PROSITE documentation PDOC00510

Glycosyl hydrolases family 10 (GH10) active site and domain profile

The microbial degradation of cellulose and xylans requires several types of enzymes such as endoglucanases (EC 3.2.1.4), cellobiohydrolases (EC 3.2.1.91) (exoglucanases), or xylanases (EC 3.2.1.8) [1,2]. Fungi and bacteria produces a spectrum of cellulolytic enzymes (cellulases) and xylanases which, on the basis of sequence similarities, can be classified into families. One of these families is known as the cellulase family F [3] or as the glycosyl hydrolases family 10 (GH10) [4,E1,E2]. All family 10 xylanases hydrolyze the glycosidic bond in a double-displacement 'retaining' mechanism using two catalytic acidic residues, where one residue acts a nucleophile (base) and the other acts as a general acid/base [6.7]. The enzymes which are currently known to belong to this family are listed below.

• Aspergillus awamori xylanase A (xynA).
• Bacillus sp. strain 125 xylanase (xynA).
• Bacillus stearothermophilus xylanase.
• Butyrivibrio fibrisolvens xylanases A (xynA) and B (xynB).
• Caldocellum saccharolyticum bifunctional endoglucanase/exoglucanase (celB). This protein consists of two domains; it is the N-terminal domain, which has exoglucanase activity, which belongs to this family.
• Caldocellum saccharolyticum xylanase A (xynA).
• Caldocellum saccharolyticum ORF4. This hypothetical protein is encoded in the xynABC operon and is probably a xylanase.
• Cellulomonas fimi exoglucanase/xylanase (cex).
• Clostridium stercorarium thermostable celloxylanase.
• Clostridium thermocellum xylanases Y (xynY) and Z (xynZ).
• Cryptococcus albidus xylanase.
• Penicillium chrysogenum xylanase (gene xylP).
• Pseudomonas fluorescens xylanases A (xynA) and B (xynB).
• Ruminococcus flavefaciens bifunctional xylanase XYLA (xynA). This protein consists of three domains: a N-terminal xylanase catalytic domain that belongs to family 11 of glycosyl hydrolases; a central domain composed of short repeats of Gln, Asn an Trp, and a C-terminal xylanase catalytic domain that belongs to family 10 of glycosyl hydrolases.
• Streptomyces lividans xylanase A (xlnA).
• Thermoanaerobacter saccharolyticum endoxylanase A (xynA).
• Thermoascus aurantiacus xylanase.
• Thermophilic bacterium Rt8.B4 xylanase (xynA).

The overall structure of the GH10 domain corresponds to an eightfold α/ β-barrel (TIM-barrel) with a typical deep groove in the centre, allowing an 'endo' type of action on the large polysaccharide backbone (see <PDB:1R85>) [6,7].

One of the conserved regions in these enzymes is centered on a conserved glutamic acid residue which has been shown [5], in the exoglucanase from Cellulomonas fimi, to be directly involved in glycosidic bond cleavage by acting as a nucleophile. We have used this region as a signature pattern. We have also developed a profile that covers the entire GH10 domain.