Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 35.33 kDa 
• Atom Count: 2632 
• Residue Count: 302 
• Unique protein chains: 1

4G3N

Mycobacterium tuberculosis gyrase type IIA topoisomerase C-terminal domain at 1.4 A resolution

• DOI: 10.2210/pdb4G3N/pdb

• Classification: ISOMERASE
• Organism(s): Mycobacterium tuberculosis H37Rv
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2012-07-15 Released: 2013-08-07 
• Deposition Author(s): Darmon, A., Piton, J., Petrella, S., Aubry, A., Mayer, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.213 
• R-Value Work: 0.185 
• R-Value Observed: 0.187 

Literature

Mycobacterium tuberculosis DNA gyrase possesses two functional GyrA-boxes.

Bouige, A., Darmon, A., Piton, J., Roue, M., Petrella, S., Capton, E., Forterre, P., Aubry, A., Mayer, C.

(2013) Biochem J 455: 285-294

• PubMed: 23869946 
• DOI: 10.1042/BJ20130430
• Primary Citation of Related Structures:  
  4G3N


• PubMed Abstract: 
  

In contrast with most bacteria which possess two type II topoisomerases (topoisomerase IV and DNA gyrase), Mycobacterium tuberculosis possesses only one, DNA gyrase, which is functionally a hybrid enzyme. Functional differences between the two type IIA topoisomerases are thought to be specified by a CTD (C-terminal DNA-binding domain), which controls DNA recognition. To explore the molecular mechanism responsible for the hybrid functions of the M. tuberculosis DNA gyrase, we conducted a series of sequence analyses and structural and biochemical experiments with the isolated GyrA CTD and the holoenzyme. Although the CTD displayed a global structure similar to that of bona fide GyrA and ParC paralogues, it harbours a second key motif similar in all respects to that of the conserved GyrA-box sequence motif. Biochemical assays showed that the GyrA-box is responsible for DNA supercoiling, whereas the second GyrA-box-l (GyrA-box-like motif) is responsible for the enhanced decatenation activity, suggesting that the mechanistic originality of M. tuberculosis DNA gyrase depends largely on the particular DNA path around the CTD allowed for by the presence of GyrA-box-l. The results of the present study also provide, through phylogenetic exploration of the entire Corynebacterineae suborder, a new and broader insight into the functional diversity of bacterial type IIA topoisomerases.

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Organizational Affiliation: 

*UPMC Université Paris 06, ER5, EA 1541, Laboratoire de Bactériologie-Hygiène, 91 bd de l'Hôpital, F 75013 Paris, France.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA gyrase subunit A	A	327	Mycobacterium tuberculosis H37Rv	Mutation(s): 1  Gene Names: gyrA, MT0006, mtct10h4.04, MTCY10H4.04, Rv0006, rv006 EC: 5.99.1.3 (PDB Primary Data), 5.6.2.2 (UniProt)
Find proteins for P9WG47 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WG47  Go to UniProtKB:  P9WG47

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.213 
• R-Value Work: 0.185 
• R-Value Observed: 0.187 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.7	α = 90
b = 80.519	β = 90
c = 88.182	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
AMoRE	phasing
BUSTER	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-07-15 
• Released Date: 2013-08-07 
Deposition Author(s): Darmon, A., Piton, J., Petrella, S., Aubry, A., Mayer, C.

Revision History 

• Version 1.0: 2013-08-07
  Type: Initial release
  
• Version 1.1: 2013-10-23
  Changes: Database references