Glycoside Hydrolase Family 29

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• Author: Gerlind Sulzenbacher
• Responsible Curator: Steve Withers

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Glycoside Hydrolase Family GH 29
Clan	GH-R
Mechanism	retaining
Active site residues	known
CAZy DB link
https://www.cazy.org/GH29.html

Substrate specificities

The glycoside hydrolases of this family are exo-acting α-fucosidases from archaeal, bacterial and eukaryotic origin. No other activities have been observed for GH29 family members. So far the only other CAZY family containing α-fucosidases is family GH95. The human enzyme FucA1 is of medical interest because its deficiency leads to fucosidosis, an autosomal recessive lysosomal storage disease [1].

Kinetics and Mechanism

GH29 α-fucosidases are retaining enzymes following a classical Koshland double-displacement mechanism, as first proposed in 1987 for human liver α-fucosidase via burst kinetics experiments and using methanol as an alternative glycone acceptor to produce methyl α-L-fucoside [2]. This has been further confirmed by ¹H NMR monitoring of the reaction catalyzed by an α-L-fucosidase from Thermus sp. [3], and a α-L-fucosidase from the marine mollusc Pecten maximus [4], as well as by COSY and ¹H-¹³C NMR spectroscopy analysis of the interglycosidic linkage of disaccharides formed by the transglycosylase action of Sulfolobus solfataricus α-L-fucosidase, Ssα-fuc [5]. GH95 α-fucosidases, in contrast, operate with inversion of the anomeric configuration.

Catalytic Residues

The catalytic nucleophile in GH29 was first identified in the Sulfolobus solfataricus α-L-fucosidase, Ssα-fuc, as Asp242 in the sequence VYFDWWI via chemical rescue of an inactive mutant with sodium azide [6]. Concomitantly the catalytic nucleophile of Thermotoga maritima α-L-fucosidase, Tmα-fuc, was confirmed to be Asp224 in the sequence LWNDMGW through trapping of the 2-deoxy-2-fluorofucosyl-enzyme intermediate and subsequent peptide mapping via LC-MS/MS technologies, as well as by chemical rescue of an inactive mutant [7]. The trapping of the 2-deoxy-2-fluorofucosyl-enzyme intermediate in Tmα-fuc was corroborated by crystallographic studies [8]. The catalytic nucleophile of the human enzyme FucA1 has recently been identified as being Asp225 [9].

Whereas the catalytic nucleophile in GH29 has been shown to be a conserved aspartate residue, the identity of the general acid/base is still controversial. Structural and mutagenesis studies of Tmα-fuc provided strong evidence for the variant Glu266 being the general acid/base [8]. In the crystal structure the carboxyl function of this residue is 5.5 Å away from that of the catalytic nucleophile Asp224, a distance commonly observed in retaining glycosidases proceeding via a classical Koshland double-displacement mechanism. Although multiple sequence alignments show that Glu266 is not conserved within GH29, the residue is structurally conserved in two 3-D structures of α-L-fucosidases from Bacteroides thetaiotaomicron VPI-5482, recently deposited in the Protein Data Bank (PDB accession numbers 3eyp and 3gza). Studies of Ssα-fuc demonstrated that mutation of the Glu residue corresponding in sequence to Tmα-fuc Glu266 barely impaired the catalytic activity of the enzyme, whereas a Glu58Gly mutant had a 4000 fold lower k_cat/K_M and could be chemically rescued [10]. In the crystal structure of Tmα-fuc in complex with fucose [8], the residue corresponding to Ssα-fuc Glu58, Glu66, is found 7.5 Å away from the catalytic nucleophile Asp224 and hydrogen bonded to the C-3 hydroxyl group of fucose, which altogether makes this residue an unlikely candidate for the function of the general acid/base. A recent study of the human α-L-fucosidase FucA1, carefully done combining bioinformatics, structural modelling, mutagenesis, chemical rescue with azide and ¹H NMR spectral analysis, identified Glu289 as the general acid/base [9]. The equivalent residue in Tmα-fuc, Glu281, as inferred from sequence alignment of FucA1 and Tmα-fuc, points to the interior of the (β/α)₈ barrel and lies about 15 Å apart form the catalytic centre.

Altogether it appears that family GH29 is a quite exceptional CAZy family in that multiple sequence alignments do not allow an unambiguous assignment of the general acid/base.

Three-dimensional structures

The first crystal structure to be solved is that of the α-L-fucosidase from T. maritima, Tmα-fuc (PDB ID 1hl8). The simultaneous solution of the structures of an enzyme-product complex (PDB ID 1odu) and of a glycosyl-enzyme intermediate (PDB ID 1hl9) allowed the unambiguous identification of the general acid/base [8], as described above. Tmα-fuc assembles as a hexamer and displays a two-domain fold, composed of a catalytic (β/α)₈-like domain and a C-terminal β-sandwich domain. The two key active site residues are located at the C-terminal ends of strands β-strands 4 (nucleophile) and 6 (acid/base). Crystallization experiments for the S. solfataricus α-L-fucosidase, Ssα-fuc, were not very fruitful, but a small angle scattering study has been reported [11], which suggests a nonameric assembly of the enzyme in solution. Two crystal structures, arising from Structural Genomics initiatives, have been deposited in the Protein Data Bank for α-L-fucosidases from Bacteroides thetaiotaomicron VPI-5482, with accession numbers 3eyp and 3gza. The catalytic domain of Tmα-fuc does not adopt the canonical TIM-barrel (β/α)₈ fold, as it lacks helices α5 and α6. Helix α5 is also missing in the structure of one of the B. thetaiotaomicron VPI-5482 α-L-fucosidases, BT3798 (PDB ID 3gza), whereas α-L-fucosidase BT2192 (PDB ID 3eyp) from the same organism adopts the canonical TIM-barrel fold. The three structures differ furthermore by the insertion/deletion of a considerable number of additional α-helices, 3₁₀ helices, and extended surface loop regions. The closest structural homologues of GH29 enzymes within the CAZy classification can be found in GH107, which together with GH29 forms Clan GH-R. GH29 also bears some structural similarity to families GH13 (Clan GH-H) and GH27 (Clan GH-D).

Transglycosylation and Glycosynthases

Transglycosylation activity had been observed in 1987 for human liver α-fucosidase [2]. The first successful transformation of an α-fucosidase into an α-transfucosidase by directed evolution has been reported for Thermotoga maritima α-fucosidase [12]. α-Fucosidases mutated in the catalytic nucleophile from both Sulfolobus solfataricus and Thermotoga maritima were successfully transformed into a type of synthetic enzyme termed a 'glycosynthase', in this case a fucosynthase, which use β-L-fucopyranosyl azide as donor substrate [13]

Family Firsts

First stereochemistry determination

Retention of anomeric stereochemistry suggested for human liver α-fucosidase by the formation of methyl α-L-fucoside using methanol as an alternative glycone acceptor [2]. Later confirmed by ¹H NMR for α-L-fucosidase from Thermus sp. [3].

First catalytic nucleophile identification

Sulfolobus solfataricus α-L-fucosidase by azide rescue of an inactivated mutant [6] and confirmed shortly thereafter by labeling of the nucleophile and peptide mapping [7].

First general acid/base residue identification

Thermotoga maritima α-fucosidase by X-ray structural analysis and mutagenesis [8].

First 3-D structure

Thermotoga maritima α-fucosidase, free enzyme (PDB 1hl8), product complex (PDB 1odu) and glycosyl-enzyme intermediate (PDB 1hl9) [8].

References

1. O'Brien JS, Willems PJ, Fukushima H, de Wet JR, Darby JK, Di Cioccio R, Fowler ML, and Shows TB. (1987). Molecular biology of the alpha-L-fucosidase gene and fucosidosis. Enzyme. 1987;38(1-4):45-53. DOI:10.1159/000469189 |
2. White WJ Jr, Schray KJ, Legler G, and Alhadeff JA. (1987). Further studies on the catalytic mechanism of human liver alpha-L-fucosidase. Biochim Biophys Acta. 1987;912(1):132-8. DOI:10.1016/0167-4838(87)90256-1 |
3. Eneyskaya EV, Kulminskaya AA, Kalkkinen N, Nifantiev NE, Arbatskii NP, Saenko AI, Chepurnaya OV, Arutyunyan AV, Shabalin KA, and Neustroev KN. (2001). An alpha-L-fucosidase from Thermus sp. with unusually broad specificity. Glycoconj J. 2001;18(10):827-34. DOI:10.1023/a:1021163720282 |
4. Berteau O, McCort I, Goasdoué N, Tissot B, and Daniel R. (2002). Characterization of a new alpha-L-fucosidase isolated from the marine mollusk Pecten maximus that catalyzes the hydrolysis of alpha-L-fucose from algal fucoidan (Ascophyllum nodosum). Glycobiology. 2002;12(4):273-82. DOI:10.1093/glycob/12.4.273 |
5. Cobucci-Ponzano B, Trincone A, Giordano A, Rossi M, and Moracci M. (2003). Identification of an archaeal alpha-L-fucosidase encoded by an interrupted gene. Production of a functional enzyme by mutations mimicking programmed -1 frameshifting. J Biol Chem. 2003;278(17):14622-31. DOI:10.1074/jbc.M211834200 |
6. Cobucci-Ponzano B, Trincone A, Giordano A, Rossi M, and Moracci M. (2003). Identification of the catalytic nucleophile of the family 29 alpha-L-fucosidase from Sulfolobus solfataricus via chemical rescue of an inactive mutant. Biochemistry. 2003;42(32):9525-31. DOI:10.1021/bi035036t |
7. Tarling CA, He S, Sulzenbacher G, Bignon C, Bourne Y, Henrissat B, and Withers SG. (2003). Identification of the catalytic nucleophile of the family 29 alpha-L-fucosidase from Thermotoga maritima through trapping of a covalent glycosyl-enzyme intermediate and mutagenesis. J Biol Chem. 2003;278(48):47394-9. DOI:10.1074/jbc.M306610200 |
8. Sulzenbacher G, Bignon C, Nishimura T, Tarling CA, Withers SG, Henrissat B, and Bourne Y. (2004). Crystal structure of Thermotoga maritima alpha-L-fucosidase. Insights into the catalytic mechanism and the molecular basis for fucosidosis. J Biol Chem. 2004;279(13):13119-28. DOI:10.1074/jbc.M313783200 |
9. Liu SW, Chen CS, Chang SS, Mong KK, Lin CH, Chang CW, Tang CY, and Li YK. (2009). Identification of essential residues of human alpha-L-fucosidase and tests of its mechanism. Biochemistry. 2009;48(1):110-20. DOI:10.1021/bi801529t |
10. Cobucci-Ponzano B, Mazzone M, Rossi M, and Moracci M. (2005). Probing the catalytically essential residues of the alpha-L-fucosidase from the hyperthermophilic archaeon Sulfolobus solfataricus. Biochemistry. 2005;44(16):6331-42. DOI:10.1021/bi047495f |
11. Rosano C, Zuccotti S, Cobucci-Ponzano B, Mazzone M, Rossi M, Moracci M, Petoukhov MV, Svergun DI, and Bolognesi M. (2004). Structural characterization of the nonameric assembly of an Archaeal alpha-L-fucosidase by synchrotron small angle X-ray scattering. Biochem Biophys Res Commun. 2004;320(1):176-82. DOI:10.1016/j.bbrc.2004.05.149 |
12. Osanjo G, Dion M, Drone J, Solleux C, Tran V, Rabiller C, and Tellier C. (2007). Directed evolution of the alpha-L-fucosidase from Thermotoga maritima into an alpha-L-transfucosidase. Biochemistry. 2007;46(4):1022-33. DOI:10.1021/bi061444w |
13. Cobucci-Ponzano B, Conte F, Bedini E, Corsaro MM, Parrilli M, Sulzenbacher G, Lipski A, Dal Piaz F, Lepore L, Rossi M, and Moracci M. (2009). beta-Glycosyl azides as substrates for alpha-glycosynthases: preparation of efficient alpha-L-fucosynthases. Chem Biol. 2009;16(10):1097-108. DOI:10.1016/j.chembiol.2009.09.013 |