Structural and Functional Analysis of the Pyridoxal Phosphate Homeostasis Protein YggS from Fusobacterium nucleatum
Abstract
:1. Introduction
2. Results and Discussion
2.1. Characterization of FnYggS
2.2. Overall Structure of FnYggS
2.3. PLP-Binding Site of FnYggS
3. Materials and Methods
3.1. Protein Preparation
3.2. Analysis of PLP Binding
3.3. Crystallization, Data Collection, and Structural Determination
3.4. Size Exclusion Chromatography
3.5. Mutagenesis
3.6. Microscale Thermophoresis
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Sample Availability
References
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Data Collection | FnYggS |
---|---|
Diffraction source | Beamline 5A, PLS-II |
Wavelength | 0.9793 |
Detector | ADSC Q315r CCD |
Rotation range per image (°) | 1 |
Total rotation range (°) | 360 |
Exposure time per image (s) | 0.5 |
Space group | P21 |
Cell dimensions | |
a, b, c (Å) | 37.929, 146.375, 74.128 |
Resolution (Å) | 36.59–2.08 |
Completeness | 96.03 (86.73) |
Redundancy | 4.2 (2.7) |
I/σ(I) | 27.1304 (4.33) |
Rsym (%) | 27.1 (60.7) |
Refinement statistics | |
Rwork (%) | 18.39 (19.59) |
Rfree (%) | 21.77 (22.86) |
B-factor (Averaged) | |
Protein | 28.83 |
R.m.s. deviations | |
Bond lengths (Å) | 0.009 |
Bond angles (°) | 1.23 |
Ramachandran plot (%) | |
favored | 97.59 |
allowed | 2.26 |
disallowed regions | 0.15 |
PDB code | 7YGF |
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He, S.; Chen, Y.; Wang, L.; Bai, X.; Bu, T.; Zhang, J.; Lu, M.; Ha, N.-C.; Quan, C.; Nam, K.H.; et al. Structural and Functional Analysis of the Pyridoxal Phosphate Homeostasis Protein YggS from Fusobacterium nucleatum. Molecules 2022, 27, 4781. https://doi.org/10.3390/molecules27154781
He S, Chen Y, Wang L, Bai X, Bu T, Zhang J, Lu M, Ha N-C, Quan C, Nam KH, et al. Structural and Functional Analysis of the Pyridoxal Phosphate Homeostasis Protein YggS from Fusobacterium nucleatum. Molecules. 2022; 27(15):4781. https://doi.org/10.3390/molecules27154781
Chicago/Turabian StyleHe, Shanru, Yuanyuan Chen, Lulu Wang, Xue Bai, Tingting Bu, Jie Zhang, Ming Lu, Nam-Chul Ha, Chunshan Quan, Ki Hyun Nam, and et al. 2022. "Structural and Functional Analysis of the Pyridoxal Phosphate Homeostasis Protein YggS from Fusobacterium nucleatum" Molecules 27, no. 15: 4781. https://doi.org/10.3390/molecules27154781