Mechanistic Insights into Substrate Recognition of Human Nucleoside Diphosphate Kinase C Based on Nucleotide-Induced Structural Changes
Abstract
:1. Introduction
2. Results and Discussion
2.1. The NDPK-C ADP Complex in the Absence and Presence of Mg2+
2.2. Comparison of Human NDPK-C Ligated with Different Nucleotides
2.3. Structure of Nucleotide-Free Human NDPK-C
2.4. Differences between the NDPK B and C Isoforms Might Contribute to Isoform-Specific Interactions
3. Materials and Methods
3.1. Cloning, Protein Preparation and Purification
3.2. Protein Characterization and Enzymatic Activity Assays
3.3. Crystallization
3.4. X-ray Data Collection
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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PDB Entry | 8QW3 | 8QVZ | 8QW0 | 8QW1 | 8QW2 | 8QVY |
---|---|---|---|---|---|---|
Ligands | ADP | cAMP | GDP | ADP, Mg2+ | UDP, Mg2+ | None |
Data Collection | ||||||
X-ray source | ESRF ID23-1 | ESRF ID30A-3 | ESRF ID30A-3 | ESRF ID23-2 | ESRF ID23-1 | ESRF ID30A-3 |
Wavelength (Å) | 1.005 | 0.9677 | 0.9677 | 0.8731 | 0.6888 | 0.9677 |
Detector | PILATUS 6M-F | EIGER X 4M | EIGER X 4M | PILATUS3 X 2M | EIGER2 X CdTe 16M | EIGER X 4M |
Space group | P1 | P1 | P21 | C2 | C2 | C2 |
Unit cell dimensions | ||||||
a (Å) | 52.32 | 52.02 | 104.3 | 106.5 | 106.5 | 106.2 |
b (Å) | 67.87 | 67.41 | 78.64 | 116.3 | 116.0 | 115.5 |
c (Å) | 68.42 | 68.15 | 112.4 | 84.07 | 83.84 | 82.61 |
α (°) | 108.5 | 108.7 | 90 | 90 | 90 | 90 |
β (°) | 112.3 | 112.4 | 97.56 | 93.05 | 93.28 | 94.32 |
γ (°) | 101.1 | 100.9 | 90 | 90 | 90 | 90 |
Vm (Å3/Da) | 1.89 | 1.86 | 2.17 | 2.47 | 2.46 | 2.40 |
Solvent content (%) | 35.1 | 34.0 | 43.5 | 50.3 | 50.0 | 48.9 |
Resolution range (Å) | 60.1–1.25 (1.28–1.25) | 45.0–1.77 (1.81–1.77) | 46.6–2.17 (2.23–2.17) | 42.0–2.10 (2.15–2.10) | 47.7–1.87 (1.94–1.87) | 47.3–2.64 (2.71–2.64) |
Rmerge (%) | 4.9 (94.7) | 12.7 (101.4) | 15.2 (138.8) | 18.4 (150.9) | 4.2 (118.7) | 12.7 (239.0) |
<I/σ(I)> | 8.6 (0.7) | 6.2 (1.2) | 9.6 (1.0) | 10.0 (1.7) | 15.0 (1.1) | 9.45 (0.9) |
CC1/2 (%) | 97.0 (40.1) | 99.3 (61.2) | 99.8 (54.9) | 99.5 (46.6) | 99.7 (69.7) | 99.2 (48.0) |
Data completeness (%) | 94.2 (89.0) | 97.3 (88.4) | 99.5 (94.2) | 95.8 (73.1) | 99.9 (99.5) | 96.4 (98.2) |
Average redundancy | 2.8 (1.8) | 4.6 (4.4) | 10.3 (7.2) | 6.6 (5.9) | 5.2 (4.9) | 7.3 (7.4) |
Wilson B (Å2) | 12.8 | 20.8 | 46.2 | 41.6 | 44.0 | 79.1 |
Refinement | ||||||
Max. resolution (Å) | 1.25 | 1.77 | 2.17 | 2.10 | 1.87 | 2.64 |
Total nr. reflections | 198,505 | 71,473 | 94,493 | 57,087 | 83,594 | 28,215 |
Test set | 2119 | 2091 | 1996 | 2382 | 2091 | 1263 |
Rwork (%) | 14.7 | 16.5 | 18.9 | 17.2 | 17.0 | 19.7 |
Rfree (%) | 17.5 | 21.0 | 22.9 | 20.5 | 20.3 | 24.7 |
Protein atoms | 7425 | 7481 | 14,483 | 7284 | 7300 | 7073 |
Other non-solvent atoms | 177 | 147 | 346 | 168 | 156 | 30 |
Solvent atoms | 542 | 408 | 303 | 399 | 313 | 0 |
RMSD bond lengths (Å) | 0.0116 | 0.0106 | 0.0112 | 0.0091 | 0.0092 | 0.0073 |
RMSD bond angles (°) | 1.671 | 1.664 | 1.812 | 1.641 | 1.618 | 1.470 |
Ramachandran | ||||||
favored (%) | 98 | 98 | 98 | 98 | 98 | 97 |
allowed (%) | 2 | 2 | 2 | 2 | 2 | 3 |
outliers (%) | 0 | 0 | 0 | 0 | 0 | 0 |
Average B (Å2) | ||||||
protein | 21.3 | 26.8 | 50.8 | 41.4 | 61.0 | 103.3 |
other non-solvent | 27.9 | 30.1 | 66.9 | 51.0 | 77.4 | 133.1 |
solvent | 30.9 | 30.1 | 41.1 | 41.8 | 57.3 | - |
PDB Entry | 8QW3 | 8QVZ | 8QW0 | 8QW1 | 8QW2 |
---|---|---|---|---|---|
Ligands | ADP | cAMP | GDP | ADP, Mg2+ | UDP, Mg2+ |
Nucleotide concentration | 1 mM | 5 mM | 3 mM | 1 mM | 2 mM |
Space group | P1 | P1 | P21 | C2 | C2 |
Crystallization condition | 6% PEG 3350 | 7% PEG 8000 | |||
150 mM Li2SO4 | 27% Glycerol | ||||
100 mM Tri-sodium citrate pH 5.4 | 40 mM KH2PO4 |
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Amjadi, R.; Werten, S.; Lomada, S.K.; Baldin, C.; Scheffzek, K.; Dunzendorfer-Matt, T.; Wieland, T. Mechanistic Insights into Substrate Recognition of Human Nucleoside Diphosphate Kinase C Based on Nucleotide-Induced Structural Changes. Int. J. Mol. Sci. 2024, 25, 9768. https://doi.org/10.3390/ijms25189768
Amjadi R, Werten S, Lomada SK, Baldin C, Scheffzek K, Dunzendorfer-Matt T, Wieland T. Mechanistic Insights into Substrate Recognition of Human Nucleoside Diphosphate Kinase C Based on Nucleotide-Induced Structural Changes. International Journal of Molecular Sciences. 2024; 25(18):9768. https://doi.org/10.3390/ijms25189768
Chicago/Turabian StyleAmjadi, Rezan, Sebastiaan Werten, Santosh Kumar Lomada, Clara Baldin, Klaus Scheffzek, Theresia Dunzendorfer-Matt, and Thomas Wieland. 2024. "Mechanistic Insights into Substrate Recognition of Human Nucleoside Diphosphate Kinase C Based on Nucleotide-Induced Structural Changes" International Journal of Molecular Sciences 25, no. 18: 9768. https://doi.org/10.3390/ijms25189768