6IMW

The complex structure of endo-beta-1,2-glucanase mutant (E262Q) from Talaromyces funiculosus with beta-1,2-glucan

Summary for 6IMW

• Entry DOI: 10.2210/pdb6imw/pdb
• Related: 6IMU
• Descriptor: Endo-beta-1,2-glucanase, beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose, beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose, ... (6 entities in total)
• Functional Keywords: glycoside hydrolase, talaromyces funiculosus, sophorose, complex, hydrolase
• Biological source: Talaromyces funiculosus
• Total number of polymer chains: 2
• Total formula weight: 117171.57

Authors

Tanaka, N.,Nakajima, M.,Narukawa-Nara, M.,Matsunaga, H.,Kamisuki, S.,Aramasa, H.,Takahashi, Y.,Sugimoto, N.,Abe, K.,Miyanaga, A.,Yamashita, T.,Sugawara, F.,Kamakura, T.,Komba, S.,Nakai, H.,Taguchi, H. (deposition date: 2018-10-23, release date: 2019-04-10, Last modification date: 2023-11-22)

Primary citation

Tanaka, N.,Nakajima, M.,Narukawa-Nara, M.,Matsunaga, H.,Kamisuki, S.,Aramasa, H.,Takahashi, Y.,Sugimoto, N.,Abe, K.,Terada, T.,Miyanaga, A.,Yamashita, T.,Sugawara, F.,Kamakura, T.,Komba, S.,Nakai, H.,Taguchi, H.
Identification, characterization, and structural analyses of a fungal endo-beta-1,2-glucanase reveal a new glycoside hydrolase family.
J.Biol.Chem., 294:7942-7965, 2019

PubMed Abstract: -β-1,2-Glucanase (SGL) is an enzyme that hydrolyzes β-1,2-glucans, which play important physiological roles in some bacteria as a cyclic form. To date, no eukaryotic SGL has been identified. We purified an SGL from (SGL), a soil fungus, to homogeneity and then cloned the complementary DNA encoding the enzyme. SGL shows no significant sequence similarity to any known glycoside hydrolase (GH) families, but shows significant similarity to certain eukaryotic proteins with unknown functions. The recombinant SGL (SGLr) specifically hydrolyzed linear and cyclic β-1,2-glucans to sophorose (Glc-β-1,2-Glc) as a main product. SGLr hydrolyzed reducing-end-modified β-1,2-gluco-oligosaccharides to release a sophoroside with the modified moiety. These results indicate that SGL is an -type enzyme that preferably releases sophorose from the reducing end of substrates. Stereochemical analysis demonstrated that SGL is an inverting enzyme. The overall structure of SGLr includes an (α/α) toroid fold. The substrate-binding mode was revealed by the structure of a Michaelis complex of an inactive SGLr mutant with a β-1,2-glucoheptasaccharide. Mutational analysis and action pattern analysis of β-1,2-gluco-oligosaccharide derivatives revealed an unprecedented catalytic mechanism for substrate hydrolysis. Glu-262 (general acid) indirectly protonates the anomeric oxygen at subsite -1 via the 3-hydroxy group of the Glc moiety at subsite +2, and Asp-446 (general base) activates the nucleophilic water via another water. SGLr is apparently different from a GH144 SGL in the reaction and substrate recognition mechanism based on structural comparison. Overall, we propose that SGL and closely-related enzymes can be classified into a new family, GH162.

PubMed: 30926603
DOI: 10.1074/jbc.RA118.007087

Experimental method

X-RAY DIFFRACTION (2.1 Å)