Computational protocol: Crystal structure of tyrosine decarboxylase and identification of key residues involved in conformational swing and substrate binding

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Protocol publication

[…] For X-ray diffraction, all crystals were equilibrated in a cryoprotectant solution containing 90% reservoir solution and 10% glycerol and then flash-cooled with liquid nitrogen. Diffraction data for SeMet-LbTDC were collected using beamline BL17A at the High Energy Accelerator Research Organization (KEK, Japan). The data for the native protein and LbTDC-PLP complex were collected using beamlines BL17U1 and BL19U1 at the Shanghai Synchrotron Radiation Facility (SSRF, China), respectively. All of the diffraction images were integrated and scaled with the HKL2000 package. The crystal parameters and data collection statistics are listed in .The phases of LbTDC were solved using the Multi-wavelength anomalous diffraction method. The position of the Se atom was identified by Autosol. Then, AutoBuild in the Phenix package was employed to automatically build the model of LbTDC. Several cycles of refinement were performed using Phenix and Coot. The structure of the LbTDC/PLP complex was solved by the molecular replacement method using Phaser in the CCP4 crystallographic suite, and the crystal structure of LbTDC was used as a search model. […]

Pipeline specifications

Software tools PHENIX, Coot, CCP4
Applications Small-angle scattering, Protein structure analysis
Organisms Lactobacillus brevis
Diseases Mitochondrial Diseases
Chemicals Alanine, Amines, Pyridoxal Phosphate, Tyramine, Tyrosine