Crystal structure of a LonA protease domain in complex with bortezomib

Experimental Data Snapshot

  • Resolution: 1.85 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.178 

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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 of 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lon protease303Meiothermus taiwanensisMutation(s): 0 
Gene Names: lonA1lon
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
  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 122.343α = 90
b = 122.343β = 90
c = 103.125γ = 120
Software Package:
Software NamePurpose
HKL-2000data processing
HKL-2000data scaling
Cootmodel building

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Ministry of Science and TechnologyTaiwan--

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