@inbook {16738,
	title = {Carbohydrases},
	booktitle = {The Encyclopedia of Catalysis},
	year = {2010},
	publisher = {John Wiley and Sons},
	organization = {John Wiley and Sons},
	edition = {2nd},
	address = {New York},
	abstract = {<p>The enzymes that catalyze the synthesis and degradation of oligo- and polysaccharides are among the most important in the biosphere, because of the key role they play in the global carbon cycle. Thanks to a long and rich history of scientific study, the catalytic mechanisms of the glycoside hydrolases and transglycosylases are generally well understood in terms of enzyme-substrate interactions and transition state structure. Recent structure-function studies of polysaccharide lyases have also begun to unravel the secrets of catalysis in these distinct classes of carbohydrate-active enzymes. Built upon a firm understanding of enzyme structure and mechanism, an impressive number of technological applications highlight the prowess of these biological catalysts.</p>},
	keywords = {biomass, carbohydrate binding module (CBM), CAZy, glycosidase, glycoside hydrolase, GLYCOSYL-ENZYME INTERMEDIATE, polysaccharide lyase, TRANSGLYCOSYLATION},
	doi = {10.1002/0471227617.eoc037},
	author = {Brumer, Harry},
	editor = {Istv{\'a}n T. Horv{\'a}th}
}
@article {713,
	title = {Characterizing the pH-dependent stability and catalytic mechanism of the family 11 xylanase from the alkalophilic Bacillus agaradhaerens},
	journal = {Carbohydrate Research},
	volume = {338},
	number = {5},
	year = {2003},
	note = {ISI Document Delivery No.: 645XBTimes Cited: 6Cited Reference Count: 38},
	month = {Feb},
	pages = {415-421},
	type = {Article},
	abstract = {The xylanase, BadX, from the alkalophilic Bacillus agaradhaerens was cloned, expressed and studied in comparison to a related family 11 xylanase, BcX, from B. circulans. Despite the alkaline versus neutral conditions under which these bacteria grow, BadX and BcX both exhibit optimal activity near pH 5.6 using the substrate omicron-nitrophenyl beta-xylobioside. Analysis of the bell-shaped activity profile of BadX yielded apparent pK(a) values of 4.2 and 7.1, assignable to its nucleophile Glu94 and general acid Glu184, respectively. In addition to having an similar to 10-fold higher k(cat)/K-m value with this substrate at pH 6 and 40 degreesC, BadX has significantly higher thermal stability than BcX under neutral and alkaline conditions. This enhanced stability, rather than a shift in its pH-optimum, may allow BadX to hydrolyze xylan under conditions of elevated temperature and pH. (C) 2003 Elsevier Science Ltd. All rights reserved.},
	keywords = {bacillus xylanase, CIRCULANS XYLANASE, CLASSIFICATION, electrostatic, extremophile, glycosidase, GLYCOSYL-ENZYME INTERMEDIATE, HYDROLASES, interactions, NMR ASSIGNMENTS, pH-dependent mechanism, PK(A), PROTEIN, STABILITY, THERMOSTABILITY},
	isbn = {0008-6215},
	url = {<Go to ISI>://000181004800004},
	author = {Poon, D. K. Y. and Webster, P. and Withers, S. G. and McIntosh, L. P.}
}
@article {5098,
	title = {Dissecting the electrostatic interactions and pH-dependent activity of a family 11 glycosidase},
	journal = {Biochemistry},
	volume = {40},
	number = {34},
	year = {2001},
	note = {ISI Document Delivery No.: 466CYTimes Cited: 56Cited Reference Count: 50},
	month = {Aug},
	pages = {10115-10139},
	type = {Article},
	abstract = {Previous studies of the low molecular mass family 11 xylanase from Bacillus circulans show that the ionization state of the nucleophile (GIu78, pK(a) 4.6) and the acid/base catalyst (Glu 172, pK(a) 6.7) gives rise to its pH-dependent activity profile. Inspection of the crystal structure of BCX reveals that Glu78 and Glu172 are in very similar environments and are surrounded by several chemically equivalent and highly conserved active site residues. Hence, there are no obvious reasons why their apparent pKa values are different. To address this question, a mutagenic approach was implemented to determine what features establish the pKa values (measured directly by C-13 NMR and indirectly by pH-dependent activity profiles) of these two catalytic carboxylic acids. Analysis of several BCX variants indicates that the ionized form of Glu78 is preferentially stabilized over that of Glu 172 in part by stronger hydrogen bonds contributed by two well-ordered residues, namely, Tyr69 and Gln127. In addition, theoretical pKa calculations show that Glu78 has a lower pKa value than Glu 172 due to a smaller desolvation energy and more favorable background interactions with permanent partial charges and ionizable groups within the protein. The pKa value of Glu172 is in turn elevated due to electrostatic repulsion from the negatively charged glutamate at position 78. The results also indicate that all of the conserved active site residues act concertedly in establishing the pKa values of Glu78 and Glu 172, with no particular residue being singly more important than any of the others. In general, residues that contribute positive charges and hydrogen bonds serve to lower the pKa values of Glu78 and Glu172. The degree to which a hydrogen bond lowers a pKa value is largely dependent on the length of the hydrogen bond (shorter bonds lower pKa values more) and the chemical nature of the donor (COOH > OH > CONH2). In contrast, neighboring carboxyl groups can either lower or raise the pKa values of the catalytic glutamic acids depending upon the electrostatic linkage of the ionization constants of the residues involved in the interaction. While the pH optimum of BCX can be shifted from -1.1 to +0.6 pH units by mutating neighboring residues within the active site, activity is usually compromised due to the loss of important ground and/or transition state interactions. These results suggest that the pH optima of an enzyme might be best engineered by making strategic amino acid substitutions, at positions outside of the "core" active site, that electrostatically influence catalytic residues without perturbing their immediate structural environment.},
	keywords = {ASSIGNMENTS, BACILLUS-CIRCULANS XYLANASE, CATALYSIS, GLYCOSYL-ENZYME INTERMEDIATE, KINETIC-ANALYSIS, MASS-SPECTROMETRY, MECHANISMS, NMR, PK(A), PROTEIN, SITE NUCLEOPHILE, structures},
	isbn = {0006-2960},
	url = {<Go to ISI>://000170627800014},
	author = {Joshi, M. D. and Sidhu, G. and Nielsen, J. E. and Brayer, G. D. and Withers, S. G. and McIntosh, L. P.}
}
@article {4780,
	title = {Analysis of the dynamic properties of Bacillus circulans xylanase upon formation of a covalent glycosyl-enzyme intermediate},
	journal = {Protein Science},
	volume = {9},
	number = {3},
	year = {2000},
	note = {ISI Document Delivery No.: 295XWTimes Cited: 16Cited Reference Count: 56},
	month = {Mar},
	pages = {512-524},
	type = {Article},
	abstract = {NMR spectroscopy was used to search for mechanistically significant differences in the local mobility of the main-chain amides of Bacillus circulans xylanase (BCX) in its native and catalytically competent covalent glycosyl-enzyme intermediate states. N-15 T-1, T-2, and N-15{H-1} NOE values were measured for similar to 120 out of 178 peptide groups in both the apo form of the protein and in BCX covalently modified at position Glu78 with a mechanism-based 2-deoxy-2-fluoro-beta-xylobioside inactivator. Employing the model-free formalism of Lipari and Szabo, the measured relaxation parameters were used to calculate a global correlation time ( tau(m)) for the protein in each form (9.2 +/- 0.2 ns for apo-BCX; 9.8 +/- 0.3 ns for the modified protein), as well as individual order parameters for the main-chain NH bond vectors. Average values of the order parameters for the protein in the apo and complexed forms were S-2 = 0.86 +/- 0.04 and S-2 = 0.91 +/- 0.04, respectively. No correlation is observed between these order parameters and the secondary structure, solvent accessibility, or hydrogen bonding patterns of amides in either form of the protein. These results demonstrate that the backbone of BCX is well ordered in both states and that formation of the,glycosyl-enzyme intermediate leads to little change, in any, in the dynamic properties of BCX on the time scales sampled by N-15-NMR relaxation measurements.},
	keywords = {ACTIVE-SITE NUCLEOPHILE, ANISOTROPIC ROTATIONAL, BACKBONE DYNAMICS, BINDING, BURIED NEUTRAL HISTIDINE, DIFFUSION, glucanase, GLYCOSYL-ENZYME INTERMEDIATE, MAGNETIC-RESONANCE RELAXATION, MODEL-FREE APPROACH, N-15 NMR RELAXATION, NMR, order parameter, PROTEIN, PROTEINS, relaxation dynamics, SIDE-CHAIN RESONANCES, STRUCTURE},
	isbn = {0961-8368},
	url = {<Go to ISI>://000085994800009},
	author = {Connelly, G. P. and Withers, S. G. and McIntosh, L. P.}
}
@article {4842,
	title = {Hydrogen bonding and catalysis: A novel explanation for how a single amino acid substitution can change the pH optimum of a glycosidase},
	journal = {Journal of Molecular Biology},
	volume = {299},
	number = {1},
	year = {2000},
	note = {ISI Document Delivery No.: 318NCTimes Cited: 96Cited Reference Count: 58},
	month = {May},
	pages = {255-279},
	type = {Article},
	abstract = {The pH optima of family 11 xylanases are well correlated with the nature of the residue adjacent to the acid/base catalyst. In xylanases that function optimally under acidic conditions, this residue is aspartic acid, whereas it is asparagine in those that function under more alkaline conditions. Previous studies of wild-type (WT) Bacillus circulans xylanase (BCX), with an asparagine residue at position 35, demonstrated that its pH-dependent activity follows the ionization states of the nucleophile Glu78 (pK(a) 4.6) and the acid/base catalyst Glu172 (pK(a) 6.7). As predicted from sequence comparisons, substitution of this asparagine residue with an aspartic acid residue (N35D BCX) shifts its pH optimum from 5.7 to 4.6, with an similar to 20 \% increase in activity. The bell-shaped pH-activity profile of this mutant enzyme follows apparent pK(a) values of 3.5 and 5.8. Based on C-13-NMR titrations, the predominant pK(a) values of its active-site carboxyl groups are 3.7 (Asp35), 5.7 (Glu78) and 8.4 (Glu172). Thus, in contrast to the WT enzyme, the pH-activity profile of N35D BCX appears to be set by Asp35 and Glu78. Mutational, kinetic, and structural studies of N35D BCX, both in its native and covalently modified 2-fluoro-xylobiosyl glycosyl-enzyme intermediate states, reveal that the xylanase still follows a double-displacement mechanism with Glu78 serving as the nucleophile. We therefore propose that Asp35 and Glu172 function together as the general acid/base catalyst, and that N35D BCX exhibits a "reverse protonation" mechanism in which it is catalytically active when Asp35, with the lower pK(a), is protonated, while Glu78, with the higher pK(a), is deprotonated. This implies that the mutant enzyme must have an inherent catalytic efficiency at least 100-fold higher than that of the parental WT, because only similar to 1\% of its population is in the correct ionization state for catalysis at its pH optimum. The increased efficiency of N35D BCX, and by inference all "acidic" family 11 xylanases, is attributed to the formation of a short (2.7 Angstrom) hydrogen bond between Asp35 and Glu172, observed in the crystal structure of the glycosyl-enzyme intermediate of this enzyme, that will substantially stabilize the transition state for glycosyl transfer. Such a mechanism may be much more commonly employed than is generally realized, necessitating careful analysis of the pH-dependence of enzymatic catalysis. (C) 2000 Academic Press.},
	keywords = {3-DIMENSIONAL STRUCTURE, 4-BETA-XYLANASES, ACTIVE-SITE, BACILLUS-CIRCULANS XYLANASE, CYCLODEXTRIN GLYCOSYLTRANSFERASE, electrostatics, ENDO-1, GLYCOSYL-ENZYME INTERMEDIATE, ISOTOPE, MOLECULAR-WEIGHT, NMR, NUCLEAR-MAGNETIC-RESONANCE, nucleophile, PANCREATIC ALPHA-AMYLASE, pH-dependent enzyme mechanism, SHIFT, TRICHODERMA-REESEI, X-RAY CRYSTALLOGRAPHY, X-ray structure},
	isbn = {0022-2836},
	url = {<Go to ISI>://000087289400019},
	author = {Joshi, M. D. and Sidhu, G. and Pot, I. and Brayer, G. D. and Withers, S. G. and McIntosh, L. P.}
}
