Protein structure homology models of C. elegans wild-type glucose-6-phosphate dehydrogenase and the D60N and R252L mutants

Published: 23 August 2021| Version 1 | DOI: 10.17632/mn3wf6v3wy.1
Contributor:
Katherine Walstrom

Description

This data folder contains protein structure homology models for glucose-6-phosphate dehydrogenase in Caenorhabditis elegans (NCBI:txid6239): GSPD-1 (B0035.5) and two mutants, D60N and R252L. The PDF file contains experimental procedures, references, and the protein structure validation results.

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Steps to reproduce

The glucose-6-phosphate dehydrogenase in Caenorhabditis elegans (NCBI:txid6239) is GSPD-1 (B0035.5). The wild-type, D60N, and R252L GSPD-1 amino acid sequences were submitted to SWISS-MODEL (1), and the predicted structures were built using ProMod3 (version 3.2.0, (2)) with the crystal structure 6E07.1.A (3) as the template. The models had GMQE and QMEAN scores (4) of 0.80 and -1.26 for wild-type GSPD-1, 0.80 and -1.29 for the D60N mutant, and 0.80 and -1.28 for the R252L mutant. The three model structures were refined by minimizing the free energy using the YASARA energy minimization server (5). The z-scores for the modeled structures were calculated using the ProSA-web tools (6, 7), the bond and rotamer angles were checked using MolProbity (8, 9), and the models passed the Verify 3D assessment (10–12). The results from these protein structure tests are shown in Figures 1-3 in the PDF file. The references are listed in the PDF file.