Structural and molecular dynamics studies of a C1‐oxidizing lytic polysaccharide monooxygenase from Heterobasidion irregulare reveal amino acids important for substrate recognition
Abstract
Lytic polysaccharide monooxygenases ( LPMO s) 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 ( H i LPMO 9B). This enzyme oxidizes cellulose at the C1 carbon of glycosidic linkages. The crystal structure of Hi LPMO 9B was determined at 2.1 Å resolution using X‐ray crystallography. Unlike the majority of the currently available C1‐specific LPMO structures, the Hi LPMO 9B 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 Hi LPMO 9B, 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 LPMOmore »
- Authors:
-
- Department of Molecular Sciences Swedish University of Agricultural Sciences Uppsala Sweden
- Department of Chemical and Materials Engineering University of Kentucky Lexington KY USA
- Department of Chemistry, Biotechnology, and Food Science Norwegian University of Life Sciences Ås Norway
- Biosciences Center National Renewable Energy Laboratory Golden CO USA
- Department of Molecular Sciences Swedish University of Agricultural Sciences Uppsala Sweden, Department of Chemical Engineering University of Patras Greece
- Department of Chemical and Materials Engineering University of Kentucky Lexington KY USA, Directorate of Engineering Division of Chemical, Bioengineering, Environmental, and Transport Systems National Science Foundation Alexandria VA USA
- Publication Date:
- Sponsoring Org.:
- USDOE
- OSTI Identifier:
- 1434537
- Resource Type:
- Publisher's Accepted Manuscript
- Journal Name:
- Federation of European Biochemical Societies (FEBS) Journal
- Additional Journal Information:
- Journal Name: Federation of European Biochemical Societies (FEBS) Journal Journal Volume: 285 Journal Issue: 12; Journal ID: ISSN 1742-464X
- Publisher:
- Wiley-Blackwell
- Country of Publication:
- United Kingdom
- Language:
- English
Citation Formats
Liu, Bing, Kognole, Abhishek A., Wu, Miao, Westereng, Bjørge, Crowley, Michael F., Kim, Seonah, Dimarogona, Maria, Payne, Christina M., and Sandgren, Mats. Structural and molecular dynamics studies of a C1‐oxidizing lytic polysaccharide monooxygenase from Heterobasidion irregulare reveal amino acids important for substrate recognition. United Kingdom: N. p., 2018.
Web. doi:10.1111/febs.14472.
Liu, Bing, Kognole, Abhishek A., Wu, Miao, Westereng, Bjørge, Crowley, Michael F., Kim, Seonah, Dimarogona, Maria, Payne, Christina M., & Sandgren, Mats. Structural and molecular dynamics studies of a C1‐oxidizing lytic polysaccharide monooxygenase from Heterobasidion irregulare reveal amino acids important for substrate recognition. United Kingdom. https://doi.org/10.1111/febs.14472
Liu, Bing, Kognole, Abhishek A., Wu, Miao, Westereng, Bjørge, Crowley, Michael F., Kim, Seonah, Dimarogona, Maria, Payne, Christina M., and Sandgren, Mats. Tue .
"Structural and molecular dynamics studies of a C1‐oxidizing lytic polysaccharide monooxygenase from Heterobasidion irregulare reveal amino acids important for substrate recognition". United Kingdom. https://doi.org/10.1111/febs.14472.
@article{osti_1434537,
title = {Structural and molecular dynamics studies of a C1‐oxidizing lytic polysaccharide monooxygenase from Heterobasidion irregulare reveal amino acids important for substrate recognition},
author = {Liu, Bing and Kognole, Abhishek A. and Wu, Miao and Westereng, Bjørge and Crowley, Michael F. and Kim, Seonah and Dimarogona, Maria and Payne, Christina M. and Sandgren, Mats},
abstractNote = {Lytic polysaccharide monooxygenases ( LPMO s) 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 ( H i LPMO 9B). This enzyme oxidizes cellulose at the C1 carbon of glycosidic linkages. The crystal structure of Hi LPMO 9B was determined at 2.1 Å resolution using X‐ray crystallography. Unlike the majority of the currently available C1‐specific LPMO structures, the Hi LPMO 9B 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 Hi LPMO 9B, 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 LPMO s, giving a molecular‐level picture of active site substrate interactions. Database The atomic coordinates and structure factors for Hi LPMO 9B have been deposited in the Protein Data Bank with accession code 5NNS .},
doi = {10.1111/febs.14472},
journal = {Federation of European Biochemical Societies (FEBS) Journal},
number = 12,
volume = 285,
place = {United Kingdom},
year = {Tue Apr 24 00:00:00 EDT 2018},
month = {Tue Apr 24 00:00:00 EDT 2018}
}
https://doi.org/10.1111/febs.14472
Web of Science
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