Structure of the two-subsite β-d-xylosidase from Selenomonas ruminantium in complex with 1,3-bis[tris(hydroxymethyl)methylamino]propane

Brunzelle, J.S.; Jordan, Douglas B.; McCaslin, Darrell R.; Ołczak, Andrzej; Wawrzak, Z.

doi:10.1016/j.abb.2008.03.007

Cited by 48 publications

(51 citation statements)

References 24 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…It is difficult, therefore, to understand how these enzymes distinguish between an Araf and Xylp at the critical Ϫ1 subsite because arabinofuranosidases that hydrolyze 4NP-Araf are not active on 4NP-Xylp. Thus, Asp 41 , Glu 215 , and Asp 168 , which function as the catalytic base, catalytic acid, and modulator of the pK a of the catalytic acid, respectively, are conserved in GH43 enzymes (8,10,11,31,32). Consistent with their catalytic function, alanine substitution of these three residues inactivates the arabinofuranosidase ( Enzyme concentrations varied from 5 nM to 10 M. Reactions were carried out at 25°C in 50 mM sodium phosphate buffer, pH 7.0.…”

Section: Subsite Interactionsmentioning

confidence: 91%

“…japonicus-Biochemical analysis of the two exo-␣-1,5-arabinofuranosidases, CJA_3012 and CJA_0806 ( Table 2), showed that both enzymes displayed the highest catalytic activity against linear arabinan and arabinooligosaccharides, releasing exclusively arabinose, probably from the non-reducing end (all exo-acting GH43 enzymes attack the non-reducing end of polysaccharides (8,11,31,32)). The two enzymes released only very small amounts of arabinose from sugar beet, reflecting the limited concentration of terminal undecorated ␣-1,5-arabinofuranose units in this highly branched polysaccharide (data not shown).…”

Section: Characterization Of Arabinan-degrading Enzymesmentioning

confidence: 99%

“…The N-and C-terminal blades, however, are in close association, and stability is provided by strong hydrogen bonds between Asp 78 in blade 1 and several residues in blade 5. CjAbf43A lacks a C-terminal ␤-jelly roll domain seen in several exo-acting GH43 enzymes (8,10,11,31).…”

Section: Three-dimensional Structure Of Cjabf43amentioning

confidence: 99%

See 2 more Smart Citations

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

View full text Add to dashboard Cite

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.

show abstract

Section: Subsite Interactionsmentioning

confidence: 91%

Section: Characterization Of Arabinan-degrading Enzymesmentioning

confidence: 99%

See 1 more Smart Citation

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

View full text Add to dashboard Cite

show abstract

“…They exhibit ␤-1,4-xylosidase (EC 3.2.1.37), ␤-1,3-xylosidase (EC 3.2.1.72), ␣-L-arabinofuranosidase (EC 3.2.1.55), arabinanase (EC 3.2.1.99), xylanase (EC 3.2.1.8), and galactan 1,3-␤-galactosidase (EC 3.2.1.145) activities. Recent biophysical studies have revealed domain organizations and catalytic mechanisms in this family (3,8,9,43,65,73). Based on their domain organization, these proteins are grouped into three different types.…”

mentioning

confidence: 99%

“…The second group includes an arabinoxylan arabinofuranohydrolase enzyme from Bacillus subtilis (BsAXH-m2,3) and, in addition to the GH43 module, the proteins in this group have a family 6 carbohydrate-binding module (CBM6) at their C termini (65). The third group, which includes a ␤-xylosidase/␣-Larabinofuranosidase from the rumen bacterium Selenomonas ruminantium (SXA) (9) and a ␤-xylosidase from Geobacillus stearothermophilus (XynB3) (8), possesses in addition to the GH43 modules a C-terminally appended ␤-sandwich fold structure composed of approximately 200 amino acid residues. GH43 proteins of similar organization as SXA and XynB3 abound in the protein databases, and they are thought to form a cluster of orthologous group of proteins (COG) with ␤-xylosidase as their functional annotation.…”

mentioning

confidence: 99%

Domain Analysis of a Modular α- l -Arabinofuranosidase with a Unique Carbohydrate Binding Strategy from the Fiber-Degrading Bacterium Fibrobacter succinogenes S85

et al. 2010

View full text Add to dashboard Cite

Family 43 glycoside hydrolases (GH43s) are known to exhibit various activities involved in hemicellulose hydrolysis. Thus, these enzymes contribute to efficient plant cell wall degradation, a topic of much interest for biofuel production. In this study, we characterized a unique GH43 protein from Fibrobacter succinogenes S85. The recombinant protein showed ␣-L-arabinofuranosidase activity, specifically with arabinoxylan. The enzyme is, therefore, an arabinoxylan arabinofuranohydrolase (AXH). The F. succinogenes AXH (FSUAXH1) is a modular protein that is composed of a signal peptide, a GH43 catalytic module, a unique ␤-sandwich module (XX domain), a family 6 carbohydrate-binding module (CBM6), and F. succinogenes-specific paralogous module 1 (FPm-1). Truncational analysis and site-directed mutagenesis of the protein revealed that the GH43 domain/XX domain constitute a new form of carbohydrate-binding module and that residue Y484 in the XX domain is essential for binding to arabinoxylan, although protein structural analyses may be required to confirm some of the observations. Kinetic studies demonstrated that the Y484A mutation leads to a higher k cat for a truncated derivative of FSUAXH1 composed of only the GH43 catalytic module and the XX domain. However, an increase in the K m for arabinoxylan led to a 3-fold decrease in catalytic efficiency. Based on the knowledge that most XX domains are found only in GH43 proteins, the evolutionary relationships within the GH43 family were investigated. These analyses showed that in GH43 members with a XX domain, the two modules have coevolved and that the length of a loop within the XX domain may serve as an important determinant of substrate specificity.

show abstract

Structure‐guided design combined with evolutionary diversity led to the discovery of the xylose‐releasing exo‐xylanase activity in the glycoside hydrolase family 43

Zanphorlin

Morais

Diogo

et al. 2019

Biotech & Bioengineering

View full text Add to dashboard Cite

Rational design is an important tool for sculpting functional and stability properties of proteins and its potential can be much magnified when combined with in vitro and natural evolutionary diversity. Herein, we report the structure‐guided design of a xylose‐releasing exo‐β‐1,4‐xylanase from an inactive member of glycoside hydrolase family 43 (GH43). Structural analysis revealed a nonconserved substitution (Lys247) that results in the disruption of the hydrogen bond network that supports catalysis. The mutation of this residue to a conserved serine restored the catalytic activity and crystal structure elucidation of the mutant confirmed the recovery of the proper orientation of the catalytically relevant histidine. Interestingly, the tailored enzyme can cleave both xylooligosaccharides and xylan, releasing xylose as the main product, being the first xylose‐releasing exo‐β‐1,4‐xylanase reported in the GH43 family. This enzyme presents a unique active‐site topology when compared with closely related β‐xylosidases, which is the absence of a hydrophobic barrier at the positive‐subsite region, allowing the accommodation of long substrates. Therefore, the combination of rational design for catalytic activation along with naturally occurring differences in the substrate binding interface led to the discovery of a novel activity within the GH43 family. In addition, these results demonstrate the importance of solvation of the β‐propeller hollow for GH43 catalytic function and expand our mechanistic understanding about the diverse modes of action of GH43 members, a key and polyspecific carbohydrate‐active enzyme family abundant in most plant cell‐wall‐degrading microorganisms.

show abstract

Structure of the two-subsite β-d-xylosidase from Selenomonas ruminantium in complex with 1,3-bis[tris(hydroxymethyl)methylamino]propane

Cited by 48 publications

References 24 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

Domain Analysis of a Modular α- l -Arabinofuranosidase with a Unique Carbohydrate Binding Strategy from the Fiber-Degrading Bacterium Fibrobacter succinogenes S85

Structure‐guided design combined with evolutionary diversity led to the discovery of the xylose‐releasing exo‐xylanase activity in the glycoside hydrolase family 43

Contact Info

Product

Resources

About