5NNS

Crystal structure of HiLPMO9B

Summary for 5NNS

• Entry DOI: 10.2210/pdb5nns/pdb
• Descriptor: Glycosyl hydrolase family 61, 2 protein, 2-acetamido-2-deoxy-beta-D-glucopyranose, COPPER (II) ION, ... (7 entities in total)
• Functional Keywords: polysaccharide oxidase, lpmo, aa9, hydrolase, oxidoreductase
• Biological source: Heterobasidion irregulare TC 32-1
• Total number of polymer chains: 2
• Total formula weight: 50679.41

Authors

Dimarogona, M.,Sandgren, M. (deposition date: 2017-04-10, release date: 2018-05-16, Last modification date: 2024-11-20)

Primary citation

Liu, B.,Kognole, A.A.,Wu, M.,Westereng, B.,Crowley, M.F.,Kim, S.,Dimarogona, M.,Payne, C.M.,Sandgren, M.
Structural and molecular dynamics studies of a C1-oxidizing lytic polysaccharide monooxygenase from Heterobasidion irregulare reveal amino acids important for substrate recognition.
FEBS J., 285:2225-2242, 2018

PubMed 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.

PubMed: 29660793
DOI: 10.1111/febs.14472

Experimental method

X-RAY DIFFRACTION (2.1 Å)