PROSITE documentation PDOC00622

Glycosyl hydrolases family 11 (GH11) active sites signatures 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 G [3] or as the glycosyl hydrolases family 11 (GH11) [4,E1,E2]. Family 11 is monospecific, only consisting of xylanases. The enzymes which are currently known to belong to this family are listed below.

• Aspergillus awamori xylanase C (xynC).
• Bacillus circulans, pumilus, stearothermophilus and subtilis xylanase (xynA).
• Clostridium acetobutylicum xylanase (xynB).
• Clostridium stercorarium xylanase A (xynA).
• Fibrobacter succinogenes xylanase C (xynC) which consist of two catalytic domains that both belong to family 10.
• Neocallimastix patriciarum xylanase A (xynA).
• 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.
• Schizophyllum commune xylanase A.
• Streptomyces lividans xylanases B (xlnB) and C (xlnC).
• Trichoderma reesei xylanases I and II.

The GH11 domain folds into a jelly-roll shape likened to a partially closed right hand (see <PDB:4HK8>). Several anti-parallel β-strands bend almost 90 degrees to produce a substrate-binding groove characteristic of the GH11 domain active sites. Two catalytic Glu residues face each other from opposite sides of the groove. The hydrolysis reaction is believed to follow a double-displacement mechanism, with one Glu residue acting as a general acid/base catalyst and the other as a nucleophile.

Two of the conserved regions in these enzymes are centered on glutamic acid residues which have both been shown [5], in Bacillus pumilis xylanase, to be necessary for catalytic activity. We have used both regions as signature patterns. We have also developed a profile that covers the entire GH11 domain.