The Experts below are selected from a list of 609 Experts worldwide ranked by ideXlab platform
Hayao Taguchi - One of the best experts on this subject based on the ideXlab platform.
-
synthesis of three deoxy Sophorose derivatives for evaluating the requirement of hydroxy groups at position 3 and or 3 of Sophorose by 1 2 β oligoglucan phosphorylases
Carbohydrate Research, 2018Co-Authors: Hiroyuki Nakai, Hayao Taguchi, Masahiro Nakajima, N Tanaka, Hiroki Aramasa, Wakako Tsuzuki, Shiro KombaAbstract:Abstract Sophorose (Sop2) is known as a powerful inducer of cellulases in Trichoderma reesei, and in recent years 1,2-β-D-oligoglucan phosphorylase (SOGP) has been found to use Sop2 in synthetic reactions. From the structure of the complex of SOGP with Sop2, it was predicted that both the 3-hydroxy group at the reducing end glucose moiety of Sop2 and the 3′-hydroxy group at the non-reducing end glucose moiety of Sop2 were important for substrate recognition. In this study, three kinds of 3- and/or 3′-deoxy-Sop2 derivatives were synthesized to evaluate this mechanism. The deoxygenation of the 3-hydroxy group of D-glucopyranose derivative was performed by radical reduction using a toluoyl group as a leaving group. The utilization of a toluoyl group that plays two roles (a leaving group for the deoxygenation and a protecting group for a hydroxy group) resulted in efficient syntheses of the three target compounds. The NMR spectra of the two final compounds (3-deoxy- and 3,3′-dideoxy-Sop2) suggested that the glucose moiety of the reducing end of Sop2 can easily take on a furanose structure (five-membered ring structure) by deoxygenation of the 3-hydroxy group of Sop2. In addition, the ratio of the five- and six-membered ring structures changed depending on the temperature. The SOGPs exhibited remarkably lower specific activity for 3′-deoxy- and 3,3′-dideoxy-Sop2, indicating that the 3′-hydroxy group of Sop2 is important for substrate recognition by SOGPs.
-
characterization and structural analysis of a novel exo type enzyme acting on β 1 2 glucooligosaccharides from parabacteroides distasonis
Biochemistry, 2018Co-Authors: Hisaka Shimizu, Hiroyuki Nakai, Akimasa Miyanaga, Yuta Takahashi, Nobukiyo Tanaka, Kaito Kobayashi, Naohisa Sugimoto, Masahiro Nakajima, Hayao TaguchiAbstract:β-1,2-Glucan is a polysaccharide produced mainly by some Gram-negative bacteria as a symbiosis and infectious factor. We recently identified endo-β-1,2-glucanase from Chitinophaga pinensis (CpSGL) as an enzyme comprising a new family. Here, we report the characteristics and crystal structure of a CpSGL homologue from Parabacteroides distasonis, an intestinal bacterium (BDI_3064 protein), which exhibits distinctive properties of known β-1,2-glucan-degrading enzymes. BDI_3064 hydrolyzed linear β-1,2-glucan and β-1,2-glucooligosaccharides with degrees of polymerization (DPs) of ≥4 to produce Sophorose specifically but did not hydrolyze cyclic β-1,2-glucan. This result indicates that BDI_3064 is a new exo-type enzyme. BDI_3064 also produced Sophorose from β-1,2-glucooligosaccharide analogues that have a modified reducing end, indicating that BDI_3064 acts on its substrates from the nonreducing end. The crystal structure showed that BDI_3064 possesses additional N-terminal domains 1 and 2, unlike CpSGL. Superi...
-
Characterization and Structural Analysis of a Novel exo-Type Enzyme Acting on β‑1,2-Glucooligosaccharides from Parabacteroides distasonis
2018Co-Authors: Hisaka Shimizu, Hiroyuki Nakai, Akimasa Miyanaga, Yuta Takahashi, Nobukiyo Tanaka, Kaito Kobayashi, Naohisa Sugimoto, Masahiro Nakajima, Hayao TaguchiAbstract:β-1,2-Glucan is a polysaccharide produced mainly by some Gram-negative bacteria as a symbiosis and infectious factor. We recently identified endo-β-1,2-glucanase from Chitinophaga pinensis (CpSGL) as an enzyme comprising a new family. Here, we report the characteristics and crystal structure of a CpSGL homologue from Parabacteroides distasonis, an intestinal bacterium (BDI_3064 protein), which exhibits distinctive properties of known β-1,2-glucan-degrading enzymes. BDI_3064 hydrolyzed linear β-1,2-glucan and β-1,2-glucooligosaccharides with degrees of polymerization (DPs) of ≥4 to produce Sophorose specifically but did not hydrolyze cyclic β-1,2-glucan. This result indicates that BDI_3064 is a new exo-type enzyme. BDI_3064 also produced Sophorose from β-1,2-glucooligosaccharide analogues that have a modified reducing end, indicating that BDI_3064 acts on its substrates from the nonreducing end. The crystal structure showed that BDI_3064 possesses additional N-terminal domains 1 and 2, unlike CpSGL. Superimposition of BDI_3064 and CpSGL complexed with ligands showed that R93 in domain 1 overlapped subsite −3 in CpSGL. Docking analysis involving a β-1,2-glucooligosaccharide with DP4 showed that R93 completely blocks the nonreducing end of the docked β-1,2-glucooligosaccharide. This indicates that BDI_3064 employs a distinct mechanism of recognition at the nonreducing end of substrates to act as an exo-type enzyme. Thus, we propose 2-β-d-glucooligosaccharide sophorohydrolase (nonreducing end) as a systematic name for BDI_3064
-
functional and structural analysis of a β glucosidase involved in β 1 2 glucan metabolism in listeria innocua
PLOS ONE, 2016Co-Authors: Masahiro Nakajima, Hiroyuki Nakai, Akimasa Miyanaga, Ryuta Yoshida, Koichi Abe, Y Takahashi, N Sugimoto, Hiroyuki Toyoizumi, Motomitsu Kitaoka, Hayao TaguchiAbstract:Despite the presence of β-1,2-glucan in nature, few β-1,2-glucan degrading enzymes have been reported to date. Recently, the Lin1839 protein from Listeria innocua was identified as a 1,2-β-oligoglucan phosphorylase. Since the adjacent lin1840 gene in the gene cluster encodes a putative glycoside hydrolase family 3 β-glucosidase, we hypothesized that Lin1840 is also involved in β-1,2-glucan dissimilation. Here we report the functional and structural analysis of Lin1840. A recombinant Lin1840 protein (Lin1840r) showed the highest hydrolytic activity toward Sophorose (Glc-β-1,2-Glc) among β-1,2-glucooligosaccharides, suggesting that Lin1840 is a β-glucosidase involved in Sophorose degradation. The enzyme also rapidly hydrolyzed laminaribiose (β-1,3), but not cellobiose (β-1,4) or gentiobiose (β-1,6) among β-linked gluco-disaccharides. We determined the crystal structures of Lin1840r in complexes with Sophorose and laminaribiose as productive binding forms. In these structures, Arg572 forms many hydrogen bonds with Sophorose and laminaribiose at subsite +1, which seems to be a key factor for substrate selectivity. The opposite side of subsite +1 from Arg572 is connected to a large empty space appearing to be subsite +2 for the binding of sophorotriose (Glc-β-1,2-Glc-β-1,2-Glc) in spite of the higher Km value for sophorotriose than that for Sophorose. The conformations of Sophorose and laminaribiose are almost the same on the Arg572 side but differ on the subsite +2 side that provides no interaction with a substrate. Therefore, Lin1840r is unable to distinguish between Sophorose and laminaribiose as substrates. These results provide the first mechanistic insights into β-1,2-glucooligosaccharide recognition by β-glucosidase.
Masahiro Nakajima - One of the best experts on this subject based on the ideXlab platform.
-
identification characterization and structural analyses of a fungal endo β 1 2 glucanase reveal a new glycoside hydrolase family
Journal of Biological Chemistry, 2019Co-Authors: N Tanaka, Masahiro Nakajima, Y Takahashi, N Sugimoto, Megumi Narukawanara, Hiroki Matsunaga, Shinji Kamisuki, Hiroki Aramasa, Koichi AbeAbstract:endo-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 Talaromyces funiculosus (TfSGL), a soil fungus, to homogeneity and then cloned the complementary DNA encoding the enzyme. TfSGL 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 TfSGL (TfSGLr) specifically hydrolyzed linear and cyclic β-1,2-glucans to Sophorose (Glc-β-1,2-Glc) as a main product. TfSGLr hydrolyzed reducing-end-modified β-1,2-gluco-oligosaccharides to release a sophoroside with the modified moiety. These results indicate that TfSGL is an endo-type enzyme that preferably releases Sophorose from the reducing end of substrates. Stereochemical analysis demonstrated that TfSGL is an inverting enzyme. The overall structure of TfSGLr includes an (α/α)6 toroid fold. The substrate-binding mode was revealed by the structure of a Michaelis complex of an inactive TfSGLr 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. TfSGLr is apparently different from a GH144 SGL in the reaction and substrate recognition mechanism based on structural comparison. Overall, we propose that TfSGL and closely-related enzymes can be classified into a new family, GH162.
-
synthesis of three deoxy Sophorose derivatives for evaluating the requirement of hydroxy groups at position 3 and or 3 of Sophorose by 1 2 β oligoglucan phosphorylases
Carbohydrate Research, 2018Co-Authors: Hiroyuki Nakai, Hayao Taguchi, Masahiro Nakajima, N Tanaka, Hiroki Aramasa, Wakako Tsuzuki, Shiro KombaAbstract:Abstract Sophorose (Sop2) is known as a powerful inducer of cellulases in Trichoderma reesei, and in recent years 1,2-β-D-oligoglucan phosphorylase (SOGP) has been found to use Sop2 in synthetic reactions. From the structure of the complex of SOGP with Sop2, it was predicted that both the 3-hydroxy group at the reducing end glucose moiety of Sop2 and the 3′-hydroxy group at the non-reducing end glucose moiety of Sop2 were important for substrate recognition. In this study, three kinds of 3- and/or 3′-deoxy-Sop2 derivatives were synthesized to evaluate this mechanism. The deoxygenation of the 3-hydroxy group of D-glucopyranose derivative was performed by radical reduction using a toluoyl group as a leaving group. The utilization of a toluoyl group that plays two roles (a leaving group for the deoxygenation and a protecting group for a hydroxy group) resulted in efficient syntheses of the three target compounds. The NMR spectra of the two final compounds (3-deoxy- and 3,3′-dideoxy-Sop2) suggested that the glucose moiety of the reducing end of Sop2 can easily take on a furanose structure (five-membered ring structure) by deoxygenation of the 3-hydroxy group of Sop2. In addition, the ratio of the five- and six-membered ring structures changed depending on the temperature. The SOGPs exhibited remarkably lower specific activity for 3′-deoxy- and 3,3′-dideoxy-Sop2, indicating that the 3′-hydroxy group of Sop2 is important for substrate recognition by SOGPs.
-
characterization and structural analysis of a novel exo type enzyme acting on β 1 2 glucooligosaccharides from parabacteroides distasonis
Biochemistry, 2018Co-Authors: Hisaka Shimizu, Hiroyuki Nakai, Akimasa Miyanaga, Yuta Takahashi, Nobukiyo Tanaka, Kaito Kobayashi, Naohisa Sugimoto, Masahiro Nakajima, Hayao TaguchiAbstract:β-1,2-Glucan is a polysaccharide produced mainly by some Gram-negative bacteria as a symbiosis and infectious factor. We recently identified endo-β-1,2-glucanase from Chitinophaga pinensis (CpSGL) as an enzyme comprising a new family. Here, we report the characteristics and crystal structure of a CpSGL homologue from Parabacteroides distasonis, an intestinal bacterium (BDI_3064 protein), which exhibits distinctive properties of known β-1,2-glucan-degrading enzymes. BDI_3064 hydrolyzed linear β-1,2-glucan and β-1,2-glucooligosaccharides with degrees of polymerization (DPs) of ≥4 to produce Sophorose specifically but did not hydrolyze cyclic β-1,2-glucan. This result indicates that BDI_3064 is a new exo-type enzyme. BDI_3064 also produced Sophorose from β-1,2-glucooligosaccharide analogues that have a modified reducing end, indicating that BDI_3064 acts on its substrates from the nonreducing end. The crystal structure showed that BDI_3064 possesses additional N-terminal domains 1 and 2, unlike CpSGL. Superi...
-
Characterization and Structural Analysis of a Novel exo-Type Enzyme Acting on β‑1,2-Glucooligosaccharides from Parabacteroides distasonis
2018Co-Authors: Hisaka Shimizu, Hiroyuki Nakai, Akimasa Miyanaga, Yuta Takahashi, Nobukiyo Tanaka, Kaito Kobayashi, Naohisa Sugimoto, Masahiro Nakajima, Hayao TaguchiAbstract:β-1,2-Glucan is a polysaccharide produced mainly by some Gram-negative bacteria as a symbiosis and infectious factor. We recently identified endo-β-1,2-glucanase from Chitinophaga pinensis (CpSGL) as an enzyme comprising a new family. Here, we report the characteristics and crystal structure of a CpSGL homologue from Parabacteroides distasonis, an intestinal bacterium (BDI_3064 protein), which exhibits distinctive properties of known β-1,2-glucan-degrading enzymes. BDI_3064 hydrolyzed linear β-1,2-glucan and β-1,2-glucooligosaccharides with degrees of polymerization (DPs) of ≥4 to produce Sophorose specifically but did not hydrolyze cyclic β-1,2-glucan. This result indicates that BDI_3064 is a new exo-type enzyme. BDI_3064 also produced Sophorose from β-1,2-glucooligosaccharide analogues that have a modified reducing end, indicating that BDI_3064 acts on its substrates from the nonreducing end. The crystal structure showed that BDI_3064 possesses additional N-terminal domains 1 and 2, unlike CpSGL. Superimposition of BDI_3064 and CpSGL complexed with ligands showed that R93 in domain 1 overlapped subsite −3 in CpSGL. Docking analysis involving a β-1,2-glucooligosaccharide with DP4 showed that R93 completely blocks the nonreducing end of the docked β-1,2-glucooligosaccharide. This indicates that BDI_3064 employs a distinct mechanism of recognition at the nonreducing end of substrates to act as an exo-type enzyme. Thus, we propose 2-β-d-glucooligosaccharide sophorohydrolase (nonreducing end) as a systematic name for BDI_3064
-
functional and structural analysis of a β glucosidase involved in β 1 2 glucan metabolism in listeria innocua
PLOS ONE, 2016Co-Authors: Masahiro Nakajima, Hiroyuki Nakai, Akimasa Miyanaga, Ryuta Yoshida, Koichi Abe, Y Takahashi, N Sugimoto, Hiroyuki Toyoizumi, Motomitsu Kitaoka, Hayao TaguchiAbstract:Despite the presence of β-1,2-glucan in nature, few β-1,2-glucan degrading enzymes have been reported to date. Recently, the Lin1839 protein from Listeria innocua was identified as a 1,2-β-oligoglucan phosphorylase. Since the adjacent lin1840 gene in the gene cluster encodes a putative glycoside hydrolase family 3 β-glucosidase, we hypothesized that Lin1840 is also involved in β-1,2-glucan dissimilation. Here we report the functional and structural analysis of Lin1840. A recombinant Lin1840 protein (Lin1840r) showed the highest hydrolytic activity toward Sophorose (Glc-β-1,2-Glc) among β-1,2-glucooligosaccharides, suggesting that Lin1840 is a β-glucosidase involved in Sophorose degradation. The enzyme also rapidly hydrolyzed laminaribiose (β-1,3), but not cellobiose (β-1,4) or gentiobiose (β-1,6) among β-linked gluco-disaccharides. We determined the crystal structures of Lin1840r in complexes with Sophorose and laminaribiose as productive binding forms. In these structures, Arg572 forms many hydrogen bonds with Sophorose and laminaribiose at subsite +1, which seems to be a key factor for substrate selectivity. The opposite side of subsite +1 from Arg572 is connected to a large empty space appearing to be subsite +2 for the binding of sophorotriose (Glc-β-1,2-Glc-β-1,2-Glc) in spite of the higher Km value for sophorotriose than that for Sophorose. The conformations of Sophorose and laminaribiose are almost the same on the Arg572 side but differ on the subsite +2 side that provides no interaction with a substrate. Therefore, Lin1840r is unable to distinguish between Sophorose and laminaribiose as substrates. These results provide the first mechanistic insights into β-1,2-glucooligosaccharide recognition by β-glucosidase.
Richard A. Gross - One of the best experts on this subject based on the ideXlab platform.
-
Glycolipid biomaterials: synthesis and solid-state properties of a poly(sophorolipid)
2009Co-Authors: Elisa Zini, Massimo Gazzano, Mariastella Scandola, Richard A. GrossAbstract:Structural complexity inherited from a microbial synthesis of glycolipids was translated into unique poly(sophorolipid) biomaterials. ROMP polymn. of natural diacetylated lactonic sophorolipids gave a high mol. wt. polymer with asym. bola-amphiphilic repeating units. The poly(sophorolipid) chain alternates C18 oleic-like aliph. segments (90% cis-configured double bonds) with bulky diacetylated disaccharide moieties. The poly(sophorolipid) is a solid at room temp. that undergoes the glass transition at 61 °C and melts at 123 °C. The crystal phase is assocd. with ordered packing of the aliph. chain segments. The semicryst. poly(sophorolipid) also displays a long-range order (d = 2.44 nm) involving Sophorose groups that persist after crystal phase melting (in high-T diffractograms) with a slightly shortened distance (2.27 nm)
-
Glycolipid Biomaterials: Solid-State Properties of a Poly(sophorolipid)
Macromolecules, 2008Co-Authors: Elisa Zini, Sabine R. Wallner, Massimo Gazzano, Mariastella Scandola, Richard A. GrossAbstract:Structural complexity inherited from a microbial synthesis of glycolipids was translated into unique poly(sophorolipid) biomaterials. ROMP polymerization of natural diacetylated lactonic sophorolipids gave a high molecular weight polymer with asymmetric bola-amphiphilic repeating units. The poly(sophorolipid) chain alternates C18 oleic-like aliphatic segments (90% cis-configured double bonds) with bulky diacetylated disaccharide moieties. The solid-state properties were investigated by means of TGA, DSC, TMDSC, and variable-temperature X-ray diffraction. The poly(sophorolipid) is a solid at room temperature that undergoes the glass transition at 61 °C and melts at 123 °C. The crystal phase is associated with ordered packing of the aliphatic chain segments. The semicrystalline poly(sophorolipid) also displays a long-range order (d = 2.44 nm) involving Sophorose groups that is found to persist after crystal phase melting (in high-T diffractograms) with a slightly shortened distance (2.27 nm). Upon annealing...
-
Glycolipid biomaterials: solid-state properties of a poly(sophorolipid)
'American Chemical Society (ACS)', 2008Co-Authors: Elisa Zini, Sabine R. Wallner, Massimo Gazzano, Mariastella Scandola, Richard A. GrossAbstract:Structural complexity inherited from a microbial synthesis of glycolipids was translated into unique poly(sophorolipid) biomaterials. ROMP polymerization of natural diacetylated lactonic sophorolipids gave a high molecular weight polymer with asymmetric bola-amphiphilic repeating units. The poly(sophorolipid) chain alternates C18 oleic-like aliphatic segments (90% cis-configured double bonds) with bulky di-acetylated disaccharide moieties. The solid-state properties were investigated by means of TGA, DSC, TMDSC and variable temperature X-ray diffraction. The poly(sophorolipid) is a solid at room temperature that undergoes the glass transition at 61\ub0C and melts at 123\ub0C. The crystal phase is associated with ordered packing of the aliphatic chain segments. The semi-crystalline poly(sophorolipid) also displays a long range order (d = 2.44 nm) involving Sophorose groups, that is found to persist after crystal phase melting (in high-T diffractograms) with a slightly shortened distance (2.27 nm). Upon annealing at 80 \ub0C the poly(sophorolipid) re-crystallizes and concomitantly the disaccharide units space out again at 2.44 nm. An exothermal phenomenon that immediately follows melting and is revealed by TMDSC might be associated with the observed adjustment of Sophorose units spacing in the melt. The peculiar structural organization of this novel biomaterial is discussed
-
Oxygen transfer rate and Sophorose lipid production by Candida bombicola
Biotechnology and bioengineering, 2002Co-Authors: Vladimir Guilmanov, Alberto Ballistreri, Giuseppe Impallomeni, Richard A. GrossAbstract:Sophorose lipids (SLs) have applications as surfactants and are produced at high levels by several yeasts. We developed a fed-batch shake-flask method for the production of SLs by Candida bombicola ATCC 22214. Optimal aeration, expressed in terms of oxygen transfer rate, was between 50 and 80 mM O(2)/L h(-1) and resulted in maximum values for both volumetric product formation (1-1.5 g/L h(-1)) and SL yield (350 g/L). The lowest aeration levels resulted in the enrichment in saturated fatty acid SLs at the expense of unsaturated fatty acid SLs.
Hiroyuki Nakai - One of the best experts on this subject based on the ideXlab platform.
-
synthesis of three deoxy Sophorose derivatives for evaluating the requirement of hydroxy groups at position 3 and or 3 of Sophorose by 1 2 β oligoglucan phosphorylases
Carbohydrate Research, 2018Co-Authors: Hiroyuki Nakai, Hayao Taguchi, Masahiro Nakajima, N Tanaka, Hiroki Aramasa, Wakako Tsuzuki, Shiro KombaAbstract:Abstract Sophorose (Sop2) is known as a powerful inducer of cellulases in Trichoderma reesei, and in recent years 1,2-β-D-oligoglucan phosphorylase (SOGP) has been found to use Sop2 in synthetic reactions. From the structure of the complex of SOGP with Sop2, it was predicted that both the 3-hydroxy group at the reducing end glucose moiety of Sop2 and the 3′-hydroxy group at the non-reducing end glucose moiety of Sop2 were important for substrate recognition. In this study, three kinds of 3- and/or 3′-deoxy-Sop2 derivatives were synthesized to evaluate this mechanism. The deoxygenation of the 3-hydroxy group of D-glucopyranose derivative was performed by radical reduction using a toluoyl group as a leaving group. The utilization of a toluoyl group that plays two roles (a leaving group for the deoxygenation and a protecting group for a hydroxy group) resulted in efficient syntheses of the three target compounds. The NMR spectra of the two final compounds (3-deoxy- and 3,3′-dideoxy-Sop2) suggested that the glucose moiety of the reducing end of Sop2 can easily take on a furanose structure (five-membered ring structure) by deoxygenation of the 3-hydroxy group of Sop2. In addition, the ratio of the five- and six-membered ring structures changed depending on the temperature. The SOGPs exhibited remarkably lower specific activity for 3′-deoxy- and 3,3′-dideoxy-Sop2, indicating that the 3′-hydroxy group of Sop2 is important for substrate recognition by SOGPs.
-
characterization and structural analysis of a novel exo type enzyme acting on β 1 2 glucooligosaccharides from parabacteroides distasonis
Biochemistry, 2018Co-Authors: Hisaka Shimizu, Hiroyuki Nakai, Akimasa Miyanaga, Yuta Takahashi, Nobukiyo Tanaka, Kaito Kobayashi, Naohisa Sugimoto, Masahiro Nakajima, Hayao TaguchiAbstract:β-1,2-Glucan is a polysaccharide produced mainly by some Gram-negative bacteria as a symbiosis and infectious factor. We recently identified endo-β-1,2-glucanase from Chitinophaga pinensis (CpSGL) as an enzyme comprising a new family. Here, we report the characteristics and crystal structure of a CpSGL homologue from Parabacteroides distasonis, an intestinal bacterium (BDI_3064 protein), which exhibits distinctive properties of known β-1,2-glucan-degrading enzymes. BDI_3064 hydrolyzed linear β-1,2-glucan and β-1,2-glucooligosaccharides with degrees of polymerization (DPs) of ≥4 to produce Sophorose specifically but did not hydrolyze cyclic β-1,2-glucan. This result indicates that BDI_3064 is a new exo-type enzyme. BDI_3064 also produced Sophorose from β-1,2-glucooligosaccharide analogues that have a modified reducing end, indicating that BDI_3064 acts on its substrates from the nonreducing end. The crystal structure showed that BDI_3064 possesses additional N-terminal domains 1 and 2, unlike CpSGL. Superi...
-
Characterization and Structural Analysis of a Novel exo-Type Enzyme Acting on β‑1,2-Glucooligosaccharides from Parabacteroides distasonis
2018Co-Authors: Hisaka Shimizu, Hiroyuki Nakai, Akimasa Miyanaga, Yuta Takahashi, Nobukiyo Tanaka, Kaito Kobayashi, Naohisa Sugimoto, Masahiro Nakajima, Hayao TaguchiAbstract:β-1,2-Glucan is a polysaccharide produced mainly by some Gram-negative bacteria as a symbiosis and infectious factor. We recently identified endo-β-1,2-glucanase from Chitinophaga pinensis (CpSGL) as an enzyme comprising a new family. Here, we report the characteristics and crystal structure of a CpSGL homologue from Parabacteroides distasonis, an intestinal bacterium (BDI_3064 protein), which exhibits distinctive properties of known β-1,2-glucan-degrading enzymes. BDI_3064 hydrolyzed linear β-1,2-glucan and β-1,2-glucooligosaccharides with degrees of polymerization (DPs) of ≥4 to produce Sophorose specifically but did not hydrolyze cyclic β-1,2-glucan. This result indicates that BDI_3064 is a new exo-type enzyme. BDI_3064 also produced Sophorose from β-1,2-glucooligosaccharide analogues that have a modified reducing end, indicating that BDI_3064 acts on its substrates from the nonreducing end. The crystal structure showed that BDI_3064 possesses additional N-terminal domains 1 and 2, unlike CpSGL. Superimposition of BDI_3064 and CpSGL complexed with ligands showed that R93 in domain 1 overlapped subsite −3 in CpSGL. Docking analysis involving a β-1,2-glucooligosaccharide with DP4 showed that R93 completely blocks the nonreducing end of the docked β-1,2-glucooligosaccharide. This indicates that BDI_3064 employs a distinct mechanism of recognition at the nonreducing end of substrates to act as an exo-type enzyme. Thus, we propose 2-β-d-glucooligosaccharide sophorohydrolase (nonreducing end) as a systematic name for BDI_3064
-
functional and structural analysis of a β glucosidase involved in β 1 2 glucan metabolism in listeria innocua
PLOS ONE, 2016Co-Authors: Masahiro Nakajima, Hiroyuki Nakai, Akimasa Miyanaga, Ryuta Yoshida, Koichi Abe, Y Takahashi, N Sugimoto, Hiroyuki Toyoizumi, Motomitsu Kitaoka, Hayao TaguchiAbstract:Despite the presence of β-1,2-glucan in nature, few β-1,2-glucan degrading enzymes have been reported to date. Recently, the Lin1839 protein from Listeria innocua was identified as a 1,2-β-oligoglucan phosphorylase. Since the adjacent lin1840 gene in the gene cluster encodes a putative glycoside hydrolase family 3 β-glucosidase, we hypothesized that Lin1840 is also involved in β-1,2-glucan dissimilation. Here we report the functional and structural analysis of Lin1840. A recombinant Lin1840 protein (Lin1840r) showed the highest hydrolytic activity toward Sophorose (Glc-β-1,2-Glc) among β-1,2-glucooligosaccharides, suggesting that Lin1840 is a β-glucosidase involved in Sophorose degradation. The enzyme also rapidly hydrolyzed laminaribiose (β-1,3), but not cellobiose (β-1,4) or gentiobiose (β-1,6) among β-linked gluco-disaccharides. We determined the crystal structures of Lin1840r in complexes with Sophorose and laminaribiose as productive binding forms. In these structures, Arg572 forms many hydrogen bonds with Sophorose and laminaribiose at subsite +1, which seems to be a key factor for substrate selectivity. The opposite side of subsite +1 from Arg572 is connected to a large empty space appearing to be subsite +2 for the binding of sophorotriose (Glc-β-1,2-Glc-β-1,2-Glc) in spite of the higher Km value for sophorotriose than that for Sophorose. The conformations of Sophorose and laminaribiose are almost the same on the Arg572 side but differ on the subsite +2 side that provides no interaction with a substrate. Therefore, Lin1840r is unable to distinguish between Sophorose and laminaribiose as substrates. These results provide the first mechanistic insights into β-1,2-glucooligosaccharide recognition by β-glucosidase.
Shigeru Ohno - One of the best experts on this subject based on the ideXlab platform.
-
molecular and crystal structures of 2 3 4 6 1 3 4 6 octa o acetyl β Sophorose methyl 2 3 4 6 3 4 6 hepta o acetyl β sophoroside and methyl 2 3 4 6 3 4 hexa o acetyl 6 deoxy β sophoroside
Carbohydrate Research, 1995Co-Authors: Masaki Ikegami, Tomoya Sato, Kouichi Suzuki, Keiichi Noguchi, Kenji Okuyama, Shinichi Kitamura, Ken'ichi Takeo, Shigeru OhnoAbstract:The molecular and crystal structures of 2,3,4,6,1′,3′,4′,6′-octa-O-acetyl-β-Sophorose (β-Sophorose octaacetate), methyl 2,3,4,6,3′,4′,6′-hepta-O-acetyl-β-sophoroside (methyl β-sophoroside heptaacetate), and methyl 2,3,4,6,3′,4′-hexa-O-acetyl-6′-deoxy-β-sophoroside (methyl 6′-deoxy-β-sophoroside heptaacetate) were determined by X-ray diffraction. All structures were obtained by the direct method and refined by the full-matrix least-squares procedure. The crystal data and final R values are as follows: (β-Sophorose octaacetate, C28O19H38, monoclinic, P21, a = 15.529(4), b = 10.958(2), c = 10.804(2) A, β = 107.73(3)°, Dobsd = 1.285 g cm−3, Dcalcd = 1.288 g cm−3, Z = 2, R = 0.052, RW = 0.052; methyl β-sophoroside heptaacetate, C27O18H38, orthorhombic, P212121, a = 20.992(5), b = 27.642(7), c = 5.730(2) A, Dobsd = 1.305 g cm−3, Dcalcd = 1.295 g cm−3, Z = 4, R = 0.064, RW = 0.066; methyl 6′-deoxy-β-sophoroside hexaacetate, C25O16H36, hexagonal, P65, a = b = 15.136(2), c = 23.534(4) A, Dcalcd = 1.264 g cm−3, Z = 6, R = 0.079, RW = 0.064. All the d-glucose residues have the 4C1 pyranose conformation. These three molecules interact with their surrounding molecules by van der Waals forces, only. Conformational angles of φ and ω at the β (1 → 2) glycosidic linkage of these compounds are similar to each other and close to the energetically minimum positions. All the primary acetate substituents at C-6 take a gauche-gauche conformation.