Cloning and characterization of arabinoxylan arabinofuranohydrolase-D3 (AXHd3) from Bifidobacterium adolescentis DSM20083

Broek, L.A.M. van den; Lloyd, Ruth; Beldman, G.; Verdoes, J.C.; McCleary, Barry V.; Voragen, A.G.J.

doi:10.1007/s00253-004-1850-9

Cited by 109 publications

(61 citation statements)

References 28 publications

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“…There is a paucity of information on enzymes that hydrolyze double substitutions. Indeed, the only other enzyme known to hydrolyze such structures is the GH43 arabinofuranosidase AXHd3 from the colonic bacterium Bifidobacterium adolescentis (44). AXHd3, however, displays broader specificity than Bt3069 or CjAbf43A because it hydrolyzes double substitutions in both arabinoxylan and arabinan.…”

Section: Discussionmentioning

confidence: 99%

The Structure and Function of an Arabinan-specific α-1,2-Arabinofuranosidase Identified from Screening the Activities of Bacterial GH43 Glycoside Hydrolases

Cartmell

McKee

Peña

et al. 2011

Journal of Biological Chemistry

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Reflecting the diverse chemistry of plant cell walls, microorganisms that degrade these composite structures synthesize an array of glycoside hydrolases. These enzymes are organized into sequence-, mechanism-, and structure-based families. Genomic data have shown that several organisms that degrade the plant cell wall contain a large number of genes encoding family 43 (GH43) glycoside hydrolases. Here we report the biochemical properties of the GH43 enzymes of a saprophytic soil bacterium, Cellvibrio japonicus, and a human colonic symbiont, Bacteroides thetaiotaomicron. The data show that C. japonicus uses predominantly exo-acting enzymes to degrade arabinan into arabinose, whereas B. thetaiotaomicron deploys a combination of endo-and side chain-cleaving glycoside hydrolases. Both organisms, however, utilize an arabinan-specific ␣-1,2-arabinofuranosidase in the degradative process, an activity that has not previously been reported. The enzyme can cleave ␣-1,2-arabinofuranose decorations in single or double substitutions, the latter being recalcitrant to the action of other arabinofuranosidases. The crystal structure of the C. japonicus arabinan-specific ␣-1,2-arabinofuranosidase, CjAbf43A, displays a fivebladed ␤-propeller fold. The specificity of the enzyme for arabinan is conferred by a surface cleft that is complementary to the helical backbone of the polysaccharide. The specificity of CjAbf43A for ␣-1,2-L-arabinofuranose side chains is conferred by a polar residue that orientates the arabinan backbone such that O2 arabinose decorations are directed into the active site pocket. A shelflike structure adjacent to the active site pocket accommodates O3 arabinose side chains, explaining how the enzyme can target O2 linkages that are components of single or double substitutions.

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Section: Discussionmentioning

confidence: 99%

The Structure and Function of an Arabinan-specific α-1,2-Arabinofuranosidase Identified from Screening the Activities of Bacterial GH43 Glycoside Hydrolases

Cartmell

McKee

Peña

et al. 2011

Journal of Biological Chemistry

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“…Recently, the AXHd3 gene was cloned and another gene preceding this sequence was also identified [33]. This gene (xylA) showed high homology with a putative endo-xylanase from Bacillus halodurans.…”

Section: Arabinoxylanmentioning

confidence: 99%

Glycosyl hydrolases from Bifidobacterium adolescentis DSM20083. An overview

Broek

Hinz

Beldman

et al. 2005

Lait

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-It is claimed that bifidobacteria have several health-promoting effects. To increase the amount of bifidobacteria in the colon the concept of probiotics and/or prebiotics can be applied. Bifidobacterium adolescentis is one of the main species of bifidobacteria in the gastro-intestinal tract of human adults. B. adolescentis is able to degrade a wide range of oligosaccharides and a number of glycosyl hydrolases have been characterized in detail. The hydrolytic activity of the glycosyl hydrolases from B. adolescentis toward prebiotics like arabinoxylan-oligosaccharides, isomalto-oligosaccharides, arabinogalactan, and sucrose-based oligosaccharides (raffinose, stachyose, and fructo-oligosaccharides) is reviewed. Alternatively, some of these glycosyl hydrolases are able to catalyze transglycosylation, which allows them to elongate oligosaccharides and to prepare potentially prebiotic oligosaccharides. Such oligosaccharides might be used to influence the microbial composition in the more distal parts of the colon. In nature, not all enzyme-substrate encounters are transglycosylating. So, the hydrolytic activity of the enzyme makes the oligosaccharide elongation less efficient than desired. Site-directed mutagenesis was applied to improve the transglycosylation reaction of the α-galactosidase from B. adolescentis.Bifidobacterium / prebiotic / glycosyl hydrolase / transglycosylation / site-directed mutagenesis Résumé -Les glycosyl hydrolases de Bifidobacterium adolescentis DSM20083. Il est affirmé que les bifidobactéries ont des propriétés bénéfiques sur la santé. Pour augmenter la teneur en bifidobactéries au niveau du colon, le concept de probiotiques et/ou prébiotiques peut être appliqué. Bifidobacterium adolescentis est l'une des principales espèces de bifidobactéries dans le tractus gastro-intestinal des adultes. Certaines des glycosyl hydrolases de B. adolescentis ont été caractérisées en détail et elles semblent dégrader un large éventail d'oligosaccharides. L'activité d'hydrolyse des glycosyl hydrolases de B. adolescentis envers des prébiotiques tels que les arabino-xylanes, isomaltooligosaccharides, arabino-galactanes et les oligosaccharides contenant du saccharose (raffinose, stachyose et fructo-oligosaccharides) est passée en revue. De plus, certaines de ces glycosyl hydrolases peuvent être utilisées pour préparer des oligosaccharides prébiotiques potentiels par transglycosylation, ce qui permet d'allonger les oligosaccharides. De tels oligosaccharides peuvent être utilisés pour influencer la composition microbienne au niveau des parties plus distales du colon. Les produits de rencontre enzymes-substrates ne sont pas tous transglycosylés naturellement et l'activité d'hydrolyse de l'enzyme entraîne une élongation de l'oligosaccharide moindre que celle désirée. La mutagenèse dirigée a été appliquée pour améliorer la réaction de transglycosylation de l'α-galactosidase de B. adolescentis. Bifidobacterium

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“…By contrast, backbone sugars, decorated at both O2 and O3 with Araf units, are particularly recalcitrant to enzymatic attack; currently only two arabinofuranosidases, defined as AXHd3s, are known to cleave these linkages (3,4) (Fig. 1).…”

Section: For Review)mentioning

confidence: 99%

Introducing endo-xylanase activity into an exo-acting arabinofuranosidase that targets side chains

McKee

Peña

Rogowski

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

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The degradation of the plant cell wall by glycoside hydrolases is central to environmentally sustainable industries. The major polysaccharides of the plant cell wall are cellulose and xylan, a highly decorated β-1,4-xylopyranose polymer. Glycoside hydrolases displaying multiple catalytic functions may simplify the enzymes required to degrade plant cell walls, increasing the industrial potential of these composite structures. Here we test the hypothesis that glycoside hydrolase family 43 (GH43) provides a suitable scaffold for introducing additional catalytic functions into enzymes that target complex structures in the plant cell wall. We report the crystal structure of Humicola insolens AXHd3 (HiAXHd3), a GH43 arabinofuranosidase that hydrolyses O3-linked arabinose of doubly substituted xylans, a feature of the polysaccharide that is recalcitrant to degradation. HiAXHd3 displays an N-terminal five-bladed β-propeller domain and a C-terminal β-sandwich domain. The interface between the domains comprises a xylan binding cleft that houses the active site pocket. Substrate specificity is conferred by a shallow arabinose binding pocket adjacent to the deep active site pocket, and through the orientation of the xylan backbone. Modification of the rim of the active site introduces endo-xylanase activity, whereas the resultant enzyme variant, Y166A, retains arabinofuranosidase activity. These data show that the active site of HiAXHd3 is tuned to hydrolyse arabinofuranosyl or xylosyl linkages, and it is the topology of the distal regions of the substrate binding surface that confers specificity. This report demonstrates that GH43 provides a platform for generating bespoke multifunctional enzymes that target industrially significant complex substrates, exemplified by the plant cell wall. biofuels | biotechnology | protein engineering | structural biology

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Cloning and characterization of arabinoxylan arabinofuranohydrolase-D3 (AXHd3) from Bifidobacterium adolescentis DSM20083

Cited by 109 publications

References 28 publications

The Structure and Function of an Arabinan-specific α-1,2-Arabinofuranosidase Identified from Screening the Activities of Bacterial GH43 Glycoside Hydrolases

The Structure and Function of an Arabinan-specific α-1,2-Arabinofuranosidase Identified from Screening the Activities of Bacterial GH43 Glycoside Hydrolases

Glycosyl hydrolases from Bifidobacterium adolescentis DSM20083. An overview

Introducing endo-xylanase activity into an exo-acting arabinofuranosidase that targets side chains

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