3WQ4

Crystal structure of beta-primeverosidase

Summary for 3WQ4

• Entry DOI: 10.2210/pdb3wq4/pdb
• Related: 3WQ5 3WQ6
• Descriptor: Beta-primeverosidase, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose, ... (4 entities in total)
• Functional Keywords: diglycosidase, diglycoside, disaccharide, glycoside hydrolase family 1 (gh1), (beta/alpha)8 barrel, specific hydrolysis of beta-primeverosides, aroma formation, oolong tea, black tea, hydrolase
• Biological source: Camellia sinensis (black tea)
• Total number of polymer chains: 2
• Total formula weight: 115297.91

Authors

Saino, H. (deposition date: 2014-01-22, release date: 2014-04-23, Last modification date: 2024-11-20)

Primary citation

Saino, H.,Shimizu, T.,Hiratake, J.,Nakatsu, T.,Kato, H.,Sakata, K.,Mizutani, M.
Crystal structures of beta-primeverosidase in complex with disaccharide amidine inhibitors.
J.Biol.Chem., 289:16826-16834, 2014

PubMed Abstract: β-Primeverosidase (PD) is a disaccharide-specific β-glycosidase in tea leaves. This enzyme is involved in aroma formation during the manufacturing process of oolong tea and black tea. PD hydrolyzes β-primeveroside (6-O-β-d-xylopyranosyl-β-d-glucopyranoside) at the β-glycosidic bond of primeverose to aglycone, and releases aromatic alcoholic volatiles of aglycones. PD only accepts primeverose as the glycone substrate, but broadly accepts various aglycones, including 2-phenylethanol, benzyl alcohol, linalool, and geraniol. We determined the crystal structure of PD complexes using highly specific disaccharide amidine inhibitors, N-β-primeverosylamidines, and revealed the architecture of the active site responsible for substrate specificity. We identified three subsites in the active site: subsite -2 specific for 6-O-β-d-xylopyranosyl, subsite -1 well conserved among β-glucosidases and specific for β-d-glucopyranosyl, and wide subsite +1 for hydrophobic aglycone. Glu-470, Ser-473, and Gln-477 act as the specific hydrogen bond donors for 6-O-β-d-xylopyranosyl in subsite -2. On the other hand, subsite +1 was a large hydrophobic cavity that accommodates various aromatic aglycones. Compared with aglycone-specific β-glucosidases of the glycoside hydrolase family 1, PD lacks the Trp crucial for aglycone recognition, and the resultant large cavity accepts aglycone and 6-O-β-d-xylopyranosyl together. PD recognizes the β-primeverosides in subsites -1 and -2 by hydrogen bonds, whereas the large subsite +1 loosely accommodates various aglycones. The glycone-specific activity of PD for broad aglycone substrates results in selective and multiple release of temporally stored alcoholic volatile aglycones of β-primeveroside.

PubMed: 24753293
DOI: 10.1074/jbc.M114.553271

Experimental method

X-RAY DIFFRACTION (1.9 Å)