1. Structural and molecular dynamics studies of a C1-oxidizing lytic polysaccharide monooxygenase from Heterobasidion irregulare reveal amino acids important for substrate recognition.
- Author
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Liu B, Kognole AA, Wu M, Westereng B, Crowley MF, Kim S, Dimarogona M, Payne CM, and Sandgren M
- Subjects
- Amino Acid Sequence, Amino Acids metabolism, Basidiomycota chemistry, Basidiomycota genetics, Catalytic Domain, Cellulose metabolism, Cloning, Molecular, Copper metabolism, Crystallography, X-Ray, Fungal Proteins genetics, Fungal Proteins metabolism, Gene Expression, Genetic Vectors chemistry, Genetic Vectors metabolism, Kinetics, Mixed Function Oxygenases genetics, Mixed Function Oxygenases metabolism, Models, Molecular, Molecular Dynamics Simulation, Oxidation-Reduction, Pichia genetics, Pichia metabolism, Protein Binding, Protein Conformation, alpha-Helical, Protein Conformation, beta-Strand, Protein Interaction Domains and Motifs, Recombinant Proteins chemistry, Recombinant Proteins genetics, Recombinant Proteins metabolism, Sequence Alignment, Sequence Homology, Amino Acid, Substrate Specificity, Amino Acids chemistry, Basidiomycota enzymology, Cellulose chemistry, Copper chemistry, Fungal Proteins chemistry, Mixed Function Oxygenases chemistry
- Abstract
Lytic polysaccharide monooxygenases (LPMOs) are a group of recently discovered enzymes that play important roles in the decomposition of recalcitrant polysaccharides. Here, we report the biochemical, structural, and computational characterization of an LPMO from the white-rot fungus Heterobasidion irregulare (HiLPMO9B). This enzyme oxidizes cellulose at the C1 carbon of glycosidic linkages. The crystal structure of HiLPMO9B was determined at 2.1 Å resolution using X-ray crystallography. Unlike the majority of the currently available C1-specific LPMO structures, the HiLPMO9B structure contains an extended L2 loop, connecting β-strands β2 and β3 of the β-sandwich structure. Molecular dynamics (MD) simulations suggest roles for both aromatic and acidic residues in the substrate binding of HiLPMO9B, with the main contribution from the residues located on the extended region of the L2 loop (Tyr20) and the LC loop (Asp205, Tyr207, and Glu210). Asp205 and Glu210 were found to be involved in the hydrogen bonding with the hydroxyl group of the C6 carbon of glucose moieties directly or via a water molecule. Two different binding orientations were observed over the course of the MD simulations. In each orientation, the active-site copper of this LPMO preferentially skewed toward the pyranose C1 of the glycosidic linkage over the targeted glycosidic bond. This study provides additional insight into cellulose binding by C1-specific LPMOs, giving a molecular-level picture of active site substrate interactions., Database: The atomic coordinates and structure factors for HiLPMO9B have been deposited in the Protein Data Bank with accession code 5NNS., (© 2018 Federation of European Biochemical Societies.)
- Published
- 2018
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