There are many kinds of xylanases, family-2b, family-10, & family-11. This enzyme belongs to the glycosidase family-11 along with the homologous enzyme (D00538), while the entries D00169, D00479 & M00160 belong to family-10. According to the literature [7], [18], [26] & [28], the catalytic reaction proceeds as follows: (1) Glu170 (of PDB;1bk1) acts as a general acid to protonate the leaving oxygen atom, leading to a oxocarbenium-like transtion state from xylan substrate. (2) pKa of Glu79 (of PDB;1bk1), which acts as a nucleophile, is modulated by Tyr70 and Tyr81. Glu79 makes a nucleophilic attack on C1 atom of the transition state, forming a glycosyl-enzyme intermediate. (2') As the glycosyl-enzyme intermediate is formed, Tyr81 switched from Glu79 to Glu170. Tyr81 may modulate the activity of Glu170 as a general base. (3) Glu170 acts as a general base to activate a water molecule. (4) The activated water makes a nucleophilic attack on the C1 atom of the intermediate. This reaction proceeds through an oxocarbenium-like transition state to complete the hydrolysis. ### According to the literature [26] & [28], this enzyme adopts 2,5B (or Boat) conformation, which places C5, O5, C1 and C2 in a planar arrangement, for the intermediate. Moreover, at the position of 37 of 1bk1, the family-11 has an aspartic acid or an aspargine residue. For high pH optimum, aspartic acid residue is used at the position, whilst an aspargine residue is adopted for lower pH optimum, according to the literature [13]. This residue makes a hydrogen bond with the acid-base, Glu170, modulating its pKa.
endo-(1->4)-beta-xylan 4-xylanohydrolase
Domains in microbial beta-1, 4-glycanases: sequence conservation, function, and enzyme families.
X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) (ISBN: 9518913625)
TRICEL Symposium on Trichoderma Reesei Cellulases and Other Hydrolases
High-resolution structures of xylanases from B.circulans and T.harzianum identify a new folding pattern and implications for the atomic basis of the catalysis.
Three-dimensional structure of endo-1,4-beta-xylanase II from Trichoderma reesei: two conformational states in the active site.
Stereochemistry of the hydrolysis of glycosidic linkage by endo-beta-1,4-xylanases of Trichoderma reesei.
Crystallization and preliminary X-ray crystallographic studies of thermostable xylanase crystals isolated from Paecilomyces varioti.
Thermostabilization of the Bacillus circulans xylanase by the introduction of disulfide bonds.
X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS), AND MUTAGENESIS.
Mutational and crystallographic analyses of the active site residues of the Bacillus circulans xylanase.
Structural comparison of two major endo-1,4-xylanases from Trichoderma reesei.
Characterisation of 4-deoxy-beta-L-threo-hex-4-enopyranosyluronic acid attached to xylan in pine kraft pulp and pulping liquor by 1H and 13C NMR spectroscopy.
Covalent binding of three epoxyalkyl xylosides to the active site of endo-1,4-xylanase II from Trichoderma reesei.
Effects of both shortening and lengthening the active site nucleophile of Bacillus circulans xylanase on catalytic activity.
The pKa of the general acid/base carboxyl group of a glycosidase cycles during catalysis: a 13C-NMR study of bacillus circulans xylanase.
Three-dimensional structure of Endo-1,4-beta-xylanase I from Aspergillus niger: molecular basis for its low pH optimum.
Xylanase homology modeling using the inverse protein folding approach.
Characterization of a buried neutral histidine residue in Bacillus circulans xylanase: NMR assignments, pH titration, and hydrogen exchange.
Secondary structure and NMR assignments of Bacillus circulans xylanase.
Endo-beta-1,4-xylanase families: differences in catalytic properties.
Structural and functional properties of low molecular weight endo-1,4-beta-xylanases.
Complete measurement of the pKa values of the carboxyl and imidazole groups in Bacillus circulans xylanase.
Catalytic thiol and carboxylate: role of cysteine and glutamic acid in the xylosidic activity of endoxylanase from Chainia sp. (NCL 82-5-1).
Characterization of a buried neutral histidine in Bacillus circulans xylanase: internal dynamics and interaction with a bound water molecule.
Thermophilic xylanase from Thermomyces lanuginosus: high-resolution X-ray structure and modeling studies.
X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF 29-210.
Crystallographic and mutational analyses of an extremely acidophilic and acid-stable xylanase: biased distribution of acidic residues and importance of Asp37 for catalysis at low pH.
Functional conformational changes of endo-1,4-xylanase II from Trichoderma reesei: a molecular dynamics study.
Sugar ring distortion in the glycosyl-enzyme intermediate of a family G/11 xylanase.
Purification and biochemical characteristics of beta-D-xylanase from a thermophilic fungus, Thermomyces lanuginosus-SSBP.
Catalysis and specificity in enzymatic glycoside hydrolysis: a 2,5B conformation for the glycosyl-enzyme intermediate revealed by the structure of the Bacillus agaradhaerens family 11 xylanase.
Family 10 and 11 xylanase genes from Caldicellulosiruptor sp. strain Rt69B.1.
Structure of XynB, a highly thermostable beta-1,4-xylanase from Dictyoglomus thermophilum Rt46B.1, at 1.8 A resolution.
Codon optimization of xylanase gene xynB from the thermophilic bacterium Dictyoglomus thermophilum for expression in the filamentous fungus Trichoderma reesei.
Hydrogen bonding and catalysis: a novel explanation for how a single amino acid substitution can change the pH optimum of a glycosidase.
The tertiary structure at 1.59 A resolution and the proposed amino acid sequence of a family-11 xylanase from the thermophilic fungus Paecilomyces varioti bainier.
Analysis of the dynamic properties of Bacillus circulans xylanase upon formation of a covalent glycosyl-enzyme intermediate.
Oligosaccharide binding to family 11 xylanases: both covalent intermediate and mutant product complexes display (2,5)B conformations at the active centre.
Crystallographic analysis of family 11 endo-beta-1,4-xylanase Xyl1 from Streptomyces sp. S38.
Dissecting the electrostatic interactions and pH-dependent activity of a family 11 glycosidase.
Simultaneous catalysis and product separation by cross-linked enzyme crystals.
ACEII, a novel transcriptional activator involved in regulation of cellulase and xylanase genes of Trichoderma reesei.
A combination of weakly stabilizing mutations with a disulfide bridge in the alpha-helix region of Trichoderma reesei endo-1,4-beta-xylanase II increases the thermal stability through synergism.
Specific characterization of substrate and inhibitor binding sites of a glycosyl hydrolase family 11 xylanase from Aspergillus niger.
Engineering of multiple arginines into the Ser/Thr surface of Trichoderma reesei endo-1,4-beta-xylanase II increases the thermotolerance and shifts the pH optimum towards alkaline pH.
Mapping the conformational itinerary of beta-glycosidases by X-ray crystallography.
MM-PBSA free energy analysis of endo-1,4-xylanase II (XynII)-substrate complexes: binding of the reactive sugar in a skew boat and chair conformation.
Long-range nature of the interactions between titratable groups in Bacillus agaradhaerens family 11 xylanase: pH titration of B. agaradhaerens xylanase.
Structural basis for inhibition of Aspergillus niger xylanase by triticum aestivum xylanase inhibitor-I.