Glycoside Hydrolase Family 51

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• Author: ^^^Yuval Shoham^^^
• Responsible Curator: ^^^Yuval Shoham^^^

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Glycoside Hydrolase Family GH51
Clan	GH-A
Mechanism	retaining
Active site residues	known
CAZy DB link
http://www.cazy.org/fam/GH51.html

Substrate specificities

The majority of the enzymes from this family hydrolyze the glycosidic bond between L-arabinofuranosides side chains of hemicelluloses such as arabinoxylan, arabinogalactan, and L-arabinan. A few enzymes of the family exhibit beta 1-4 endoglucanase activity towards carboxy methyl cellulose and xylan [1].

This is an example of how to make references to a journal article [2]. (See the References section below). Multiple references can go in the same place like this [2, 3]. You can even cite books using just the ISBN [4]. References that are not in PubMed can be typed in by hand [5].

Kinetics and Mechanism

Family GH51 L-arabinfuranosidases are retaining enzymes and follow a classical Koshland double-displacement mechanism. Due to the fast mutarotation and tautomerization rates of arabinose, the stereochemical course of the reaction was determined in presence of methanol and followed by NMR spectroscopy [6, 7, 8]. Enzymes that have been well studied kinetically include the Geobacillus stearothermophilus T-6 and Thermobacillus xylanilyticus alpha L-arabinofuranosidases, for which a detailed kinetic study was performed including kinetics with aryl-α-L-arabinofuranosides bearing various leaving groups, Brønsted plots for the E175A acid-base catalytic residue and azide-rescue for the E294A nucleophilc mutant [7, 8, 9].

Catalytic Residues

The catalytic acid-base was first identified in Thermobacillus xylanilyticus (Glu176) [7] and in Geobacillus stearothermophilus T-6 (Glu175) alpha-arabinofuranosidases [8] using kinetic analysis, pH dependence profiles, and azide rescue of the catalytic mutant. The catalytic nucleophile was first identified in Geobacillus stearothermophilus alpha-arabinofuranosidase through detailed kinetic studies for the catalytic mutant including azide rescue.

Three-dimensional structures

Three-dimensional structures for GH51 arabinofuranosidases are available for G. stearothermophilus [10] C. thermocellum [11] and Thermobacillus xylanilyticus [12]. The enzyme in solution is a hexamer (can be described as a trimer of dimmers) and each monomer is organized into two domains: a ‘clan GH-A’ catalytic (β/α)8 domain and a 12-stranded beta sandwich with a jelly-roll topology.

Family Firsts

First sterochemistry determination

Cite some reference here, with a short (1-2 sentence) explanation [2].

First catalytic nucleophile identification

Cite some reference here, with a short (1-2 sentence) explanation [5].

First general acid/base residue identification

Cite some reference here, with a short (1-2 sentence) explanation [3].

First 3-D structure

Cite some reference here, with a short (1-2 sentence) explanation [4].

References

1. Eckert K and Schneider E. (2003). A thermoacidophilic endoglucanase (CelB) from Alicyclobacillus acidocaldarius displays high sequence similarity to arabinofuranosidases belonging to family 51 of glycoside hydrolases. Eur J Biochem. 2003;270(17):3593-602. DOI:10.1046/j.1432-1033.2003.03744.x |
2. 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 |
3. 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 |
4. Robert V. Stick and Spencer J. Williams. (2009) Carbohydrates. Elsevier Science.

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

6. Pitson SM, Voragen AG, and Beldman G. (1996). Stereochemical course of hydrolysis catalyzed by arabinofuranosyl hydrolases. FEBS Lett. 1996;398(1):7-11. DOI:10.1016/s0014-5793(96)01153-2 |
7. Debeche T, Bliard C, Debeire P, and O'Donohue MJ. (2002). Probing the catalytically essential residues of the alpha-L-arabinofuranosidase from Thermobacillus xylanilyticus. Protein Eng. 2002;15(1):21-8. DOI:10.1093/protein/15.1.21 |
8. Shallom D, Belakhov V, Solomon D, Gilead-Gropper S, Baasov T, Shoham G, and Shoham Y. (2002). The identification of the acid-base catalyst of alpha-arabinofuranosidase from Geobacillus stearothermophilus T-6, a family 51 glycoside hydrolase. FEBS Lett. 2002;514(2-3):163-7. DOI:10.1016/s0014-5793(02)02343-8 |
9. Shallom D, Belakhov V, Solomon D, Shoham G, Baasov T, and Shoham Y. (2002). Detailed kinetic analysis and identification of the nucleophile in alpha-L-arabinofuranosidase from Geobacillus stearothermophilus T-6, a family 51 glycoside hydrolase. J Biol Chem. 2002;277(46):43667-73. DOI:10.1074/jbc.M208285200 |
10. Hövel K, Shallom D, Niefind K, Belakhov V, Shoham G, Baasov T, Shoham Y, and Schomburg D. (2003). Crystal structure and snapshots along the reaction pathway of a family 51 alpha-L-arabinofuranosidase. EMBO J. 2003;22(19):4922-32. DOI:10.1093/emboj/cdg494 |
11. Taylor EJ, Smith NL, Turkenburg JP, D'Souza S, Gilbert HJ, and Davies GJ. (2006). Structural insight into the ligand specificity of a thermostable family 51 arabinofuranosidase, Araf51, from Clostridium thermocellum. Biochem J. 2006;395(1):31-7. DOI:10.1042/BJ20051780 |
12. Paës G, Skov LK, O'Donohue MJ, Rémond C, Kastrup JS, Gajhede M, and Mirza O. (2008). The structure of the complex between a branched pentasaccharide and Thermobacillus xylanilyticus GH-51 arabinofuranosidase reveals xylan-binding determinants and induced fit. Biochemistry. 2008;47(28):7441-51. DOI:10.1021/bi800424e |