Crystal structure of the catalytic unit of thermostable GH87 α-1,3-glucanase from Streptomyces thermodiastaticus strain HF3-3

Itoh, Takafumi; Panti, Niphawan; Hayashi, Junji; Toyotake, Yosuke; Matsui, Daisuke; Yano, Shigekazu; Wakayama, Mamoru; Hibi, Takao

doi:10.1016/j.bbrc.2020.09.133

Cited by 6 publications

(7 citation statements)

References 28 publications

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“…The melting temperature ( T m ) of Agl-ST and YgjK was 46.9 ± 0.1 °C and 45.9 ± 0.5 °C, respectively. It was consistent with the previous reference, which reported that the T m of CatAgl-KA was 51 °C . Consequently, 40 °C can be regarded as the preferred temperature for the Agl-ST-/YgjK dual-enzyme system.…”

Section: Resultssupporting

confidence: 92%

“…By analyzing the structure of Agl-ST enzyme, no binding domain was identified. 25 Agl-ST cleaves the chain in the middle, whose soluble products are not only glucose but also oligomers, e.g., nigerose, nigerotriose, and nigerotetraose, contributing to the rapid decline in mass (rapid increase in Δf, Figure 4A). It is suspected that the rate of degradation was faster than the rate of loading and binding of Agl-ST, resulting in a situation where the theoretical increase in mass from enzyme loading was offset by the decrease in mass due to the removal of degradation products.…”

Section: In Situ and Real-time Monitoring Of α-13-glucan Degradation ...mentioning

confidence: 99%

“…Agl-ST and YgjK. The synthetic α-1,3-glucanase genes of Agl-ST (endotype, PDB ID:7C7D), 25 YgjK (exotype, PDB ID: 3W7S), 26 Agl-KA (endotype, PDB ID: 5ZRU), LIGH31 (exotype, PDB ID:7WJ9), IMO-2446 (exotype, PDB ID: 4KMQ), and TpL-182 (exotype, PDB ID:5F7S) were synthesized in vector pET-28a(+) and transformed into the host strain E. coli BL21 (DE3) (gene sequences are listed in the Supporting Information). Preculture for protein expression was performed in 6 mL of LB medium supplemented with 40 μg/mL kanamycin for 8 h (37 °C, 200 rpm).…”

Section: Expression and Purification Of α-13-glucanasementioning

confidence: 99%

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Synergism of Endo and Exo-α-1,3-Glucanases in α-1,3-Glucan Degradation: A Kinetic Study

Dong,

Zhang,

Kralj

et al. 2024

ACS Sustainable Chem. Eng.

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Biobased materials are promising alternatives to traditional fossil-derived synthetic polymers to mitigate greenhouse gas emissions and to provide end-of-life benefits addressing increasing environmental concerns. Biobased polymers with advantaged degradation and reuse characteristics have attracted increasing attention. In this work, a dual-enzyme system (combining endo α-1,3-glucanase Agl-ST from Streptomyces thermodiastaticus HF 3–3 and exo α-1,3-glucanase YgjK from Escherichia coli K12) was identified for the targeted degradation of α-1,3-glucan. The effects of pH, metal ions, enzyme concentration, temperature, and reaction time were investigated to assess the degradation characteristics of α-1,3-glucan using the synergistic enzyme system. After degradation under model conditions for 10 h, the dual-enzyme system achieved a weight loss rate of 29%, releasing 4.0 mM reducing sugar from 1% α-1,3-glucan. Binding behavior and degradation kinetics of α-1,3-glucanase on α-1,3-glucan were studied by a quartz crystal microbalance with dissipation monitoring. This dual-α-1,3-glucanase enzyme cocktail is a promising example for efficient biobased α-1,3-glucan polymer degradation, thereby contributing toward the concept of a circular economy.

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Section: Resultssupporting

confidence: 92%

Section: In Situ and Real-time Monitoring Of α-13-glucan Degradation ...mentioning

confidence: 99%

Section: Expression and Purification Of α-13-glucanasementioning

confidence: 99%

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Synergism of Endo and Exo-α-1,3-Glucanases in α-1,3-Glucan Degradation: A Kinetic Study

Dong,

Zhang,

Kralj

et al. 2024

ACS Sustainable Chem. Eng.

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“…The CBM from these proteins was most similar to a CBM1 domain from GH10 enzyme from Bacteroides intestinalis (PDB 4qpw) [37], CBM35 from a GH31 enzyme from Paenibacillus sp. 598K (PDB 5x7s) [38], and the Ig-like domain from a GH86 enzyme from Bacteroides uniformis (PDB 5ta1) [39] and the β-sandwich domain from a GH87 enzyme from Streptomyces thermodiastaticus (PDB 7c7d) [40] (Dali Z-scores between 6.4 and 6.9, RMSDs 3.3-4.2 Å over 94-102 Cα atoms) (Figure S2). Based on a more detailed comparison with the structure of the CBM1 in complex with xylotriose (Figure S2), the CBM from PbeAcXE and CspAcXE does not appear to have an equivalent ligand binding pocket due to the positioning of the loops 73-82 and 146-160; however, conformational changes in this area in the presence of the appropriate ligand may open a binding pocket.…”

Section: Structural Determinants Of the New Ce Familymentioning

confidence: 99%

Elucidating Sequence and Structural Determinants of Carbohydrate Esterases for Complete Deacetylation of Substituted Xylans

et al. 2022

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Acetylated glucuronoxylan is one of the most common types of hemicellulose in nature. The structure is formed by a β-(1→4)-linked D-xylopyranosyl (Xylp) backbone that can be substituted with an acetyl group at O-2 and O-3 positions, and α-(1→2)-linked 4-O-methylglucopyranosyluronic acid (MeGlcpA). Acetyl xylan esterases (AcXE) that target mono- or doubly acetylated Xylp are well characterized; however, the previously studied AcXE from Flavobacterium johnsoniae (FjoAcXE) was the first to remove the acetyl group from 2-O-MeGlcpA-3-O-acetyl-substituted Xylp units, yet structural characteristics of these enzymes remain unspecified. Here, six homologs of FjoAcXE were produced and three crystal structures of the enzymes were solved. Two of them are complex structures, one with bound MeGlcpA and another with acetate. All homologs were confirmed to release acetate from 2-O-MeGlcpA-3-O-acetyl-substituted xylan, and the crystal structures point to key structural elements that might serve as defining features of this unclassified carbohydrate esterase family. Enzymes comprised two domains: N-terminal CBM domain and a C-terminal SGNH domain. In FjoAcXE and all studied homologs, the sequence motif around the catalytic serine is Gly-Asn-Ser-Ile (GNSI), which differs from other SGNH hydrolases. Binding by the MeGlcpA-Xylp ligand is directed by positively charged and highly conserved residues at the interface of the CBM and SGNH domains of the enzyme.

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“…GH87 enzymes were mainly found in gram-positive bacteria such as Bacillus , Paenibacillus , and Streptomyces 21 – 23 . Some GH87 enzymes from gram-positive bacteria were characterized, and X-ray crystallographic analysis of the catalytic domain was performed (e.g., Agl-KA of Bacillus circulans KA-304, Agl-FH1 of Paenibacillus glycanilyticus FH11, and Agl-ST of Streptomyces thermodiastaticus HF3-3) 24 – 26 . For gram-negative bacteria, α-1,3-glucanases have been isolated from Flavobacterium , Pseudomonas , Bacteroides orali , and Paracoccus mutanolyticus 27 – 30 .…”

Section: Introductionmentioning

confidence: 99%

α-1,3-Glucanase from the gram-negative bacterium Flavobacterium sp. EK-14 hydrolyzes fungal cell wall α-1,3-glucan

Takahashi,

Yano,

Horaguchi

et al. 2023

Sci Rep

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The glycoside hydrolase (GH) 87 α-1,3-glucanase (Agl-EK14) gene was cloned from the genomic DNA of the gram-negative bacterium Flavobacterium sp. EK14. The gene consisted of 2940 nucleotides and encoded 980 amino acid residues. The deduced amino acid sequence of Agl-EK14 included a signal peptide, a catalytic domain, a first immunoglobulin-like domain, a second immunoglobulin-like domain, a ricin B-like lectin domain, and a carboxyl-terminal domain (CTD) involved in extracellular secretion. Phylogenetic analysis of the catalytic domain of GH87 enzymes suggested that Agl-EK14 is distinct from known clusters, such as clusters composed of α-1,3-glucanases from bacilli and mycodextranases from actinomycetes. Agl-EK14 without the signal peptide and CTD hydrolyzed α-1,3-glucan, and the reaction residues from 1 and 2% substrates were almost negligible after 1440 min reaction. Agl-EK14 hydrolyzed the cell wall preparation of Aspergillus oryzae and released glucose, nigerose, and nigero-triose from the cell wall preparation. After treatment of A. oryzae live mycelia with Agl-EK14 (at least 0.5 nmol/ml), mycelia were no longer stained by red fluorescent protein-fused α-1,3-glucan binding domains of α-1,3-glucanase Agl-KA from Bacillus circulans KA-304. Results suggested that Agl-EK14 can be applied to a fungal cell wall lytic enzyme.

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Crystal structure of the catalytic unit of thermostable GH87 α-1,3-glucanase from Streptomyces thermodiastaticus strain HF3-3

Cited by 6 publications

References 28 publications

Synergism of Endo and Exo-α-1,3-Glucanases in α-1,3-Glucan Degradation: A Kinetic Study

Synergism of Endo and Exo-α-1,3-Glucanases in α-1,3-Glucan Degradation: A Kinetic Study

Elucidating Sequence and Structural Determinants of Carbohydrate Esterases for Complete Deacetylation of Substituted Xylans

α-1,3-Glucanase from the gram-negative bacterium Flavobacterium sp. EK-14 hydrolyzes fungal cell wall α-1,3-glucan

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