Dissecting the Cytochrome P450 OleP Substrate Specificity: Evidence for a Preferential Substrate
Abstract
:1. Introduction
2. Materials and Methods
2.1. Chemicals
2.2. OleP Expression and Purification
2.3. Equilibrium Binding Analysis
2.4. Crystallization, X-Ray Data Collection, and Analysis
2.5. Structure Determination and Refinement
2.6. Molecular Docking
3. Results and Discussion
3.1. Binding Properties of OleP to the Aglycone Substrate
3.2. The Structure of OleP Bound to the Oleandolide, DEO
3.3. Docking of L-O-DEO and Crystallographic Structure of OleP Bound to DEO and L-Rhamnose
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Data Collection | OleP–DEOLS | OleP–DEOHS | OleP–DEO-Rhamnose | OleP–6DEB–Rhamnose |
---|---|---|---|---|
PDB ID | 6ZI2 | 6ZHZ | 6ZI7 | 6ZI3 |
Crystallization Conditions | 0.2 M NaCl 0.1 M Tris·HCl pH 7.4 25% PEG 3350 (seeding) | 4 M HCOONa (10% glycerol) | 4.4 M HCOONa | 4.2 M HCOONa (20% glycerol) |
Space group | P1 | C2 | C2 | C2 |
Unit cell (Å, °) | a = 112.07, b = 116.64, c = 125.17, α = 104.43, β = 104.25, γ = 113.91 | a = 247.47, b = 111.22, c = 159.20, β = 129.4 | a = 247.53, b = 110.68, c = 159.28, β = 129.5 | a = 247.38, b = 111.15, c = 159.14, β = 129.4 |
Resolution (å) | 39.89–2.87 (3.05–2.87) | 37.7–2.20 (2.33–2.20) | 50.0–2.11 (2.24–2.11) | 50.0–1.96 (2.08–1.96) |
Total measurements | 411,472 | 574,285 | 1,262,482 | 1,251,578 |
Unique reflections | 115,590 | 168,218 | 373,419 | 462,663 |
Completeness (%) | 98.2 (95.9) | 98.9 (97.3) | 99.1 (99.0) | 97.7 (96.7) |
Redundancy | 3.56 (3.64) | 3.41 (3.37) | 3.38 (3.30) | 2.70 (2.54) |
Rmerge a (%) | 16.5 (92.4) | 5.6 (112.7) | 7.2 (147.1) | 6.4 (163.6) |
cc/2 (%) | 99.0 (68.8) | 99.8 (51.4) | 99.8 (48.4) | 99.7 (36.2) |
I/σ (I) | 7.29 (1.36) | 12.10 (1.05) | 10.52 (0.72) | 7.80 (0.52) |
Wilson B-value (Å2) | 44.1 | 44.9 | 56.7 | 53.5 |
Refinement | ||||
Molecules per asymmetric unit | 9 | 6 | 6 | 6 |
Resolution Range (Å) | 39.89–2.93 | 37.73–2.2 | 47.92–2.28 | 48.09–2.08 |
Rwork/Rfree b (%) | 24.0/29.1 | 18.7/24.3 | 18.4/24.7 | 17.2/22.5 |
Deviations from ideal geometry | ||||
Bond (Å) | 0.011 | 0.012 | 0.013 | 0.011 |
Angles (°) | 1.78 | 2.16 | 2.16 | 1.75 |
Ramachandran (%) Favored/allowed/outliers * | 96.6/3.4/0.0 | 96.1/3.9/0.0 | 96.6/3.4/0.0 | 97.0/3.0/0.0 |
Mean B-factors (Å2) | ||||
Protein | 56.9 | 45.2 | 59.5 | 59.6 |
HEM/DEO/6DEB/RAM | 51.3/53.5/-/- | 31.7/44.7/-/- | 43.1/46.8/-/54.6 | 42.8/-/47.2/75.7 |
H2O/Na/FMT/GOL/TRS | 13.5/-/-/-/- | 62.2/58.5/87.5/81.6/64.4 | 59.6/56.1/76.4/- | 63.9/86.7/55.9/83.3/87.6 |
RSCC (per monomer in the asymmetric unit) | ||||
DEO | 0.88/0.96/0.95/0.91/0.88/0.88/0.88/0.88/0.80 | 0.97/0.96/0.97/0.95/0.95/0.95 | 0.97/0.97/0.97/0.97/0.96/0.96 | |
6DEB | 0.98/0.93/0.96/0.93/0.97/0.97 | |||
RAM (bound to the solvent cavity) | 0.91;0.86/0.81/-/0.85/-/- | 0.87/0.80/0.86/0.87/0.85/- | ||
No of Atoms | ||||
Protein | 26350 | 18824 | 19903 | 20575 |
HEM/DEO/6DEB/RAM | 387/234/-/- | 258/156/-/- | 258/156/-/33 | 258/-/162/77+ |
H2O/Na+/FMT/GOL/TRS | 96/-/-/-/- | 763/5/249/90/24 | 1369/6/642/-/- | 1145/7/609/36/24 |
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Parisi, G.; Freda, I.; Exertier, C.; Cecchetti, C.; Gugole, E.; Cerutti, G.; D’Auria, L.; Macone, A.; Vallone, B.; Savino, C.; et al. Dissecting the Cytochrome P450 OleP Substrate Specificity: Evidence for a Preferential Substrate. Biomolecules 2020, 10, 1411. https://doi.org/10.3390/biom10101411
Parisi G, Freda I, Exertier C, Cecchetti C, Gugole E, Cerutti G, D’Auria L, Macone A, Vallone B, Savino C, et al. Dissecting the Cytochrome P450 OleP Substrate Specificity: Evidence for a Preferential Substrate. Biomolecules. 2020; 10(10):1411. https://doi.org/10.3390/biom10101411
Chicago/Turabian StyleParisi, Giacomo, Ida Freda, Cécile Exertier, Cristina Cecchetti, Elena Gugole, Gabriele Cerutti, Lucia D’Auria, Alberto Macone, Beatrice Vallone, Carmelinda Savino, and et al. 2020. "Dissecting the Cytochrome P450 OleP Substrate Specificity: Evidence for a Preferential Substrate" Biomolecules 10, no. 10: 1411. https://doi.org/10.3390/biom10101411