PROSITE documentation PDOC00794

Glycosyl hydrolases family 16 (GH16) signature and domain profile

The glycosyl hydrolases family 16 (GH16) [1,E1] contains functionally heterogeneous members, including β-agarases, endo-1,3-β-glucanases (laminarinases), endo-β-1,3-1,4-glucanases (lichenases), kappa-carrageenases, endo-β-galactosidases and xyloglucan endotransferases. These enzymes share a common ancestor and have diverged significantly in their primary sequence.

The GH16 catalytic domain has a classical sandwich-like β-jelly roll fold, formed by two main, closely packed and curved antiparallel β sheets, creating a deep channel harboring the catalytic machinery (see <PDB:1DYP>). Even though the GH16 domains have now diverged significantly in their primary sequences, they all feature a common catalytic motif, E-[ILV]-D-[IVAF]-[VILMF](0,1)-E. The two glutamic acid residues in the conserved motif are the nucleophile and the general base involved in catalysis, whereas the aspartic acid residue is important in maintaining the relative position of these catalytic amino acids [2,3].

Some proteins known to contain a GH16 domain are listed below:

• Bacterial β-1,3-1,4-glucanases, or lichenases, (EC 3.2.1.73) mainly from Bacillus but also from Clostridium thermocellum (gene licB), Fibrobacter succinogenes and Rhodothermus marinus (gene bglA).
• Bacillus circulans β-1,3-glucanase A1 (EC 3.2.1.39) (gene glcA).
• Alteromonas carrageenovora kappa-carrageenase (EC 3.2.1.83) (gene cgkA).
• Rhizobium meliloti endo-1,3-1,4-β-glycanase exoK.
• Streptomyces coelicolor agarase (EC 3.2.1.81) (gene dagA).
• Zobellia galactanivorans β-agarase A (EC 3.2.1.81) (gene agaA).
• Zobellia galactanivorans β-agarase B (EC 3.2.1.81) (gene agaB).
• Saccharophagus sp. AG21 β-agarase (gene agy1), includes a GH16 domain and two CBM6 (carbohydrate binding type-6) domain (see <PDOC51175>).
• Microbulbifer thermotolerans agarase (agaA).
• Thermotoga maritima laminarinase.
• Saccharomyces cerevisiae β-glucan synthesis-associated protein SKN1 [5].
• Saccharomyces cerevisiae β-glucan synthesis-associated protein KRE6 [5].

Two closely clustered conserved glutamates have been shown [6] to be involved in the catalytic activity of Bacillus licheniformis lichenase. We used the region that contains these residues as a signature pattern. We have also developed a profile that covers the entire GH16 domain.