4AK5

Native crystal structure of BpGH117

4AK5 の概要

• エントリーDOI: 10.2210/pdb4ak5/pdb
• 関連するPDBエントリー: 4AK6 4AK7
• 分子名称: ANHYDRO-ALPHA-L-GALACTOSIDASE, CHLORIDE ION, 1,2-ETHANEDIOL, ... (5 entities in total)
• 機能のキーワード: hydrolase, marine glycoside hydrolase, marine polysaccharide degradation, marine cazymes, agar metabolism, seaweed biofuels
• 由来する生物種: BACTEROIDES PLEBEIUS
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 92150.50

構造登録者

Hehemann, J.H.,Smyth, L.,Yadav, A.,Vocadlo, D.J.,Boraston, A.B. (登録日: 2012-02-21, 公開日: 2012-03-14, 最終更新日: 2024-05-08)

主引用文献

Hehemann, J.H.,Smyth, L.,Yadav, A.,Vocadlo, D.J.,Boraston, A.B.
Analysis of Keystone Enzyme in Agar Hydrolysis Provides Insight Into the Degradation (of a Polysaccharide from) Red Seaweeds.
J.Biol.Chem., 287:13985-, 2012

PubMed Abstract: Agars are abundant polysaccharides from marine red algae, and their chemical structure consists of alternating D-galactose and 3,6-anhydro-L-galactose residues, the latter of which are presumed to make the polymer recalcitrant to degradation by most terrestrial bacteria. Here we study a family 117 glycoside hydrolase (BpGH117) encoded within a recently discovered locus from the human gut bacterium Bacteroides plebeius. Consistent with this locus being involved in agarocolloid degradation, we show that BpGH117 is an exo-acting 3,6-anhydro-α-(1,3)-L-galactosidase that removes the 3,6-anhydrogalactose from the non-reducing end of neoagaro-oligosaccharides. A Michaelis complex of BpGH117 with neoagarobiose reveals the distortion of the constrained 3,6-anhydro-L-galactose into a conformation that favors catalysis. Furthermore, this complex, supported by analysis of site-directed mutants, provides evidence for an organization of the active site and positioning of the catalytic residues that are consistent with an inverting mechanism of catalysis and suggests that a histidine residue acts as the general acid. This latter feature differs from the vast majority of glycoside hydrolases, which use a carboxylic acid, highlighting the alternative strategies that enzymes may utilize in catalyzing the cleavage of glycosidic bonds.

PubMed: 22393053
DOI: 10.1074/JBC.M112.345645

実験手法

X-RAY DIFFRACTION (1.7 Å)