The structure of a family GH25 lysozyme fromAspergillus fumigatus

Lysins are important biomolecules which cleave the bacterial cell-wall polymer peptidoglycan. They are finding increasing commercial and medical application. In order to gain an insight into the mechanism by which these enzymes operate, the X-ray structure of a CAZy family GH25 `lysozyme' fromAspergillus fumigatuswas determined. This is the first fungal structure from the family and reveals a modified α/β-barrel-like fold in which an eight-stranded β-barrel is flanked by three α-helices. The active site lies toward the bottom of a negatively charged pocket and its layout has much in common with other solved members of the GH25 and related GH families. A conserved active-site DXE motif may be implicated in catalysis, lending further weight to the argument that this glycoside hydrolase family operatesviaa `substrate-assisted' catalytic mechanism.

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Epoxyalkyl glycosides of d-xylose and xylo-oligosaccharides are active-site markers of xylanases from glycoside hydrolase family 11, not from family 10

Biochemical Journal ◽

10.1042/bj3470865 ◽

2000 ◽

Vol 347 (3) ◽

pp. 865-873 ◽

Cited By ~ 5

Author(s):

Patricia NTARIMA ◽

Wim NERINCKX ◽

Klaus KLARSKOV ◽

Bart DEVREESE ◽

Mahalingeshwara K. BHAT ◽

...

Keyword(s):

Active Site ◽

Glycoside Hydrolase ◽

Glycoside Hydrolases ◽

Thermomyces Lanuginosus ◽

Glycoside Hydrolase Family ◽

Active Site Residues ◽

X Ray ◽

Order Of Magnitude ◽

Site Markers ◽

Hydrolase Family

A series of Ω-epoxyalkyl glycosides of D-xylopyranose, xylobiose and xylotriose were tested as potential active-site-directed inhibitors of xylanases from glycoside hydrolase families 10 and 11. Whereas family-10 enzymes (Thermoascus aurantiacus Xyn and Clostridium thermocellum Xyn Z) are resistant to electrophilic attack of active-site carboxyl residues, glycoside hydrolases of family 11 (Thermomyces lanuginosus Xyn and Trichoderma reesei Xyn II) are irreversibly inhibited. The apparent inactivation and association constants (ki, 1/Ki) are one order of magnitude higher for the xylobiose and xylotriose derivatives. The effects of the aglycone chain length can clearly be described. Xylobiose and n-alkyl β-D-xylopyranosides are competitive ligands and provide protection against inactivation. MS measurements showed 1:1 stoichiometries in most labelling experiments. Electrospray ionization MS/MS analysis revealed the nucleophile Glu86 as the modified residue in the T. lanuginosus xylanase when 2,3-epoxypropyl β-D-xylopyranoside was used, whereas the acid/base catalyst Glu178 was modified by the 3,4-epoxybutyl derivative. The active-site residues Glu86 and Glu177 in T. reesei Xyn II are similarly modified, confirming earlier X-ray crystallographic data [Havukainen, Törrönen, Laitinen and Rouvinen (1996) Biochemistry 35, 9617-9624]. The inability of the Ω-epoxyalkyl xylo(oligo)saccharide derivatives to inactivate family-10 enzymes is discussed in terms of different ligand-subsite interactions.

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Two distinct catalytic pathways for GH43 xylanolytic enzymes unveiled by X-ray and QM/MM simulations

Nature Communications ◽

10.1038/s41467-020-20620-3 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Mariana A. B. Morais ◽

Joan Coines ◽

Mariane N. Domingues ◽

Renan A. S. Pirolla ◽

Celisa C. C. Tonoli ◽

...

Keyword(s):

Active Site ◽

Catalytic Mechanism ◽

Open Architecture ◽

Reaction Pathways ◽

Main Reaction ◽

Glycoside Hydrolase Family ◽

X Ray ◽

Glycoside Hydrolase Family 43 ◽

Xylanolytic Enzymes ◽

Hydrolase Family

AbstractXylanolytic enzymes from glycoside hydrolase family 43 (GH43) are involved in the breakdown of hemicellulose, the second most abundant carbohydrate in plants. Here, we kinetically and mechanistically describe the non-reducing-end xylose-releasing exo-oligoxylanase activity and report the crystal structure of a native GH43 Michaelis complex with its substrate prior to hydrolysis. Two distinct calcium-stabilized conformations of the active site xylosyl unit are found, suggesting two alternative catalytic routes. These results are confirmed by QM/MM simulations that unveil the complete hydrolysis mechanism and identify two possible reaction pathways, involving different transition state conformations for the cleavage of xylooligosaccharides. Such catalytic conformational promiscuity in glycosidases is related to the open architecture of the active site and thus might be extended to other exo-acting enzymes. These findings expand the current general model of catalytic mechanism of glycosidases, a main reaction in nature, and impact on our understanding about their interaction with substrates and inhibitors.

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Crystallization and preliminary X-ray diffraction study of two complexes of a TAXI-type xylanase inhibitor with glycoside hydrolase family 11 xylanases fromAspergillus nigerandBacillus subtilis

Acta Crystallographica Section D Biological Crystallography ◽

10.1107/s0907444903029330 ◽

2004 ◽

Vol 60 (3) ◽

pp. 555-557 ◽

Cited By ~ 8

Author(s):

Stefaan Sansen ◽

Camiel J. De Ranter ◽

Kurt Gebruers ◽

Kristof Brijs ◽

Christophe M. Courtin ◽

...

Keyword(s):

Diffraction Study ◽

Glycoside Hydrolase ◽

Glycoside Hydrolase Family ◽

X Ray Diffraction ◽

X Ray ◽

Xylanase Inhibitor ◽

Hydrolase Family

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Functional metagenomics identifies an exosialidase with an inverting catalytic mechanism that defines a new glycoside hydrolase family (GH156)

Journal of Biological Chemistry ◽

10.1074/jbc.ra118.003302 ◽

2018 ◽

Vol 293 (47) ◽

pp. 18138-18150 ◽

Cited By ~ 7

Author(s):

Léa Chuzel ◽

Mehul B. Ganatra ◽

Erdmann Rapp ◽

Bernard Henrissat ◽

Christopher H. Taron

Keyword(s):

Glycoside Hydrolase ◽

Catalytic Mechanism ◽

Recombinant Expression ◽

Biochemical Property ◽

Environmental Dna ◽

Thermal Spring ◽

Sialic Acid Residue ◽

Glycoside Hydrolases ◽

Glycoside Hydrolase Family ◽

Hydrolase Family

Exosialidases are glycoside hydrolases that remove a single terminal sialic acid residue from oligosaccharides. They are widely distributed in biology, having been found in prokaryotes, eukaryotes, and certain viruses. Most characterized prokaryotic sialidases are from organisms that are pathogenic or commensal with mammals. However, in this study, we used functional metagenomic screening to seek microbial sialidases encoded by environmental DNA isolated from an extreme ecological niche, a thermal spring. Using recombinant expression of potential exosialidase candidates and a fluorogenic sialidase substrate, we discovered an exosialidase having no homology to known sialidases. Phylogenetic analysis indicated that this protein is a member of a small family of bacterial proteins of previously unknown function. Proton NMR revealed that this enzyme functions via an inverting catalytic mechanism, a biochemical property that is distinct from those of known exosialidases. This unique inverting exosialidase defines a new CAZy glycoside hydrolase family we have designated GH156.

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