5E7S

Hexameric structure of a LonA protease domain in active state


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.03 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.227 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural Basis for the Magnesium-Dependent Activation and Hexamerization of the Lon AAA+ Protease

Su, S.-C.Lin, C.-C.Tai, H.-C.Chang, M.-Y.Ho, M.-R.Babu, C.S.Liao, J.-H.Wu, S.-H.Chang, Y.-C.Lim, C.Chang, C.-I.

(2016) Structure 24: 676-686

  • DOI: 10.1016/j.str.2016.03.003
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The Lon AAA+ protease (LonA) plays important roles in protein homeostasis and regulation of diverse biological processes. LonA behaves as a homomeric hexamer in the presence of magnesium (Mg(2+)) and performs ATP-dependent proteolysis. However, it is ...

    The Lon AAA+ protease (LonA) plays important roles in protein homeostasis and regulation of diverse biological processes. LonA behaves as a homomeric hexamer in the presence of magnesium (Mg(2+)) and performs ATP-dependent proteolysis. However, it is also found that LonA can carry out Mg(2+)-dependent degradation of unfolded protein substrate in an ATP-independent manner. Here we show that in the presence of Mg(2+) LonA forms a non-secluded hexameric barrel with prominent openings, which explains why Mg(2+)-activated LonA can operate as a diffusion-based chambered protease to degrade unstructured protein and peptide substrates efficiently in the absence of ATP. A 1.85 Å crystal structure of Mg(2+)-activated protease domain reveals Mg(2+)-dependent remodeling of a substrate-binding loop and a potential metal-binding site near the Ser-Lys catalytic dyad, supported by biophysical binding assays and molecular dynamics simulations. Together, these findings reveal the specific roles of Mg(2+) in the molecular assembly and activation of LonA.


    Organizational Affiliation

    Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan 11529, ROC.,Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan 11529, ROC; Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan 10617, ROC.,Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan 11529, ROC.,Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan 11529, ROC; Department of Chemistry, National Tsing Hua University, Hsinchu, Taiwan 30013, ROC.,Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan 11529, ROC; Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan 10617, ROC. Electronic address: chungi@gate.sinica.edu.tw.,Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan 11529, ROC.,Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan 11529, ROC; Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan 30013, ROC.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lon protease
A, B, C, D, E, F, G, H, I, J, K, L
298Meiothermus taiwanensisMutation(s): 0 
Gene Names: lonA1 (lon)
EC: 3.4.21.53
Find proteins for A0A059VAZ3 (Meiothermus taiwanensis)
Go to UniProtKB:  A0A059VAZ3
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.03 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.227 
  • Space Group: C 1 2 1
  • Diffraction Data DOI: 
    10.15785/SBGRID/316 SBGrid
Unit Cell:
Length (Å)Angle (°)
a = 116.309α = 90.00
b = 212.787β = 100.80
c = 178.921γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
Cootmodel building
REFMACrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-03-16
    Type: Initial release
  • Version 1.1: 2016-04-20
    Type: Database references
  • Version 1.2: 2016-05-18
    Type: Database references, Experimental preparation