Structure Prediction, Molecular Dynamics Simulation and Docking Studies of D-Specific Dehalogenase from Rhizobium sp. RC1
Abstract
:1. Introduction
2. Results and Discussion
2.1. The Primary and Secondary Structure of DehD
2.2. The Three-Dimensional (3D) Structure of DehD
2.3. Structural Model Refinement
2.4. Structural Model Validation
2.5. Identification of the Binding Site and Catalytic Residues Lining the Active Site of DehD
2.6. Identification of the Key Catalytic Residues of DehD by Docking
2.7. Docking of Other Substrates into DehD Active Site
3. Experimental Section
3.1. The Primary and Secondary Structure of DehD
3.2. Three-Dimensional (3D) Model of DehD
3.3. Structure Refinement and Validation
3.4. Identification of Catalytic Residues and Substrate Docking into the Active Site of DehD
4. Conclusions
Supplementary Information
ijms-13-15724-s001.pdfAcknowledgments
- Conflict of InterestThe authors declare that they have no conflict of interest and are responsible for the content of the paper.
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Number of amino acid residues in the loop | Loop length | Number of amino acid residues in the helix | Helix length |
---|---|---|---|
24 | M1–T24 | 33 | G5–A37 |
5 | F38–W42 | 8 | M43–I50 |
2 | P51–I52 | 16 | S53–G68 |
1 | T69 | 18 | R70–V87 |
14 | E88–K101 | 9 | T102–S110 |
3 | G111–S113 | 28 | E114–R141 |
25 | G142–G166 | 3 | T167–G169 |
24 | F170–D193 | 17 | E194–I210 |
9 | L211–R219 | 4 | G220–I223 |
4 | S224–V227 | 37 | G228–L264 |
1 | P265 | ||
Total (percentage) | 112 (42.26%) | 173 (65.28%) |
Stereochemical parameter | Parameter value | Typical value | Bandwidth | Number of bandwidths from mean |
---|---|---|---|---|
Percentage residues in favored region | 79.6 | 76.6 | 10.0 | 0.3 |
Omega angle standard deviation (degrees) | 8.4 | 6.0 | 3.0 | 0.8 |
Number of bad contacts/100 residues | 0.0 | 10.5 | 10.0 | −1.1 |
Zeta angle standard deviation (degrees) | 5.6 | 3.1 | 1.6 | 1.6 |
Hydrogen bond standard deviation | 0.8 | 0.9 | 0.2 | −0.7 |
Overall G-factor | −0.8 | −0.6 | 0.3 | −0.6 |
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Sudi, I.Y.; Wong, E.L.; Joyce-Tan, K.H.; Shamsir, M.S.; Jamaluddin, H.; Huyop, F. Structure Prediction, Molecular Dynamics Simulation and Docking Studies of D-Specific Dehalogenase from Rhizobium sp. RC1. Int. J. Mol. Sci. 2012, 13, 15724-15754. https://doi.org/10.3390/ijms131215724
Sudi IY, Wong EL, Joyce-Tan KH, Shamsir MS, Jamaluddin H, Huyop F. Structure Prediction, Molecular Dynamics Simulation and Docking Studies of D-Specific Dehalogenase from Rhizobium sp. RC1. International Journal of Molecular Sciences. 2012; 13(12):15724-15754. https://doi.org/10.3390/ijms131215724
Chicago/Turabian StyleSudi, Ismaila Yada, Ee Lin Wong, Kwee Hong Joyce-Tan, Mohd Shahir Shamsir, Haryati Jamaluddin, and Fahrul Huyop. 2012. "Structure Prediction, Molecular Dynamics Simulation and Docking Studies of D-Specific Dehalogenase from Rhizobium sp. RC1" International Journal of Molecular Sciences 13, no. 12: 15724-15754. https://doi.org/10.3390/ijms131215724