Glycoside Hydrolase Family 84

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• Author: ^^^Ian Greig^^^
• Responsible Curator: ^^^David Vocadlo^^^

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Glycoside Hydrolase Family GH84
Clan	none
Mechanism	retaining
Active site residues	known
CAZy DB link
http://www.cazy.org/GH84.html

Substrate specificities

GH84 contains β-N-acetylglucosaminidases and β-N-acetylhyaluronidase activities. Human O-GlcNAcase is a nucleocytoplasmic enzyme whose in vivo targets are glycoprotein serine and threonine residues modified by a single β-linked GlcNAc residue. In contrast to the β-hexosaminidases of GH20 a relaxed specificity for substitutions of the N-acyl group is observed with residues significantly more bulky than the N-acyl group being tolerated.[1]

Kinetics and Mechanism

Members of GH84 utilize a mechanism of neighbouring group participation, this originally being established through the use of free-energy relationship-based studies of human O-GlNAcase.[1] More recent studies of this enzyme have investigated variations in rates of reaction (V/K) with both nucleophile and leaving group structures.[2] For substrates possessing the naturally-occurring acetyl nucleophile a pre-chemical step is rate-determining on V/K for leaving groups with a pK_a below 11 (with the chemical step rate-determining for substrates with higher pK_a values). Studies of substrates possessing fluoroacetyl nucleophiles highlighted that a dissociative (D_N*A_N) mechanism involving general acid catalysis operates for the hydrolysis of substrates possessing leaving groups with a pK_a greater than approximately 7; a concerted (A_ND_N) mechanism, not employing general acid catalysis was found for substrates possessing leaving groups with lower pK_as (consistent with prior studies of S-glucosaminide hydrolysis[3]). Substrate distortion.[2, 4] A truncated, nuclear-localized isoform of human O-GlcNAcase lacking the putative C-terminal histone acetyl transferase domain retains similar kinetic properties and inhibitory patterns as the full-length cytosolic isoform and is consistent with hexosaminidase activity residing in the N-terminal domain.[5]

Catalytic Residues

Studies of two mutants of human O-GlcNAcase established that adjacent aspartate residues, Asp174 and Asp175, act as critical components of the catalytic machinery of this enzyme.[6]

The mutant Asp175Ala displayed marked reductions in activity (V and (V/K)) towards aryl N-acetylglucosaminides possessing poor leaving groups with smaller reductions being observed for both O-aryl and S-aryl N-acetylglucosaminides substrates possessing better leaving groups. Exogenous azide was found to partially rescue the activity of human O-GlcNAcase towards 3,4-dinitrophenylglucosaminide. These results identify Asp175 as the general acid catalyst.

The mutant Asp174Ala showed decreased activity towards O-aryl N-acetylglucosaminides possessing good leaving groups and it was argued that this is consistent with its role as a residue responsible for the orientation and polarization of the N-acyl nucleophile.

Three-dimensional structures

The reported crystallization of Clostridium perfringens NagJ[7] was followed by solved structures for that enzyme[8] and Bacteroides thetaiotaomicron β-hexosaminidase[8]. In common with the chitinases of family GH18 and the exo-acting β-hexosaminidases of GH20 the catalytic domain is a (βα)₈-barrel structure. The structure of human O-GlcNAcase has not been solved but Bacteroides thetaiotaomicron β-hexosaminidase was originally reported as a good structural mimic of both the active site and catalytic domain of human O-GlcNAcase. More recently the structure of the GH84 β-hexosaminidase from Oceanicola granulosus has been solved and shown to possess an improved sequence identity with the catalytic domain of the human enzyme.[9] Furthermore, the C-terminal domain of this protein also displays notable sequence identity with the spacer domain (separating the domains possessing O-GlcNAcase and histone acetyltransferase activities) of the human enzyme.

Defining the conformational itinerary of a GH84 enzyme. Azepane (i) binds with a boat-like conformation to Bacteroides thetaiotaomicron β-hexosaminidase (BtOG). This binding mode is confirmed by the structure of a bound substrate (ii). Thiazoline (iii) binds to wild-type BtOG, 5-fluoro-oxazoline (iv) binds to the Asp243Asn mutant of BtOG, and oxazoline (v) binds to the Asp242Asn mutant of BtOG in the ⁴C₁ conformation.

A series of crystallographic studies on Bacteroides thetaiotaomicron β-hexosaminidase have used a variety of small molecules to define define the conformational itinerary for this family of enzymes. Substrate distortion from the ⁴C₁ conformation found in solution to a bound ^1,4B / ¹S₃ conformation was supported by the crystal structure of the wild-type enzyme in complex with the 7-membered azepane. [10] This distortion was confirmed by the structure the wild-type enzyme in complex with the substrate, 3,4-difluorophenyl 2-deoxy-2-difluoroacetamido-β-D-glucopyranoside.[11] Earlier studies of the wild-type-bound thiazoline show that this intermediate is found in a ⁴C₁conformation.[1] Subsequent studies have shown that oxazoline intermediates are bound to the mutant enzymes in this conformation.[11].

Family Firsts

First sterochemistry determination

¹H-NMR studies of human O-GlcNAcase established that the β-configured hemiacetal product is formed prior to anomerisation.[2].

First catalytic nucleophile identification

This family of enzymes uses a mechanism of neighbouring group participation, which was first establishes through the use of free energy relationships studies.[1].

First general acid/base residue identification

Studies of human O-GlcNAcase mutant Asp175Ala identify reactivity patterns (free energy relationships, pH-activity profiles) consistent with the action of Asp175 as the catalytic general acid/base.[6].

First 3-D structure

The structures of Bacteroides thetaiotaomicron O-GlcNAcase[12] and Clostridium perfringens NagJ[8].

References

1. Macauley MS, Whitworth GE, Debowski AW, Chin D, and Vocadlo DJ. (2005). O-GlcNAcase uses substrate-assisted catalysis: kinetic analysis and development of highly selective mechanism-inspired inhibitors. J Biol Chem. 2005;280(27):25313-22. DOI:10.1074/jbc.M413819200 |
2. Greig IR, Macauley MS, Williams IH, and Vocadlo DJ. (2009). Probing synergy between two catalytic strategies in the glycoside hydrolase O-GlcNAcase using multiple linear free energy relationships. J Am Chem Soc. 2009;131(37):13415-22. DOI:10.1021/ja904506u |
3. Macauley MS, Stubbs KA, and Vocadlo DJ. (2005). O-GlcNAcase catalyzes cleavage of thioglycosides without general acid catalysis. J Am Chem Soc. 2005;127(49):17202-3. DOI:10.1021/ja0567687 |
4. He Y, Macauley MS, Stubbs KA, Vocadlo DJ, and Davies GJ. (2010). Visualizing the reaction coordinate of an O-GlcNAc hydrolase. J Am Chem Soc. 2010;132(6):1807-9. DOI:10.1021/ja9086769 |
5. Macauley MS and Vocadlo DJ. (2009). Enzymatic characterization and inhibition of the nuclear variant of human O-GlcNAcase. Carbohydr Res. 2009;344(9):1079-84. DOI:10.1016/j.carres.2009.04.017 |

6. Cetinbaş N, Macauley MS, Stubbs KA, Drapala R, Vocadlo DJ. Identification of Asp174 and Asp175 as the key catalytic residues of human O-GlcNAcase by functional analysis of site-directed mutants. Biochemistry. 2006 Mar 21;45(11):3835-44.

   Note: Due to a problem with PubMed data, this reference is not automatically formatted. Please see these links out: DOI:10.1021/bi052370b PMID:16533067

7. Ficko-Blean E and Boraston AB. (2005). Cloning, recombinant production, crystallization and preliminary X-ray diffraction studies of a family 84 glycoside hydrolase from Clostridium perfringens. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2005;61(Pt 9):834-6. DOI:10.1107/S1744309105024012 |
8. Rao FV, Dorfmueller HC, Villa F, Allwood M, Eggleston IM, and van Aalten DM. (2006). Structural insights into the mechanism and inhibition of eukaryotic O-GlcNAc hydrolysis. EMBO J. 2006;25(7):1569-78. DOI:10.1038/sj.emboj.7601026 |
8. Schimpl M, Schüttelkopf AW, Borodkin VS, and van Aalten DM. (2010). Human OGA binds substrates in a conserved peptide recognition groove. Biochem J. 2010;432(1):1-7. DOI:10.1042/BJ20101338 |
10. Marcelo F, He Y, Yuzwa SA, Nieto L, Jiménez-Barbero J, Sollogoub M, Vocadlo DJ, Davies GD, and Blériot Y. (2009). Molecular basis for inhibition of GH84 glycoside hydrolases by substituted azepanes: conformational flexibility enables probing of substrate distortion. J Am Chem Soc. 2009;131(15):5390-2. DOI:10.1021/ja809776r |
11. He Y, Macauley MS, Stubbs KA, Vocadlo DJ, and Davies GJ. (2010). Visualizing the reaction coordinate of an O-GlcNAc hydrolase. J Am Chem Soc. 2010;132(6):1807-9. DOI:10.1021/ja9086769 |
12. Dennis RJ, Taylor EJ, Macauley MS, Stubbs KA, Turkenburg JP, Hart SJ, Black GN, Vocadlo DJ, and Davies GJ. (2006). Structure and mechanism of a bacterial beta-glucosaminidase having O-GlcNAcase activity. Nat Struct Mol Biol. 2006;13(4):365-71. DOI:10.1038/nsmb1079 |
13. Comfort DA, Bobrov KS, Ivanen DR, Shabalin KA, Harris JM, Kulminskaya AA, Brumer H, and Kelly RM. (2007). Biochemical analysis of Thermotoga maritima GH36 alpha-galactosidase (TmGalA) confirms the mechanistic commonality of clan GH-D glycoside hydrolases. Biochemistry. 2007;46(11):3319-30. DOI:10.1021/bi061521n |
14. He S and Withers SG. (1997). Assignment of sweet almond beta-glucosidase as a family 1 glycosidase and identification of its active site nucleophile. J Biol Chem. 1997;272(40):24864-7. DOI:10.1074/jbc.272.40.24864 |

16. Sinnott, M.L. (1990) Catalytic mechanisms of enzymic glycosyl transfer. Chem. Rev. 90, 1171-1202. DOI: 10.1021/cr00105a006