5H40

Crystal Structure of 1,2-beta-oligoglucan phosphorylase from Lachnoclostridium phytofermentans in complex with sophorose

Summary for 5H40

• Entry DOI: 10.2210/pdb5h40/pdb
• Related: 5H3Z 5H41 5H42
• Descriptor: Uncharacterized protein, beta-D-glucopyranose-(1-2)-beta-D-glucopyranose, GLYCEROL, ... (5 entities in total)
• Functional Keywords: beta-1, 2-glucan, glycoside phosphorylase, transferase
• Biological source: Clostridium phytofermentans ISDg
• Total number of polymer chains: 2
• Total formula weight: 258372.61

Authors

Nakajima, M.,Tanaka, N.,Furukawa, N.,Nihira, T.,Kodutsumi, Y.,Takahashi, Y.,Sugimoto, N.,Miyanaga, A.,Fushinobu, S.,Taguchi, H.,Nakai, H. (deposition date: 2016-10-28, release date: 2017-03-01, Last modification date: 2023-11-15)

Primary citation

Nakajima, M.,Tanaka, N.,Furukawa, N.,Nihira, T.,Kodutsumi, Y.,Takahashi, Y.,Sugimoto, N.,Miyanaga, A.,Fushinobu, S.,Taguchi, H.,Nakai, H.
Mechanistic insight into the substrate specificity of 1,2-beta-oligoglucan phosphorylase from Lachnoclostridium phytofermentans
Sci Rep, 7:42671-42671, 2017

PubMed Abstract: Glycoside phosphorylases catalyze the phosphorolysis of oligosaccharides into sugar phosphates. Recently, we found a novel phosphorylase acting on β-1,2-glucooligosaccharides with degrees of polymerization of 3 or more (1,2-β-oligoglucan phosphorylase, SOGP) in glycoside hydrolase family (GH) 94. Here, we characterized SOGP from Lachnoclostridium phytofermentans (LpSOGP) and determined its crystal structure. LpSOGP is a monomeric enzyme that contains a unique β-sandwich domain (Ndom1) at its N-terminus. Unlike the dimeric GH94 enzymes possessing catalytic pockets at their dimer interface, LpSOGP has a catalytic pocket between Ndom1 and the catalytic domain. In the complex structure of LpSOGP with sophorose, sophorose binds at subsites +1 to +2. Notably, the Glc moiety at subsite +1 is flipped compared with the corresponding ligands in other GH94 enzymes. This inversion suggests the great distortion of the glycosidic bond between subsites -1 and +1, which is likely unfavorable for substrate binding. Compensation for this disadvantage at subsite +2 can be accounted for by the small distortion of the glycosidic bond in the sophorose molecule. Therefore, the binding mode at subsites +1 and +2 defines the substrate specificity of LpSOGP, which provides mechanistic insights into the substrate specificity of a phosphorylase acting on β-1,2-glucooligosaccharides.

PubMed: 28198470
DOI: 10.1038/srep42671

Experimental method

X-RAY DIFFRACTION (2.2 Å)