5CA3
Crystal structure of the glycosynthase mutant D324N of Escherichia coli GH63 glycosidase in complex with glucose and lactose
Summary for 5CA3
| Entry DOI | 10.2210/pdb5ca3/pdb |
| Related | 3D3I 3W7S 3W7T 3W7U 3W7W 3W7X 5CA4 |
| Related PRD ID | PRD_900008 |
| Descriptor | Glucosidase YgjK, beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose, CALCIUM ION, ... (7 entities in total) |
| Functional Keywords | glycoside hydrolase, gh63, alpha/alpha barrel, hydrolase |
| Biological source | Escherichia coli (strain K12) |
| Total number of polymer chains | 2 |
| Total formula weight | 173205.65 |
| Authors | Miyazaki, T.,Tonozuka, T. (deposition date: 2015-06-29, release date: 2016-08-10, Last modification date: 2024-10-16) |
| Primary citation | Miyazaki, T.,Nishikawa, A.,Tonozuka, T. Crystal structure of the enzyme-product complex reveals sugar ring distortion during catalysis by family 63 inverting alpha-glycosidase. J.Struct.Biol., 2016 Cited by PubMed Abstract: Glycoside hydrolases are divided into two groups, known as inverting and retaining enzymes, based on their hydrolytic mechanisms. Glycoside hydrolase family 63 (GH63) is composed of inverting α-glycosidases, which act mainly on α-glucosides. We previously found that Escherichia coli GH63 enzyme, YgjK, can hydrolyze 2-O-α-d-glucosyl-d-galactose. Two constructed glycosynthase mutants, D324N and E727A, which catalyze the transfer of a β-glucosyl fluoride donor to galactose, lactose, and melibiose. Here, we determined the crystal structures of D324N and E727A soaked with a mixture of glucose and lactose at 1.8- and 2.1-Å resolutions, respectively. Because glucose and lactose molecules are found at the active sites in both structures, it is possible that these structures mimic the enzyme-product complex of YgjK. A glucose molecule found at subsite -1 in both structures adopts an unusual S skew-boat conformation. Comparison between these structures and the previously determined enzyme-substrate complex structure reveals that the glucose pyranose ring might be distorted immediately after nucleophilic attack by a water molecule. These structures represent the first enzyme-product complex for the GH63 family, as well as the structurally-related glycosidases, and it may provide insight into the catalytic mechanism of these enzymes. PubMed: 27688023DOI: 10.1016/j.jsb.2016.09.015 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.8 Å) |
Structure validation
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