Glycoside Hydrolase Family 66

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• Author: Ryuichiro Suzuki
• Responsible Curator: Zui Fujimoto

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Glycoside Hydrolase Family GH66
Clan	none, (β/α)8
Mechanism	retaining
Active site residues	known
CAZy DB link
https://www.cazy.org/GH66.html

Substrate specificities

Glycoside hydrolases of family GH66 include endo-acting dextranases (Dex; EC 3.2.1.11) and cycloisomaltooligosaccharide glucanotransferases (CITase; EC 2.4.1.248). Family GH66 enzymes are classified into the following three types: Type I Dexs, Type II Dexs with low CITase activity, and Type III CITases [1, 2].

Dex enzymes hydrolyze α-1,6-linkages of dextran and produce isomaltooligosaccharides (IGs) of varying length. Dex enzymes from oral streptococci have been studied since the 1970s [3, 4, 5]. Dexs are classified into families GH49 and GH66.

CITases catalyze intramolecular transglucosylation to produce cycloisomaltooligosaccharides (CIs; cyclodextrans) with degree of polymerization of 7-17 [6]. CITases produce CIs from IG4 and larger IGs [7]. CITase from Bacillus sp. T-3040 (CITase-T3040) produced CI-8 predominantly from dextran 40, whereas the major product of CITase from Paenibacillus sp. 598K (CITase-598K) was CI-7 [7, 8]. CITases contain a CITase-specific insertion (about 90 residues) inside the catalytic domain. The insertion region is a family 35 carbohydrate-binding module (CBM35) domain [8]. Some Dexs displaying strong dextranolytic activity with low cyclization activity have been discovered [1, 2].

Kinetics and Mechanism

GH66 enzymes are retaining enzymes, as first shown by structural analysis of cyclic dextrins formed by transglycosylation from a-1,6-glucan by Bacillus sp. T-3040 CITase-T3040 [9]. This has been supported by subsequent structural [10] and chemical rescue studies [1]. GH66 enzymes appear to operate through a classical Koshland retaining mechanism. The k_cat and K_M values of Dex from Bacteroides thetaiotaomicron VPI-5482 (BtDex) toward dextran T2000 were determined to be 86.7 s^-1 and 0.029 mM, respectively [2]. Both CITase-T3040 and CITase-598K showed the same K_M value for dextran 40 (0.18 mM) [7]. The k_cat values of CITase-T3040 and CITase-598K against dextran 40 were 3.2 s^-1 and 5.8 s^-1, respectively [7]. Dexs from family GH49 are inverting enzymes.

Catalytic Residues

Catalytic residues of several GH66 enzymes have been identified by mutational and structural studies [1, 7, 10, 11]. The catalytic nucleophile is aspartic acid and the general acid/base is glutamic acid. Asp385 and Glu453 are nucleophile and acid/base catalyst, respectively, in Dex from Streptococcus mutans (SmDex) [10, 11], Asp340 and Glu412 in Dex from Paenibacillus sp. (PsDex) [1], Asp270 and Glu342 in CITase-T3040 [7, 12], and Asp269 and Glu341 in CITase-598K [7].

Three-dimensional structures

Crystal structures of a truncated mutant of Streptococcus mutans SmDex (lacking the N-terminal 99 and C-terminal 118 residues) have been reported as the first three-dimensional structure of a GH66 enzyme [10]. Three structures, ligand free (PDB ID 3vmn), in complex with IG3 (PDB ID 3vmo), and in complex with 4’,5’-epoxypentyl α-D-glucopyranoside (PDB ID 3vmp), have been solved [10]. The catalytic domain of SmDex is a (β/α)₈-barrel fold, accompanied by N-terminal immunoglobulin-like β-sandwich fold and C-terminal β-sandwich structure containing two Greek key motifs. These three domains are the common structural components in GH66 enzymes.

A structure for a GH66 CITase-T3040 (PDB ID 3wnk-3wno) has been reported [12]. CITase-T3040 has a similar domain arrangement to that of SmDex, but a CBM35 domain is inserted into the catalytic module, which assists substrate uptake and production of the dominant cyclooctylisomaltoside (CI-8).

Family Firsts

First stereochemistry determination

Bacillus sp. T-3040 CITase-T3040 by structural analysis of transglycosylation products using ¹H-NMR and ¹³C-NMR spectroscopy [9].

First catalytic nucleophile identification

Streptococcus mutans SmDex and Paenibacillus sp. PsDex by structural study [10] and chemical rescue approach [1], respectively.

First general acid/base residue identification

SmDex and PsDex by structural study [10] and chemical rescue approach [1], respectively.

First 3-D structure

Truncated mutant of SmDex [10].

References

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9. Oguma T, Horiuchi T, and Kobayashi M. Novel Cyclic Dextrins, Cycloisomaltooligosaccharides, from Bacillus sp. T-3040 Culture. Biosci Biotechnol Biochem. 1993 57(7):1225-1227. DOI:10.1271/bbb.57.1225