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Insights into the mechanism(s) of digestion of crystalline cellulose by plant class C GH9 endoglucanases

  • Siddhartha KunduEmail author
Original Paper
  • 43 Downloads

Abstract

Biofuels such as γ-valerolactone, bioethanol, and biodiesel are derived from potentially fermentable cellulose and vegetable oils. Plant class C GH9 endoglucanases are CBM49-encompassing hydrolases that cleave the β (1 → 4) glycosidic linkage of contiguous D-glucopyranose residues of crystalline cellulose. Here, I analyse 3D-homology models of characterised and putative class C enzymes to glean insights into the contribution of the GH9, linker, and CBM49 to the mechanism(s) of crystalline cellulose digestion. Crystalline cellulose may be accommodated in a surface groove which is imperfectly bounded by the GH9_CBM49, GH9_linker, and linker_CBM49 surfaces and thence digested in a solvent accessible subsurface cavity. The physical dimensions and distortions thereof, of the groove, are mediated in part by the bulky side chains of aromatic amino acids that comprise it and may also result in a strained geometry of the bound cellulose polymer. These data along with an almost complete absence of measurable cavities, along with poorly conserved, hydrophobic, and heterogeneous amino acid composition, increased atomic motion of the CBM49_linker junction, and docking experiements with ligands of lower degrees of polymerization suggests a modulatory rather than direct role for CBM49 in catalysis. Crystalline cellulose is the de facto substrate for CBM-containing plant and non-plant GH9 enzymes, a finding supported by exceptional sequence- and structural-homology. However, despite the implied similarity in general acid-base catalysis of crystalline cellulose, this study also highlights qualitative differences in substrate binding and glycosidic bond cleavage amongst class C members. Results presented may aid the development of novel plant-based GH9 endoglucanases that could extract and utilise potential fermentable carbohydrates from biomass.

Graphical Abstract

Crystalline cellulose digestion by plant class C GH9 endoglucanases - an in silico assessment of function.

Keywords

Active-site geometry Carbohydrate binding module Class C GH9 endoglucanases Crystalline cellulose Glycoside hydrolase Homology modelling Interaction surface 

Abbreviations

AA

Amino acids

CBM

Carbohydrate binding module

DP

Degree of polymerization

EC

Enzyme commission

FL

Full length

GH

Glycoside hydrolase

IS

Interaction surface

L

Linker

NMA

Normal mode analysis

T

Truncated

Notes

Acknowledgments

SK wishes to formally thank Dr. Rita Sharma for her suggestions and unflinching moral support.

Author contribution

SK collated the data, conducted the analysis, developed the scoring indices, wrote all the necessary code, and the manuscript.

Supplementary material

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© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Department of BiochemistryArmy College of Medical SciencesNew DelhiIndia

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