DFT studies of the copper active site in AA13 polysaccharide monooxygenase

Abstract

AA13 polysaccharide monooxygenases (AA13 PMOs) are novel enzymes that break down starch using a copper active site in a substrate binding groove on a solvent-exposed surface. The structure of the copper active site is influenced by the residues in the groove, while the crystal structure of Cu(II)-AA13 was damaged by photoreduction and lacked two exogenous ligands. We utilized density functional theory (DFT) calculations to obtain insights into the structure of Cu(II)-AA13 in the presence and absence of a key residue (G89) of the groove that interferes with the distal coordination site. Results show that the copper active site of AA13 PMOs can exhibit both 6-coordinate and a 5-coordinate structures depending on position of G89. The active site features are intermediate to those in AA9 and AA10 PMOs, which are the most abundant and well characterized PMO families. In addition, the superoxo species of AA13 has structural parameters halfway between those in AA9 and AA10 PMOs. The structural relationship between the active site and intermediates of AA13 with AA9 and AA10 PMOs is also consistent with their evolutionary relationship.