Crystal Structure and Computational Characterization of the Lytic Polysaccharide Monooxygenase GH61D from the Basidiomycota Fungus Phanerochaete chrysosporium

• Published in: The Journal of biological chemistry 2013-05, Vol.288 (18), p.12828-12839
• Main Authors: Wu, Miao, Beckham, Gregg T., Larsson, Anna M., Ishida, Takuya, Kim, Seonah, Payne, Christina M., Himmel, Michael E., Crowley, Michael F., Horn, Svein J., Westereng, Bjørge, Igarashi, Kiyohiko, Samejima, Masahiro, Ståhlberg, Jerry, Eijsink, Vincent G.H., Sandgren, Mats
• Format: Article
• Language: English
• Subjects: Biochemistry and Molecular Biology; Biofuel; Biokemi och molekylärbiologi; Carbohydrate-binding Protein; Catalytic Domain; CBM33; Cellobiose - chemistry; Cellobiose - metabolism; Copper - chemistry; Copper - metabolism; Copper Monooxygenase; Crystallography, X-Ray; Enzymology; Fungal Proteins - chemistry; Fungal Proteins - metabolism; Förnyelsebar bioenergi; GH61; Glycoside Hydrolases; Lytic Polysaccharide Monooxygenase; Mixed Function Oxygenases - chemistry; Mixed Function Oxygenases - metabolism; Molecular Dynamics; Phanerochaete - enzymology; Phanerochaete chrysosporium; Renewable Bioenergy Research; Structural Biology; Strukturbiologi
• ISSN: 0021-9258; 1083-351X; 1083-351X
• DOI: 10.1074/jbc.M113.459396

Carbohydrate structures are modified and degraded in the biosphere by a myriad of mostly hydrolytic enzymes. Recently, lytic polysaccharide mono-oxygenases (LPMOs) were discovered as a new class of enzymes for cleavage of recalcitrant polysaccharides that instead employ an oxidative mechanism. LPMOs employ copper as the catalytic metal and are dependent on oxygen and reducing agents for activity. LPMOs are found in many fungi and bacteria, but to date no basidiomycete LPMO has been structurally characterized. Here we present the three-dimensional crystal structure of the basidiomycete Phanerochaete chrysosporium GH61D LPMO, and, for the first time, measure the product distribution of LPMO action on a lignocellulosic substrate. The structure reveals a copper-bound active site common to LPMOs, a collection of aromatic and polar residues near the binding surface that may be responsible for regio-selectivity, and substantial differences in loop structures near the binding face compared with other LPMO structures. The activity assays indicate that this LPMO primarily produces aldonic acids. Last, molecular simulations reveal conformational changes, including the binding of several regions to the cellulose surface, leading to alignment of three tyrosine residues on the binding face of the enzyme with individual cellulose chains, similar to what has been observed for family 1 carbohydrate-binding modules. A calculated potential energy surface for surface translation indicates that P. chrysosporium GH61D exhibits energy wells whose spacing seems adapted to the spacing of cellobiose units along a cellulose chain. Background: Lytic polysaccharide monooxygenases (LPMOs) represent a recently discovered enzymatic route to cleave carbohydrates. Results: We report the first basidiomycete LPMO structure and describe enzyme-cellulose interactions with simulation. Conclusion: We characterize the copper-containing active site and identify loops important for substrate recognition and binding. Significance: This structure is the first LPMO from a model basidiomycete fungus that contains many LPMO genes.