Computational protocol: Structural insights into the production of 3-hydroxypropionic acid by aldehyde dehydrogenase from Azospirillum brasilense

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Protocol publication

[…] The structure of apo-form of AbKGSADH was determined by molecular replacement with the CCP4 version of MOLREP, using the structure of Succinic-semialdehyde dehydrogenase (SSADH) from Homo sapiens (PDB code 2W8R) as a search model. Further model building was performed manually using the program WinCoot, and refinement was performed with CCP4 refmac5. The structure of AbKGSADH in complex with NAD+ was solved by molecular replacement using the crystal structure of the apo-form of AbKGSADH. The data statistics are summarized in . The refined model of the apo-form of AbKGSADH and that in complex with NAD+ were deposited in the Protein Data Bank with PDB codes of 5X5T and 5X5U, respectively. [...] Molecular docking simulations of α-KGSA, SSA and 3-HPA to AbKGSADH structure were performed by AutoDock Vina software. AbKGSADH structure in complex with NAD+ cofactor (PDB code of 5X5U) and the α-KGSA, SSA and 3-HPA ligands were prepared using the JLigand software. For the docking simulation, the pdbqt files were generated using AutoDock Tools, and all steps for simulation and grid box creation were performed according to the AutoDock Vina manual. The grid size for α-KGSA was x = 40, y = 50, z = 36, and grid center was designated at x = −35.377, y = −49.707, z = −4.816. And the grid size for SSA was x = 28, y = 50, z = 34, and grid center was designated at x = −37.77, y = −49.853, z = −4.29. Last, the grid size for 3-HPA was x = 26, y = 32, z = 34, and grid center was designated at x = −37.903, y = −46.826, z = −4.534. The final conformations produced in this simulation were checked using PyMOL software. […]

Pipeline specifications

Software tools AutoDock Vina, PyMOL
Application Protein interaction analysis
Organisms Azospirillum brasilense
Chemicals Acetaldehyde, Amino Acids, Glycerol, Hydrogen, NAD, Hydroxyl Radical, Acrylamide