Supporting Information Mechanism of hydrogen peroxide formation by lytic polysaccharide monooxygenase

Content Provider	Semantic Scholar
Author	Caldararu, Octav Oksanen, Esko Ryde, Ulf Hedegård, Erik Donovan
Copyright Year	2019
Abstract	Protein setup The starting coordinates for QM/MM calculations were taken from the joint refinement reported in the main paper. The structure is a dimer that contains 288 amino acids, 299 crystal water molecules, amounting to 5105 atoms in total. The crystal structure contained 203 amino-acid residues and 105 water residues with atoms in alternative conformations. We included in the calculations only the conformation with highest occupation or the first conformation if the occupation numbers were equal. Hydrogen atom coordinates were taken from the joint refinement reported in the main paper. The individual residues were additionally visually inspected and their solvent exposure and hydrogen-bond network were assessed. Based on this, we concluded that all arginines and lysines are protonated (+1) and the aspartic and glutamic acids are in their carboxylate form (−1). In both chains, Arg41 and Arg154 forms ionic pairs with the carboxylate groups of Asp169 and Glu115, while His149 (doubly protonated, see below) forms an ionic pair with Asp119. In one case, a ionic pair is formed between the two chains: The ammonium group of Lys68 in chain A forms a ionic pair with the carboxylate group of Glu60 in chain B. The protein contains four cysteine residues in each chain (Cys45, Cys54, Cys73 and Cys167) that are cross-linked by disulfide bridges. Residues 1-31 were missing and no attempt to build these missing residues was done. Concerning the histidine residues, these can have two possible protonation sites. The dimer has 5 histidine residues in each chain. In the following, we denote histidines as HIE (Nε2 protonated), HID (Nδ1 protonated) or HIP (both nitrogens protonated). The N-terminal histidine is a special case since Nδ1 (and the terminal N) coordinates to the Cu ion. In some LPMOs, the imidazole ring of the terminal histidine is methylated on the Nε2 atom, but this is not the case for the one studied here. For the remaining histidine residues, we employed the protonation states HID109, HIP123, HIP139 and HIP149. HID109 coordinates to Cu through Nε2. The two residues HIP123 and HIP139 are close to the surface, and therefore chosen to be doubly protonated. The last histidine, HIP149, is also on the surface and forms additionally hydrogen bonds to the carbonyl O of Thr115 through Nε2, and to the carboxylate Oδ2 of Asp119 through Nδ1 (cf. description of ionic pairs above). The total charge of the simulated system in the [CuO2] + state was -12 (for the dimer).
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Language	English
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Resource Type	Article