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Protein homology modeling, docking, and phylogenetic analyses of an endo-1,4-β-xylanase GH11 of Colletotrichum lindemuthianum

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Abstract

Endo-1,4-β-xylanase (EC 3.2.1.8) is a crucial enzyme that randomly cleaves the β-1,4-glycosidic linkages of the xylan backbone, releasing xylooligomers of different lengths. The three-dimensional structure of the endo-β-1,4-xylanase protein (xyl1) from Colletotrichum lindemuthianum was modeled and docked with various xylan model compounds. Docking analyses revealed significantly higher stability of C. lindemuthianum XYL1 with the xylopentaose oligomer. Residues interacting with the model oligomers at the respective enzyme active sites were found to be in accord with their role in xylan degradation. Nevertheless, docking analyses of xylanases GH11 from Colletotrichum sp. revealed significative differences in structure, integration of the substrate into the active site, and in the glutamate residues of the catalytic site involved in substrate hydrolysis; of these proteins, 36%, 60%, and 4% integrated xylotetraose, xylopentaose, and xylohexaose in the active site, respectively. Since endoxylanases GH11 from Colletotrichum species interact much more efficiently with xylopentaose and xylotetraose, and xylanases GH11 from different fungi do not seem to have the same substrate binding subsites, we propose that they are enzymes with different affinity to xylooligosaccharides. In agreement with this idea, phylogenetic analyses of xylanases from Colletotrichum sp. show four lineages, suggesting diversifying selection. Most likely, the polydiversity or structural polymolecularity of xylan in plant cell walls processed by these organisms play a determinant role in diversifying selection.

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Acknowledgements

The authors thank the financial support provided by Secretaría de Educación Pública-Consejo Nacional de Ciencia y Tecnología (SEP-CONACyT), México (project 2012-01-182755 to María G. Zavala-Páramo), Coordinación de la Investigación, Universidad Michoacana de San Nicolás de Hidalgo (project 2014-2015 to Horacio Cano-Camacho), Consejo Nacional de Ciencia y Tecnología, México, for scholarship number 209148 granted to Ulises Conejo-Saucedo and scholarship number 233565 granted to Maria G. Villa-Rivera, and Universidad Nacional Autónoma de México for postdoctoral fellowship program 2012-14 granted to Alicia Lara-Márquez.

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  1. Centro Multidisciplinario de Estudios en Biotecnología, FMVZ, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, Mexico

    Ulises Conejo-Saucedo, Horacio Cano-Camacho, Maria G. Villa-Rivera & María G. Zavala-Páramo

  2. Escuela Nacional de Estudios Superiores, Universidad Nacional Autónoma de México, Morelia, Michoacán, Mexico

    Alicia Lara-Márquez

  3. Departamento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Mexico

    Everardo López-Romero

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  1. Ulises Conejo-Saucedo
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Conejo-Saucedo, U., Cano-Camacho, H., Villa-Rivera, M.G. et al. Protein homology modeling, docking, and phylogenetic analyses of an endo-1,4-β-xylanase GH11 of Colletotrichum lindemuthianum . Mycol Progress 16, 577–591 (2017). https://doi.org/10.1007/s11557-017-1291-3

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