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.
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.
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