Unique Structural Fold of LonBA Protease from Bacillus subtilis, a Member of a Newly Identified Subfamily of Lon Proteases
Abstract
:1. Introduction
2. Results and Discussion
2.1. Analysis of the Primary Structures of Lon Proteases Belonging to ID Group S16.005
2.2. Preparation, Limited Proteolysis, and Preliminary Characterization of the Recombinant BsLonBA
2.3. Crystal Structure of the P Domain of BsLonBA
2.4. The Mode of Binding of Bortezomib to the P Domain of LonBA and Other Lon Proteases
2.5. Comparison of the BsLonBA P Domain with Its Counterparts in Other Lon Proteases
2.6. Model Building of the ATPase Domain of BsLonBA
2.7. Comparison of the Functionally Important Elements in the AAA+ Module of BsLonBA with Their Counterparts in LonA and LonB
2.8. A Model of the Full-Length BsLonBA
3. Materials and Methods
3.1. Analysis of the Amino acid Sequences of Lon Proteases
3.2. Molecular Cloning, Purification, Characterization, and Limited Proteolysis of the Recombinant BsLonBA
3.3. Cloning, Protein Expression, and Purification of the Protease Domain of BsLonBA
3.4. Crystallographic Procedures
3.5. Modeling Procedures
4. Conclusions
A Proposal to Assign LonBA as a Separate Lon Subfamily
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
References
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Data Collection | LonBA |
---|---|
Space group | P63 |
Unit cell parameters a, b, c (Å) α, β, γ (˚) | 89.9, 89.9, 83.95 90, 120, 90 |
Temperature (K) | 100 |
Wavelength (Å) | 1.000 |
Resolution (Å) | 84–1.9 (1.94–1.90) |
Rmerge (%) | 4.4 (82.7) |
Completeness (%) | 99.9 (99.0) |
Mean I/σ(I) | 30.1 (1.8) |
Total reflections | 294,057 (10,969) |
Unique reflections | 30,425 (1942) |
Redundancy | 9.7 |
CC1/2 | 1.000 (0.797) |
B factor from Wilson plot (Å2) | 39.6 |
No. of molecules in a.u. | 2 |
Refinement statistics | |
Resolution (Å) | 30–1.9 (1.95–1.90) |
Working set: no. of reflections | 28,500 |
Rfactor (%) | 19.4 (31.6) |
Test set: no. of reflections | 951 |
Rfree (%) | 23.7 (34.2) |
Protein atoms | 2831 |
Solvent atoms | 159 |
Ligand atoms | 58 |
Geometry statistics | |
R.m.s.d. bond distance (Å) | 0.01 |
R.m.s.d. bond angle (°) | 1.65 |
Isotropic average B-factor (Å2) | 47.0 |
Ramachandran plot (%) | |
Favored regions | 97 |
Allowed regions | 3 |
Disallowed regions | 0 |
PDB ID | 8dvh |
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Gustchina, A.; Li, M.; Andrianova, A.G.; Kudzhaev, A.M.; Lountos, G.T.; Sekula, B.; Cherry, S.; Tropea, J.E.; Smirnov, I.V.; Wlodawer, A.; et al. Unique Structural Fold of LonBA Protease from Bacillus subtilis, a Member of a Newly Identified Subfamily of Lon Proteases. Int. J. Mol. Sci. 2022, 23, 11425. https://doi.org/10.3390/ijms231911425
Gustchina A, Li M, Andrianova AG, Kudzhaev AM, Lountos GT, Sekula B, Cherry S, Tropea JE, Smirnov IV, Wlodawer A, et al. Unique Structural Fold of LonBA Protease from Bacillus subtilis, a Member of a Newly Identified Subfamily of Lon Proteases. International Journal of Molecular Sciences. 2022; 23(19):11425. https://doi.org/10.3390/ijms231911425
Chicago/Turabian StyleGustchina, Alla, Mi Li, Anna G. Andrianova, Arsen M. Kudzhaev, George T. Lountos, Bartosz Sekula, Scott Cherry, Joseph E. Tropea, Ivan V. Smirnov, Alexander Wlodawer, and et al. 2022. "Unique Structural Fold of LonBA Protease from Bacillus subtilis, a Member of a Newly Identified Subfamily of Lon Proteases" International Journal of Molecular Sciences 23, no. 19: 11425. https://doi.org/10.3390/ijms231911425