1EI1

DIMERIZATION OF E. COLI DNA GYRASE B PROVIDES A STRUCTURAL MECHANISM FOR ACTIVATING THE ATPASE CATALYTIC CENTER


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.166 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Dimerization of Escherichia coli DNA-gyrase B provides a structural mechanism for activating the ATPase catalytic center.

Brino, L.Urzhumtsev, A.Mousli, M.Bronner, C.Mitschler, A.Oudet, P.Moras, D.

(2000) J Biol Chem 275: 9468-9475

  • DOI: 10.1074/jbc.275.13.9468
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • DNA-gyrase exhibits an unusual ATP-binding site that is formed as a result of gyrase B subunit dimerization, a structural transition that is also essential for DNA capture during the topoisomerization cycle. Previous structural studies on Escherichia ...

    DNA-gyrase exhibits an unusual ATP-binding site that is formed as a result of gyrase B subunit dimerization, a structural transition that is also essential for DNA capture during the topoisomerization cycle. Previous structural studies on Escherichia coli DNA-gyrase B revealed that dimerization is the result of a polypeptidic exchange involving the N-terminal 14 amino acids. To provide experimental data that dimerization is critical for ATPase activity and enzyme turnover, we generated mutants with reduced dimerization by mutating the two most conserved residues of the GyrB N-terminal arm (Tyr-5 and Ile-10 residues). Our data demonstrate that the hydrophobic Ile-10 residue plays an important role in enzyme dimerization and the nucleotide-protein contact mediated by Tyr-5 side chain residue helps the dimerization process. Analysis of ATPase activities of mutant proteins provides evidence that dimerization enhances the ATP-hydrolysis turnover. The structure of the Y5S mutant of the N-terminal 43-kDa fragment of E. coli DNA GyrB subunit indicates that Tyr-5 residue provides a scaffold for the ATP-hydrolysis center. We describe a channel formed at the dimer interface that provides a structural mechanism to allow reactive water molecules to access the gamma-phosphate group of the bound ATP molecule. Together, these results demonstrate that dimerization strongly contributes to the folding and stability of the catalytic site for ATP hydrolysis. A role for the essential Mg(2+) ion for the orientation of the phosphate groups of the bound nucleotide inside the reactive pocket was also uncovered by superposition of the 5'-adenylyl beta-gamma-imidodiphosphate (ADPNP) wild-type structure to the salt-free ADPNP structure.


    Related Citations: 
    • Isoleucine 10 is Essential for DNA Gyrase B Function in Escherichia coli.
      Brino, L., Bronner, C., Oudet, P., Mousli, M.
      (1999) Biochimie 81: 973
    • Expression in Escherichia coli of Y5-mutant and N-terminal Domain-deleted DNA Gyrase B Proteins Affects Strongly Plasmid Maintenance.
      Brino, L., Mousli, M., Oudet, P., Weiss, E.
      (1997) Plasmid 38: 188

    Organizational Affiliation

    Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS/INSERM, Université Louis Pasteur, BP 163, 1 Rue Laurent Fries, 67404 Illkirch Cedex, France.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA GYRASE BA, B391Escherichia coliMutation(s): 1 
EC: 5.99.1.3 (PDB Primary Data), 5.6.2.2 (UniProt)
Find proteins for P0AES6 (Escherichia coli (strain K12))
Explore P0AES6 
Go to UniProtKB:  P0AES6
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ANP
Query on ANP

Download CCD File 
A, B
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A, B
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.166 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.7α = 90
b = 137.4β = 90
c = 78.9γ = 90
Software Package:
Software NamePurpose
AMoREphasing
X-PLORrefinement
XDSdata reduction
AUTOMARdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-03-31
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2012-02-22
    Changes: Structure summary
  • Version 1.4: 2017-10-04
    Changes: Refinement description