Crystal Structure of the Multidomain Pectin Methylesterase PmeC5 from Butyrivibrio fibrisolvens D1T
Abstract
:1. Introduction
2. Materials and Methods
2.1. Molecular Modelling
2.2. Protein Expression and Purification
2.3. Crystallization
2.4. Data Collection and Structure Determination
3. Results and Discussion
3.1. The Pectin Methylesterase Pmec5 Structure from B. Fibrisolvens D1T
3.2. The Substrate Binding Domain of Pmec5
4. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Data Collection Statistics * | Items |
---|---|
Space group | P1211 |
Unit cell parameters: a, b, c (Å) α, β, γ (°) | 43.30, 61.95, 77.37 90.00, 105.39, 90.00 |
Wavelength (Å) | 0.953722 |
Temperature (K) | 100 |
Resolution Range (Å) | 47.66–1.33 |
No. of observed ref. | 624,009 (30,348) |
No. of unique ref. | 89,955 (4440) |
Rsym a | 0.045 (0.274) |
Rpim b | 0.028 (0.171) |
Completeness (%) | 99.4 (98.4) |
Multiplicity | 6.9 (6.8) |
I/σ(I) | 23.3 (5.8) |
CC1/2 | 1.000 (0.958) |
Refinement statistics | |
Resolution range (Å) | 47.66–1.33 |
All reflections used | 90,509 |
Size Rfree set (%) | 5 |
All reflections (Rfree) | 4472 |
R-values | |
Rcryst (%) | 11.97 |
Rfree (%) | 14.01 |
Matthews coefficient (Å3 Da−1) | 1.74 |
Solvent content (%) | 28.70 |
RMSD ** | |
Rms Bond Length (Å) | 0.0127 |
Rms Bond Angle (°) | 1.8987 |
Ramachandran plot | |
Residues in favored regions (%) | 96.9 |
Residues in allowed regions (%) | 3.1 |
Average B factors (Å2) | |
Protein | 9.055 |
Water (HOH) | 23.282 |
Mg2+ Na | 20.333 18.173 |
Organism and Gene | Class | PDB Monomer | Z-Score a | RMSD b | Lali c | %id d |
---|---|---|---|---|---|---|
Dickeya dadantii 3937 Gene Name: PEMA, PEM EC: 3.1.1.11 | Pectinesterase | 2NTP-A | 33.2 | 2.4 | 289 | 27 |
Aspergillus niger ATCC 1015 Gene Name: ASPNIDRAFT_214857 EC: 3.1.1.11 | Pectinesterase | 5C1C-A | 32.7 | 2.1 | 271 | 30 |
Erwinia chrysanthemi Gene Name: PEMA EC: 3.1.1.11 | Pectin methylesterase | 1QJV-A | 32.7 | 2.4 | 290 | 27 |
Daucus carota Protein sequence: P83218, PME EC: 3.1.1.11 | Pectinesterase | 1GQ8-A | 31.5 | 2.4 | 284 | 27 |
Escherichia coli K-12 Gene Names: b0772, JW0755, ybhC EC: 3.1.2 | Acyl-CoA thioester hydrolase | 3GRH-A | 28.9 | 2.4 | 269 | 19 |
Sitophilus oryzae Gene Name: CE8-1 EC: 3.1.1.11 | Pectinesterase | 4PMH-A | 28.6 | 2.2 | 261 | 26 |
Butyrivibrio fibrisolvens Gene Name: SAMN02745229_01989 EC: 3.1.1.11 | Pectinesterase | 8TMS-A | 25.0 | 2.9 | 229 | 22 |
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Carbone, V.; Reilly, K.; Sang, C.; Schofield, L.R.; Kelly, W.J.; Ronimus, R.S.; Attwood, G.T.; Palevich, N. Crystal Structure of the Multidomain Pectin Methylesterase PmeC5 from Butyrivibrio fibrisolvens D1T. Biomolecules 2025, 15, 720. https://doi.org/10.3390/biom15050720
Carbone V, Reilly K, Sang C, Schofield LR, Kelly WJ, Ronimus RS, Attwood GT, Palevich N. Crystal Structure of the Multidomain Pectin Methylesterase PmeC5 from Butyrivibrio fibrisolvens D1T. Biomolecules. 2025; 15(5):720. https://doi.org/10.3390/biom15050720
Chicago/Turabian StyleCarbone, Vincenzo, Kerri Reilly, Carrie Sang, Linley R. Schofield, William J. Kelly, Ron S. Ronimus, Graeme T. Attwood, and Nikola Palevich. 2025. "Crystal Structure of the Multidomain Pectin Methylesterase PmeC5 from Butyrivibrio fibrisolvens D1T" Biomolecules 15, no. 5: 720. https://doi.org/10.3390/biom15050720
APA StyleCarbone, V., Reilly, K., Sang, C., Schofield, L. R., Kelly, W. J., Ronimus, R. S., Attwood, G. T., & Palevich, N. (2025). Crystal Structure of the Multidomain Pectin Methylesterase PmeC5 from Butyrivibrio fibrisolvens D1T. Biomolecules, 15(5), 720. https://doi.org/10.3390/biom15050720