Computational protocol: A Cell Cycle-Regulated Toxoplasma Deubiquitinase, TgOTUD3A, Targets Polyubiquitins with Specific Lysine Linkages

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Protocol publication

[…] Putative TgOTUs were identified using text and OTU domain motif (Pfam accession number PF02338) searches () in the Toxoplasma genome database (http://www.toxodb.org). The putative hits were further verified for OTU domain and other structural features by BLAST searches in the EMBL Pfam database (http://pfam.xfam.org/), SMART (http://smart.embl-heidelberg.de/), and PROSITE (http://prosite.expasy.org/) analysis program. Conservation of active site residues was demonstrated by MUSCLE alignment, and the phylogenetic tree was drawn with the UPGMA (unweighted pair group method using average linkages) tree building method using Geneious version 6.1.8 (). Predicted structures of wild-type and catalytically inactive TgOTUD3A (C229A) were determined using the primary amino acid sequences on a template-based protein structure modeling program, RaptorX (http://raptorx.uchicago.edu/StructurePrediction) (). The structure alignment analysis and labeling of active site residues were done by using PyMOL1.7.4.4 Edu (Schrodinger, LLC). […]

Pipeline specifications

Software tools Geneious, RaptorX, PyMOL
Applications Phylogenetics, Protein structure analysis
Organisms Toxoplasma gondii, Homo sapiens
Diseases Ovarian Neoplasms