Protein Structure Homology Models of C. elegans cytoplasmic and mitochondrial malate dehydrogenases

Published: 5 August 2021| Version 1 | DOI: 10.17632/3crjnzfwkm.1
Contributor:
Katherine Walstrom

Description

This data folder contains protein structure homology models for the two malate dehydrogenase (MDH) isozymes in Caenorhabditis elegans (NCBI:txid6239): cytoplasmic MDH-1 (F46E10.10) and mitochondrial MDH-2 (F20H11.3). The PDF file contains experimental procedures, references, and the protein structure validation results.

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The two malate dehydrogenase (MDH) isozymes in Caenorhabditis elegans (NCBI:txid6239) are cytoplasmic MDH-1 (F46E10.10) and mitochondrial MDH-2 (F20H11.3). The MDH-2 sequence was analyzed using MitoProt II v1.101 (1) and MitoFates (2) to determine the cleavage site for the mitochondrial import sequence, and the import sequence was removed. Then the MDH-1 and MDH-2 amino acid sequences were submitted to SWISS-MODEL (3), and the predicted structures were built using ProMod3 (version 3.2.0, (4)) with the crystal structures 1BMD.1.A (5) and 2DFD.1.A (unpublished structure from the Structural Genomics Consortium) as the templates, respectively. The models had GMQE and QMEAN scores (6) of 0.79 and -0.62, respectively, for MDH-1 and 0.78 and -0.04, respectively, for MDH-2. The structure of the MDH-1 model was refined by minimizing the free energy using the YASARA energy minimization server (7). The z-scores for the modeled structures were calculated using the ProSA-web tools (8, 9), the bond and rotamer angles were checked using MolProbity (10, 11), and the models passed the Verify 3D assessment (12–14). The results from these protein structure tests are shown in Figures 1-3. The list of references is available in the PDF file in this data folder.