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Comparative homology modeling of pyruvate dehydrogenase kinase isozymes from Xenopus tropicalis reveals structural basis for their subfunctionalization

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Abstract

Structural–functional divergence is responsible for the preservation of highly homologous genes. Protein functions affected by mutagenesis in divergent sequences require investigation on an individual basis. In the present study, comparative homology modeling and predictive bioinformatics analysis were used to reveal for the first time the subfunctionalization of two pyruvate dehydrogenase kinase (PDK) isozymes in the western clawed frog Xenopus tropicalis. Three-dimensional structures of the two proteins were built by homology modeling based on the crystal structures of mammalian PDKs. A detailed comparison of them revealed important structural differences that modify the accessibility of the nucleotide binding site in the two isozymes. Based on the generated models and bioinformatics data analysis, the differences between the two proteins in terms of kinetic parameters, metabolic regulation, and tissue distribution are predicted. The results obtained are consistent with the idea that one of the xtPDKs is the major isozyme responsible for metabolic control of PDC activity in X. tropicalis, whereas the other one has more specialized functions. Hence, this study provides a rationale for the existence of two closely related PDK isozymes in X. tropicalis, thereby enhancing our understanding of the functional evolution of PDK family genes.

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Authors and Affiliations

  1. Research Center for Environmental Genomics and Graduate School of Science, Kobe University, Rokko dai 1-1, Nada, Kobe, 657-8501, Japan

    Alexander A. Tokmakov

  2. RIKEN Systems and Structural Biology Center, Yokohama, Japan

    Alexander A. Tokmakov

Authors
  1. Alexander A. Tokmakov
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Correspondence to Alexander A. Tokmakov.

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Table S1

Interaction energies (kJ/mol) of amino acid residues located in the xtPDK3 ATP lid. (PDF 66 kb)

Table S2

Interaction energies (kJ/mol) of amino acid residues located in the xtPDK4 ATP lid. (PDF 40 kb)

Fig. S1

Ramachandran plot of the xtPDK3 model obtained by PROCHECK. (PDF 243 kb)

Fig. S2

Ramachandran plot of the xtPDK4 model obtained by PROCHECK. (PDF 251 kb)

Fig. S3

Estimation of absolute quality (left) and density plot of the QMEAN score (right) for the xtPDK3 model. (PDF 82 kb)

Fig. S4

Estimation of absolute quality (left) and density plot of the QMEAN score (right) for the xtPDK4 model. (PDF 219 kb)

Fig. S5

Estimated residue error in the models of xtPDK3 (a) and xtPDK4 (b) visualized using a color gradient. (PDF 88 kb)

Fig. S6

Analysis of xtPDK4 flexibility. Backbone and sequence of the modeled xtPDK4 protein are shown, colored by B factor. (PDF 166 kb)

Fig. S7

Structure predictions for the C-terminal regions of the xtPDKs. The results of secondary structure predictions obtained using the Jpred3 proteomics server are shown. (PDF 36 kb)

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Tokmakov, A.A. Comparative homology modeling of pyruvate dehydrogenase kinase isozymes from Xenopus tropicalis reveals structural basis for their subfunctionalization. J Mol Model 18, 2567–2576 (2012). https://doi.org/10.1007/s00894-011-1281-3

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  • DOI: https://doi.org/10.1007/s00894-011-1281-3

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