4GIT

Crystal structure of alpha sub-domain of Lon protease from Brevibacillus thermoruber


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.88 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.206 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis for DNA-mediated allosteric regulation facilitated by the AAA(+) module of Lon protease.

Lee, A.Y.Chen, Y.D.Chang, Y.Y.Lin, Y.C.Chang, C.F.Huang, S.J.Wu, S.H.Hsu, C.H.

(2014) Acta Crystallogr D Biol Crystallogr 70: 218-230

  • DOI: https://doi.org/10.1107/S139900471302631X
  • Primary Citation of Related Structures:  
    4GIT

  • PubMed Abstract: 

    Lon belongs to a unique group of AAA+ proteases that bind DNA. However, the DNA-mediated regulation of Lon remains elusive. Here, the crystal structure of the α subdomain of the Lon protease from Brevibacillus thermoruber (Bt-Lon) is presented, together with biochemical data, and the DNA-binding mode is delineated, showing that Arg518, Arg557 and Arg566 play a crucial role in DNA binding. Electrostatic interactions contributed by arginine residues in the AAA+ module are suggested to be important to DNA binding and allosteric regulation of enzymatic activities. Intriguingly, Arg557, which directly binds DNA in the α subdomain, has a dual role in the negative regulation of ATPase stimulation by DNA and in the domain-domain communication in allosteric regulation of Bt-Lon by substrate. In conclusion, structural and biochemical evidence is provided to show that electrostatic interaction in the AAA+ module is important for DNA binding by Lon and allosteric regulation of its enzymatic activities by DNA and substrate.


  • Organizational Affiliation

    Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lon protease
A, B
124Brevibacillus thermoruberMutation(s): 0 
Gene Names: lon
EC: 3.4.21.53
UniProt
Find proteins for Q84FG5 (Brevibacillus thermoruber)
Explore Q84FG5 
Go to UniProtKB:  Q84FG5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ84FG5
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.88 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.206 
  • Space Group: P 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.283α = 90
b = 94.283β = 90
c = 94.283γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-09-11
    Type: Initial release
  • Version 1.1: 2014-03-05
    Changes: Database references
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description