5E7S | pdb_00005e7s

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 (Depositor), 0.257 (DCC) 
  • R-Value Work: 
    0.227 (Depositor) 
  • R-Value Observed: 
    0.230 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 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: https://doi.org/10.1016/j.str.2016.03.003
  • Primary Citation Related Structures: 
    4YPM, 5E7S

  • 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 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 Biochemical Sciences, National Taiwan University, Taipei, Taiwan 10617, ROC.

Macromolecule Content 

  • Total Structure Weight: 391.25 kDa 
  • Atom Count: 26,298 
  • Modeled Residue Count: 3,443 
  • Deposited Residue Count: 3,576 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Lon protease
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
298Meiothermus taiwanensisMutation(s): 0 
Gene Names: lonA1lon
EC: 3.4.21.53
UniProt
Find proteins for A0A059VAZ3 (Meiothermus taiwanensis)
Explore A0A059VAZ3 
Go to UniProtKB:  A0A059VAZ3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A059VAZ3
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.03 Å
  • R-Value Free:  0.279 (Depositor), 0.257 (DCC) 
  • R-Value Work:  0.227 (Depositor) 
  • R-Value Observed: 0.230 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.309α = 90
b = 212.787β = 100.8
c = 178.921γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
Cootmodel building

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-03-16
    Type: Initial release
  • Version 1.1: 2016-04-20
    Changes: Database references
  • Version 1.2: 2016-05-18
    Changes: Database references, Experimental preparation
  • Version 1.3: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description