Structural and biochemical characterization of a multidomain alginate lyase reveals a novel role of CBM32 in CAZymes

Lyu, Qianqian; Zhang, Keke; Zhu, Qiaoyun; Z, Li; Liu, Yujie; Fitzek, Elisabeth; Yohe, Tanner; Zhao, Liming; Li, Weihua; Liu, Tao; Yin, Yanbin; Liu, Weizhi

doi:10.1016/j.bbagen.2018.05.024

Cited by 42 publications

(53 citation statements)

References 30 publications

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“…We suppose that these flexible loops may adjust the substrate binding pocket to assist the active site in catalyzing different substrates. This result is similar with active site in AlyB [41]. It has been speculated that the flexibility of these loops is essential for both substrate recognition and binding.…”

Section: Molecular Modeling and Docking Analysis Of Aly7asupporting

confidence: 80%

“…The linker is not shown in the domain analysis ( Figure 1A) but found in the molecular modeling as a helix ( Figure 6). These secondary structures of Aly7A are similar to AlyB [41]. Aly7A contained two domains which were linked by a sequence named "Linker".…”

Section: Molecular Modeling and Docking Analysis Of Aly7amentioning

confidence: 80%

“…Otherwise, the catalytic activities of Aly7A towards alginate were 15,718 U/mg, 35,524 U/mg and 18,770 U/mg, while the catalytic activities of Aly7A-CD were 14,010 U/mg, 29,321 U/mg and 22,941 U/mg. Therefore, we concluded that the CBM in full-length Aly7A mainly aids the formation of trisaccharides instead of increasing the enzymatic activity of the catalytic domain [41].…”

Section: Analysis Of Aly7a and Aly7a-cd Degradation Productsmentioning

confidence: 83%

“…We concluded that the substrate chain could then slide into the binding pocket to position the next trisaccharide for cleavage ( Figure 7A). As Lyu et al have reported, a putative role for the alpha-helical linker is to keep the CBM and CD at an appropriately mutual location and distance between the two binding pockets to ensure that the alginate substrate enters the catalytic cavity in a precise manner during this processive movement [41]. Therefore, we propose that the CBM and the alpha helix linker, in combination, act as a "controller" that is responsible for product distribution and ensures a consistent release of trisaccharide products.…”

Section: Molecular Modeling and Docking Analysis Of Aly7amentioning

confidence: 99%

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Elucidation of a Unique Pattern and the Role of Carbohydrate Binding Module of an Alginate Lyase

Zhu

et al. 2019

Marine Drugs

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Alginate oligosaccharides with different degrees of polymerization (DPs) possess diverse physiological activities. Therefore, in recent years, increasing attention has been drawn to the use of enzymes for the preparation of alginate oligosaccharides for food and industrial applications. Previously, we identified and characterized a novel bifunctional alginate lyase Aly7A, which can specifically release trisaccharide from three different substrate types with a unique degradation pattern. Herein, we investigated its degradation pattern by modular truncation and molecular docking. The results suggested that Aly7A adopted a unique action mode towards different substrates with the substrate chain sliding into the binding pocket of the catalytic domain to position the next trisaccharide for cleavage. Deletion of the Aly7A carbohydrate binding module (CBM) domain resulted in a complex distribution of degradation products and no preference for trisaccharide formation, indicating that the CBM may act as a “controller” during the trisaccharide release process. This study further testifies CBM as a regulator of product distribution and provides new insights into well-defined generation of alginate oligosaccharides with associated CBMs.

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Section: Molecular Modeling and Docking Analysis Of Aly7asupporting

confidence: 80%

Section: Molecular Modeling and Docking Analysis Of Aly7amentioning

confidence: 80%

Section: Analysis Of Aly7a and Aly7a-cd Degradation Productsmentioning

confidence: 83%

Section: Molecular Modeling and Docking Analysis Of Aly7amentioning

confidence: 99%

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Elucidation of a Unique Pattern and the Role of Carbohydrate Binding Module of an Alginate Lyase

Zhu

et al. 2019

Marine Drugs

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“…Extensive biochemical data, and sequence comparisons have indicated that enzymes involved in carbohydrate chemistry possess a modular structure, as a part of which a catalytic module is associated with one or more non-catalytic modules in a multifunctional polypeptide chain (23). This type of architecture is common for many PL family enzymes, but it is less common for alginate lyases, although, in some, but not all enzymes belonging to the PL7 family, accessory modules belonging to CBM13, CBM16 and CBM32 have been identified (24)(25)(26). Currently, the precise roles of these domains in alginate lyases are poorly understood with only weak binding of the CBM32 domains to the oligosaccharide being reported (25,27).…”

Section: Analysis Of the Alginate Binding Properties Of The Non-catalmentioning

confidence: 99%

The molecular basis of endolytic activity of a multidomain alginate lyase from Defluviitalea phaphyphila, a representative of a new lyase family, PL39

Dix

Aziz

et al. 2019

Journal of Biological Chemistry

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Alginate is a polymer containing two uronic acid epimers,-D-mannuronate (M) and-L-guluronate (G), and is a major component of brown seaweed that is depolymerized by alginate lyases. These enzymes have diverse specificity, cleaving the chain with endo-or exotype activity and with differential selectivity for the sequence of M or G at the cleavage site. Dp0100 is a 201-kDa multimodular, broad-specificity endotype alginate lyase from the marine thermophile Defluviitalea phaphyphila, which uses brown algae as a carbon source, converting it to ethanol, and bioinformatics analysis suggested that its catalytic domain

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Design and characterization of a chimeric alginate lyase for immobilization to produce well‐defined oligosaccharides

Zhang

Lyu

Liu

et al. 2022

Food Bioengineering

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Recently, a novel two-domain alginate lyase (AlyAL01) was cloned from Algibacter sp. and successfully overexpressed in Escherichia coli BL21(DE3). Biochemical analysis showed that the N-terminal carbohydrate-binding module (CBM) of AlyAL01 had no effect on the enzyme activity and product distributions. Therefore, the N-terminal CBM was substituted with CBM3 to confer the designed chimeric protein with the ability to specifically bind to regenerated amorphous cellulose. As anticipated, the designed chimeric protein (CBM3-L1) exhibited a similar enzyme activity. Moreover, it was found that the CBM3-L1 combined the purification and immobilization in one step with high immobilized efficiency of 65.8%. The immobilized enzyme exhibited good storage stability and moderate reusability. The immobilized enzyme could keep 85% activity when incubated at 4°C for 60 days and 70% activity when incubated at 25°C for 30 days. Furthermore, the immobilized CBM3-L1 kept about 50% of its initial activity after being reused five times. Finally, immobilized CBM3-L1 successively produced well-defined alginate oligosaccharides (AOS) with DPs of 2-6 by controlling reaction time. In sum, our current study provided a feasible strategy for well-defined AOS production.K E Y W O R D S alginate lyase, alginate oligosaccharides, cellulose-binding domain, immobilized enzyme

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Structural and biochemical characterization of a multidomain alginate lyase reveals a novel role of CBM32 in CAZymes

Cited by 42 publications

References 30 publications

Elucidation of a Unique Pattern and the Role of Carbohydrate Binding Module of an Alginate Lyase

Elucidation of a Unique Pattern and the Role of Carbohydrate Binding Module of an Alginate Lyase

The molecular basis of endolytic activity of a multidomain alginate lyase from Defluviitalea phaphyphila, a representative of a new lyase family, PL39

Design and characterization of a chimeric alginate lyase for immobilization to produce well‐defined oligosaccharides

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