Analysis of functional divergence within two structurally related glycoside hydrolase families

Abstract

Two glycoside hydrolase (GH) families were analyzed to detect the presence of functional divergence using the program DIVERGE. These two families, GH7 and GH16, each contain members related by amino acid sequence similarity, retaining hydrolytic mechanisms, and catalytic residue identity. GH7 and GH16 comprise GH Clan B, with a shared beta-jelly roll topology and mechanism. GH7 contains fungal cellobiohydrolases and endoglucanases and is divided into five main subfamilies, four of the former and one of the latter. Cluster comparisons between three of the cellobiohydrolase subfamilies and the endoglucanase subfamily identified specific amino acid residues that play a role in the functional divergence between the two enzyme types. GH16 contains subfamilies of bacterial agarases, xyloglucosyl transferases, 1,3-beta-D-glucanases, lichenases, and other enzymes with various substrate specificities and product profiles. Four cluster comparisons between these four main subfamilies again have identified amino acid residues involved in functional divergence between the subfamilies. (c) 2009 Wiley Periodicals, Inc. Biopolymers 91: 478-495, 2009.

Bioinformatic characterisation of genes encoding cell wall degrading enzymes in the Phytophthora parasitica genome

“…The β-1,4-linked glucose residues that form cellulose can be degraded by enzymes that fall into four broad categories: endo- and exo-β-1,4-glucanases [17, 18, 64], cellobiohydrolases [64, 65] and β-glucosidases [66]. There are also AA proteins that assist in cellulose breakdown through direct or indirect enzyme activity [21], and CBMs that bind to cellulose and act to concentrate enzyme activities.…”

“…GH6 enzymes act at the non-reducing end of the polysaccharide chain. The five P. parasitica GH7 proteins share 29% amino acid identity and contain the ExDxxE motif typical of the GH7 family [65]. The GH7 family includes cellobiohydrolases that release the disaccharide cellobiose from the reducing end of cellulose chains, endo-β-1,4-glucanases and β-1,3-1,4 glucanases.…”

“…Sequence alignment showed that the GH7 proteins could be split into two subfamilies but specific functions could not be assigned to individual GH7 proteins, although two [PPTG_07012 and 07017] sharing 71% amino acid identity showed sequence similarities with β-1,3:1,4 glucanases from Bispora sp. [e. g. NCBI: ACT53749, [80]] and the other three showed more similarity to endoglucanases from Trichoderma reesei [65]. Using sequence data from two orthologous genes [PPTG_11504 P10297 and 16275 P10297 ] from another P. parasitica isolate to predict full-length versions of truncated proteins in the INRA-310 isolate, the 14 P. parasitica GH12 proteins were shown to contain the six GH12 consensus boxes described in Goedegebuur et al [81].…”

“…In P. parasitica , the GH1, GH3, GH12 and GH30 families include proteins that act on xyloglucan backbones [18, 66, 68]. Breakage of the β-1,4-linked glucans can also be achieved by xyloglucan-specific endo-β-1,4-glucanases from the diverse GH16 family [65]. The GH16 family members also act on β-1,3-galactans in AGPs, β-1,3:1,4-glucans and β-1,3-glucans [94, 95].…”

Genomics Review of Holocellulose Deconstruction by Aspergilli

“…3B) are similar to GH16 enzymes found in plants and to bacterial agarases, cleaving ␤-1,3-and/or ␤-1,4-glycosidic linkages. Members are related by amino acid sequence similarity, the retaining hydrolytic mechanism, and catalytic residue identity (117). These endoglucanases share the ␤-jelly-roll topology and the retaining catalytic mechanism (118)(119)(120).…”