5T7K

X-ray crystal structure of AA13 LPMO

Summary for 5T7K

• Entry DOI: 10.2210/pdb5t7k/pdb
• Descriptor: AoAA13, 2-acetamido-2-deoxy-beta-D-glucopyranose, ZINC ION, ... (4 entities in total)
• Functional Keywords: enzyme, aspergillus oryzae aa13 lpmo, metal binding protein
• Biological source: Aspergillus oryzae RIB40 (Yellow koji mold)
• Total number of polymer chains: 1
• Total formula weight: 26173.90

Authors

Frandsen, K.E.H.,Poulsen, J.-C.N.,Tovborg, M.,Johansen, K.S.,Lo Leggio, L. (deposition date: 2016-09-05, release date: 2017-01-18, Last modification date: 2024-01-17)

Primary citation

Frandsen, K.E.,Poulsen, J.C.,Tovborg, M.,Johansen, K.S.,Lo Leggio, L.
Learning from oligosaccharide soaks of crystals of an AA13 lytic polysaccharide monooxygenase: crystal packing, ligand binding and active-site disorder.
Acta Crystallogr D Struct Biol, 73:64-76, 2017

PubMed Abstract: Lytic polysaccharide monooxygenases (LPMOs) are a class of copper-dependent enzymes discovered within the last ten years. They oxidatively cleave polysaccharides (chitin, lignocellulose, hemicellulose and starch-derived), presumably making recalcitrant substrates accessible to glycoside hydrolases. Recently, the first crystal structure of an LPMO-substrate complex was reported, giving insights into the interaction of LPMOs with β-linked substrates (Frandsen et al., 2016). The LPMOs acting on α-linked glycosidic bonds (family AA13) display binding surfaces that are quite different from those of LPMOs that act on β-linked glycosidic bonds (families AA9-AA11), as revealed from the first determined structure (Lo Leggio et al., 2015), and thus presumably the AA13s interact with their substrate in a distinct fashion. Here, several new structures of the same AA13 enzyme, Aspergillus oryzae AA13, are presented. Crystals obtained in the presence of high zinc-ion concentrations were used, as they can be obtained more reproducibly than those used to refine the deposited copper-containing structure. One structure with an ordered zinc-bound active site was solved at 1.65 Å resolution, and three structures from crystals soaked with maltooligosaccharides in solutions devoid of zinc ions were solved at resolutions of up to 1.10 Å. Despite similar unit-cell parameters, small rearrangements in the crystal packing occur when the crystals are depleted of zinc ions, resulting in a more occluded substrate-binding surface. In two of the three structures maltooligosaccharide ligands are bound, but not at the active site. Two of the structures presented show a His-ligand conformation that is incompatible with metal-ion binding. In one of these structures this conformation is the principal one (80% occupancy), giving a rare atomic resolution view of a substantially misfolded enzyme that is presumably rendered inactive.

PubMed: 28045386
DOI: 10.1107/S2059798316019641

Experimental method

X-RAY DIFFRACTION (1.3 Å)