.

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Organizational Affiliation: 

Department of Molecular and Cell Biology, 237 Hildebrand Hall #3206, University of California, Berkeley, Berkeley, CA 94720-3206, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Topoisomerase IV subunit A	A	716	Escherichia coli	Mutation(s): 0  Gene Names: parC EC: 5.99.1 (PDB Primary Data), 5.6.2.2 (UniProt)
Find proteins for P0AFI2 (Escherichia coli (strain K12)) Explore P0AFI2  Go to UniProtKB:  P0AFI2

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.296 
• R-Value Work: 0.240 
• R-Value Observed: 0.243 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 257.99	α = 90
b = 62.141	β = 90
c = 63.998	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-06-02 
• Released Date: 2005-07-05 
Deposition Author(s): Corbett, K.D., Schoeffler, A.J., Thomsen, N.D., Berger, J.M.

Revision History 

• Version 1.0: 2005-07-05
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance