Structural Analysis of Glucuronoxylan-specific Xyn30D and Its Attached CBM35 Domain Gives Insights into the Role of Modularity in Specificity*

Sainz-Polo, M.A.; Valenzuela, Susana V.; González, Beatriz; Pastor, F. I. Javier; Sanz‐Aparicio, Julia

doi:10.1074/jbc.m114.597732

Cited by 33 publications

(21 citation statements)

References 49 publications

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“…They generally differ from the endoxylanases in family 10 by having high selectivity for glucuronoxylan and XOS substituted with glucuronic acid (GlcA) or methylglucuronic acid (MeGlcA) via an α-1,2 linkage. This is combined with lower selectivity for unsubstituted xylan, AX, and XOS, which may be structurally reflected by more open-binding clefts (Sainz-Polo et al 2014 ). (At least one exception from this rule is however known as the enzyme from C. papyrosolvens (St John et al 2014 ) is active on non-substituted xylan).…”

Section: Gh30 Glucuronoarabinoxylan Endoxylanasesmentioning

confidence: 99%

“…Other enzymes are shown to be connected to a CBM, e.g. CBM35 of Xyn30D from Paenibacillus barcinonensis (Sainz-Polo et al 2014 ) that is reported to be glucuronoxylan binding. Overall, GH30_8 candidates differ in modularity, some enzymes being single module, while others are connected to binding modules or parts of cellulosomes.…”

Section: Gh30 Glucuronoarabinoxylan Endoxylanasesmentioning

confidence: 99%

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Endo-xylanases as tools for production of substituted xylooligosaccharides with prebiotic properties

Karlsson

Schmitz

Linares-Pastén

et al. 2018

Appl Microbiol Biotechnol

135

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Xylan has a main chain consisting of β-1,4-linked xylose residues with diverse substituents. Endoxylanases cleave the xylan chain at cleavage sites determined by the substitution pattern and thus give different oligosaccharide product patterns. Most known endoxylanases belong to glycoside hydrolase (GH) families 10 and 11. These enzymes work well on unsubstituted xylan but accept substituents in certain subsites. The GH11 enzymes are more restricted by substituents, but on the other hand, they are normally more active than the GH10 enzymes on insoluble substrates, because of their smaller size. GH5 endoxylanases accept arabinose substituents in several subsites and require it in the − 1 subsite. This specificity makes the GH5 endoxylanases very useful for degradation of highly arabinose-substituted xylans and for the selective production of arabinoxylooligosaccharides, without formation of unsubstituted xylooligosaccharides. The GH30 endoxylanases have a related type of specificity in that they require a uronic acid substituent in the − 2 subsite, which makes them very useful for the production of uronic acid substituted oligosaccharides. The ability of dietary xylooligosaccharides to function as prebiotics in humans is governed by their substitution patterns. Endoxylanases are thus excellent tools to tailor prebiotic oligosaccharides to stimulate various types of intestinal bacteria and to cause fermentation in different parts of the gastrointestinal tract. Continuously increasing knowledge on the function of the gut microbiota and discoveries of novel endoxylanases increase the possibilities to achieve health-promoting effects.

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Section: Gh30 Glucuronoarabinoxylan Endoxylanasesmentioning

confidence: 99%

Section: Gh30 Glucuronoarabinoxylan Endoxylanasesmentioning

confidence: 99%

Endo-xylanases as tools for production of substituted xylooligosaccharides with prebiotic properties

Karlsson

Schmitz

Linares-Pastén

et al. 2018

Appl Microbiol Biotechnol

135

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“…Here, we determined the structure of CtXyn30A in its native form and that of the CtXyn30A-E225A mutant bound to xylotetraose. Comparison of the GH30 structure with those of XynA from E. chrysanthemi (Urbá niková et al, 2011), XynC from B. subtilis (St John et al, 2011), CpC71 from C. papyrosolvens (St John et al, 2014) and XynD from P. barcinonensis (Sainz-Polo et al, 2014) revealed remarkable conservation in the catalytic machinery of both mesophilic and thermophilic glucuronoxylan endo--1,4-xylanases.…”

Section: Introductionmentioning

confidence: 99%

Conservation in the mechanism of glucuronoxylan hydrolysis revealed by the structure of glucuronoxylan xylanohydrolase (CtXyn30A) fromClostridium thermocellum

Freire

Verma

Bule

et al. 2016

Acta Cryst Sect D Struct Biol

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Glucuronoxylan endo-β-1,4-xylanases cleave the xylan chain specifically at sites containing 4-O-methylglucuronic acid substitutions. These enzymes have recently received considerable attention owing to their importance in the cooperative hydrolysis of heteropolysaccharides. However, little is known about the hydrolysis of glucuronoxylans in extreme environments. Here, the structure of a thermostable family 30 glucuronoxylan endo-β-1,4-xylanase (CtXyn30A) from Clostridium thermocellum is reported. CtXyn30A is part of the cellulosome, a highly elaborate multi-enzyme complex secreted by the bacterium to efficiently deconstruct plant cell-wall carbohydrates. CtXyn30A preferably hydrolyses glucuronoxylans and displays maximum activity at pH 6.0 and 70°C. The structure of CtXyn30A displays a (β/α) TIM-barrel core with a side-associated β-sheet domain. Structural analysis of the CtXyn30A mutant E225A, solved in the presence of xylotetraose, revealed xylotetraose-cleavage oligosaccharides partially occupying subsites -3 to +2. The sugar ring at the +1 subsite is held in place by hydrophobic stacking interactions between Tyr139 and Tyr200 and hydrogen bonds to the OH group of Tyr227. Although family 30 glycoside hydrolases are retaining enzymes, the xylopyranosyl ring at the -1 subsite of CtXyn30A-E225A appears in the α-anomeric configuration. A set of residues were found to be strictly conserved in glucuronoxylan endo-β-1,4-xylanases and constitute the molecular determinants of the restricted specificity displayed by these enzymes. CtXyn30A is the first thermostable glucuronoxylan endo-β-1,4-xylanase described to date. This work reveals that substrate recognition by both thermophilic and mesophilic glucuronoxylan endo-β-1,4-xylanases is modulated by a conserved set of residues.

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“…Paenibacillus barcinonensis BP-23 is a powerful xylanolytic bacterial strain isolated from rice field soil (15) that produces a complex secretome, including different xylanases from families GH10, GH11, and GH30 that have already been cloned and characterized (16)(17)(18)(19). Some of these enzymes have been successfully evaluated in industrial applications (20,21).…”

Section: Importancementioning

confidence: 99%

The Glycoside Hydrolase Family 8 Reducing-End Xylose-Releasing Exo-oligoxylanase Rex8A from Paenibacillus barcinonensis BP-23 Is Active on Branched Xylooligosaccharides

Valenzuela

López

Biely

et al. 2016

Appl Environ Microbiol

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A GH8 family enzyme involved in xylan depolymerization has been characterized. The enzyme, Rex8A, is a reducing-end xylosereleasing exo-oligoxylanase (Rex) that efficiently hydrolyzes xylooligosaccharides and shows minor activity on polymeric xylan. Rex8A hydrolyzes xylooligomers of 3 to 6 xylose units to xylose and xylobiose in long-term incubations. Kinetic constants of Rex8A were determined on xylotriose, showing a K m of 1.64 ؎ 0.03 mM and a k cat value of 118.8 s ؊1 . Besides linear xylooligosaccharides, the enzyme hydrolyzed decorated xylooligomers. The catalytic activity on branched xylooligosaccharides, i.e., the release of xylose from the reducing end, is a newly described trait of xylose-releasing exo-oligoxylanases, as the exo-activity on these substrates has not been reported for the few of these enzymes characterized to date. Modeling of the three-dimensional (3D) structure of Rex8A shows an (␣/␣) 6 barrel fold where the loops connecting the ␣-helices contour the active site. These loops, which show high sequence diversity among GH8 enzymes, shape a catalytic cleft with a ؊2 subsite that can accommodate methyl-glucuronic acid decorations. The hydrolytic ability of Rex8A on branched oligomers can be crucial for the complete depolymerization of highly substituted xylans, which is indispensable to accomplish biomass deconstruction and to generate efficient catalysts. IMPORTANCEA GH8 family enzyme involved in xylan depolymerization has been characterized. The Rex8A enzyme from Paenibacillus barcinonensis is involved in depolymerization of glucuronoxylan, a major component of the lignocellulosic substrates. The study shows that Rex8A is a reducing-end xylose-releasing exo-oligoxylanase that efficiently hydrolyzes xylose from neutral and acidic xylooligosaccharides generated by the action of other xylanases also secreted by the strain. The activity of a Rex enzyme on branched xylooligosaccharides has not been described to date. This report provides original and useful information on the properties of a new example of the rarely studied Rex enzymes. Depolymerization of highly substituted xylans is crucial for biomass valorization as a platform for generation of biofuels, chemicals, and solvents. P lant biomass is the most abundant source of organic carbon on the planet; therefore, it has become one of the most powerful and sustainable alternatives to petroleum as a platform for generation of biofuels, chemicals, and solvents (1). Nevertheless, plant cell walls are recalcitrant to biological depolymerization, as the extensive interactions between polysaccharides, and between polysaccharides and lignin, restrict access to the battery of degrading enzymes that break down these composite structures (2, 3). Celluloses and hemicelluloses are the most abundant polysaccharides in plants; thus, their separation and degradation are crucial for biomass valorization. Xylan is the major component of hemicelluloses, and it is composed of a backbone of ␤-D-xylopyranosyl residues that can be variably acetylated an...

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Structural Analysis of Glucuronoxylan-specific Xyn30D and Its Attached CBM35 Domain Gives Insights into the Role of Modularity in Specificity*

Cited by 33 publications

References 49 publications

Endo-xylanases as tools for production of substituted xylooligosaccharides with prebiotic properties

Endo-xylanases as tools for production of substituted xylooligosaccharides with prebiotic properties

Conservation in the mechanism of glucuronoxylan hydrolysis revealed by the structure of glucuronoxylan xylanohydrolase (CtXyn30A) fromClostridium thermocellum

The Glycoside Hydrolase Family 8 Reducing-End Xylose-Releasing Exo-oligoxylanase Rex8A from Paenibacillus barcinonensis BP-23 Is Active on Branched Xylooligosaccharides

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