Glycoside Hydrolase Family 67

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• Author: Harry Gilbert
• Responsible Curator: Harry Gilbert

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Glycoside Hydrolase Family GHnn
Clan	none
Mechanism	inverting
Active site residues	Proposed
CAZy DB link
https://www.cazy.org/GH67.html

Substrate specificities =

Glycoside hydrolases of this family display alpha-glucuronidase activity. The enzymes target the glucuronic acid appended to the C2-OH of the xylose at the non-reducing end of xylooligosaccharides. The enzymes display a preference for 4-O-methyl-D-glucuronic acid side chains. The length of the oligosaccharide does not influence catalytic rate indicating that the enzyme only interacts with the uronic acid and the linked xylose. These enzymes do not remove glucuronic acid from internal regions of xylan [1, 2]. The enzymes are generally intracellular or membrane associated [3, 4] suggesting that they play a terminal role in uncapping decorated xyloooligosaccharides, making these molecules available to beta-xylosidases produced by the host.

Kinetics and Mechanism

Alpha-glucuronidases are inverting enzymes that hydrolyse their target glycoside bond through a single displacement mechanism assisted by general acid and general base residues. Thus the glucuronic acid is formed in a beta configuration [5].

Catalytic Residues

Typical of inverting glycoside hydrolases, GH67 enzymes contain a general acid that protonates the scissile glycosidic oxygen promoting leaving group departure. This residue, Glu292 in the Cellvibrio japonicus GH67 [6] and Glu285 in the Geobacillus stearothermophilus GH67 enzymes [7] is a conserved glutamate within GH67. There are a pair of carboxylic acids that make hydrogen bonds with the catalytic water (attacks the anomeric carbon of the scissile glycosidic bond), and are predicted to activate the solvent molecule, thus acting as the general base. Which of these highly conserved residues, Glu393/Asp365 and Glu392/Asp364 in the C. japonicus and G. stearothermophilus enzymes, respectively, act as the general base is unclear. Mutational studies suggested that Asp365 in the C. japonicus enzyme may be the catalytic base [6], although similar mutagenesis studies on the Geobacillus glucuronidase indicate that mutation of either possible catalytic bases results in almost complete inactivation of the enzyme [8].

Three-dimensional structures

GH67 enzymes contain three distinct domains [9, 10]. The N-terminal domain forms a two-layer β sandwich, the central domain, the catalytic domain, is a classical (β/α)8 barrel whose catalytic center is located on the opposite, "C-terminal" side of the barrel to the N-terminal domain. The remaining, C-terminal domain is mainly α-helical. It wraps around the catalytic domain, making additional interactions both with the N-terminal domain of its parent monomer and also forming the majority of the dimer-surface with the equivalent C-terminal domain of the other monomer of the dimer. The active site comprises a deep, partially hydrophobic, pocket.

Family Firsts

First sterochemistry determination

¹H NMR demonstrated that the released 4-methyl-D-glucuronic acid was a beta anomer and thus that the enzyme is an inverter [11].

First general base residue identification

The general base was suggested by mutagenesis studies only and there remains two potential candidates [12]

First general acid residue identification

The general acid residue was suggested by mutagenesis studies [12]

First 3-D structure

Two reports on the crystal structure of GH67 glucuronidases were published within 18 months of each other [9, 10]

References

1. Ruile P, Winterhalter C, and Liebl W. (1997). Isolation and analysis of a gene encoding alpha-glucuronidase, an enzyme with a novel primary structure involved in the breakdown of xylan. Mol Microbiol. 1997;23(2):267-79. DOI:10.1046/j.1365-2958.1997.2011568.x |
2. Bronnenmeier K, Meissner H, Stocker S, and Staudenbauer WL. (1995). alpha-D-glucuronidases from the xylanolytic thermophiles Clostridium stercorarium and Thermoanaerobacterium saccharolyticum. Microbiology (Reading). 1995;141 ( Pt 9):2033-40. DOI:10.1099/13500872-141-9-2033 |
3. Shulami S, Gat O, Sonenshein AL, and Shoham Y. (1999). The glucuronic acid utilization gene cluster from Bacillus stearothermophilus T-6. J Bacteriol. 1999;181(12):3695-704. DOI:10.1128/JB.181.12.3695-3704.1999 |
4. Nagy T, Emami K, Fontes CM, Ferreira LM, Humphry DR, and Gilbert HJ. (2002). The membrane-bound alpha-glucuronidase from Pseudomonas cellulosa hydrolyzes 4-O-methyl-D-glucuronoxylooligosaccharides but not 4-O-methyl-D-glucuronoxylan. J Bacteriol. 2002;184(17):4925-9. DOI:10.1128/JB.184.17.4925-4929.2002 |
5. Biely P, de Vries RP, Vrsanská M, and Visser J. (2000). Inverting character of alpha-glucuronidase A from Aspergillus tubingensis. Biochim Biophys Acta. 2000;1474(3):360-4. DOI:10.1016/s0304-4165(00)00029-5 |
6. Nurizzo D, Nagy T, Gilbert HJ, and Davies GJ. (2002). The structural basis for catalysis and specificity of the Pseudomonas cellulosa alpha-glucuronidase, GlcA67A. Structure. 2002;10(4):547-56. DOI:10.1016/s0969-2126(02)00742-6 |
7. Golan G, Shallom D, Teplitsky A, Zaide G, Shulami S, Baasov T, Stojanoff V, Thompson A, Shoham Y, and Shoham G. (2004). Crystal structures of Geobacillus stearothermophilus alpha-glucuronidase complexed with its substrate and products: mechanistic implications. J Biol Chem. 2004;279(4):3014-24. DOI:10.1074/jbc.M310098200 |
8. Zaide G, Shallom D, Shulami S, Zolotnitsky G, Golan G, Baasov T, Shoham G, and Shoham Y. (2001). Biochemical characterization and identification of catalytic residues in alpha-glucuronidase from Bacillus stearothermophilus T-6. Eur J Biochem. 2001;268(10):3006-16. DOI:10.1046/j.1432-1327.2001.02193.x |