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Glycoside Hydrolase Family 93

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Glycoside Hydrolase Family GH93
Clan GH-E
Mechanism retaining
Active site residues known
CAZy DB link

Substrate specificities

The characterized glycoside hydrolases of family GH93 are known to hydrolyse linear α-1,5-L-arabinan. [1, 2], EC:3.2.1-.

Kinetics and Mechanism

GH93 enzymes are exo-acting enzymes that only release arabinobiose from the non-reducing end of α-1,5-L-arabinan. These enzymes are proposed to be retaining enzymes based on the net retention of the configuration of the anomeric carbon is proposed from the products of the transglycosylation activity of the protein Abnx from Penicillium chrysogenum [3]. This proposal obtained support from the crystal structures of the Arb93A enzyme from Fusarium graminearum and Abnx both in complex with arabinobiose [2, 4]. α-L-Arabinofuranosylated pyrrolidines were shown to be good inhibitors of Arb93A. The Arb93A complex structure with a deoxyiminosugar equivalent of arabinobiose revealed a 4TN twist conformation expected for the Michaelis complex, as seen for several retaining GH51 α-L-arabinofuranosidases. [5]

Catalytic Residues

From the crystal structure of Arb93A, Glu170 and Glu242 are proposed to act as catalytic nucleophile and general acid/base respectively. Mutagenesis experiment support their role in catalysis and they are strictly conserved among the family members. [2] Recent structures and mutagenesis studies for the arabinanase Abnx from Penicillium chrysogenum 31B strengthened this assignment. Mutations to alanine or glutamine of their equivalent Glu174 and Glu246 lead to inactive enzyme. [4]

Three-dimensional structures

The crystal structure of Arb93A reveals a six-bladed β-propeller fold characteristic of sialidases of clan GH-E. [2, 4], The catalytic machinery is however very different from that of sialidases. [6]

Arb93A inhibitor

Family Firsts

First sterochemistry determination

This was determined with the Penicillium chrysogenum Abxn enzyme using 1H-NMR to identify the transglycosylation products [3]

First catalytic nucleophile identification This was proposed based on the structure of Fusarium graminearum Arb93A [2]

First general acid/base residue identification This was proposed based on the structure of Fusarium graminearum Arb93A [2]

First 3-D structure Determined for Fusarium graminearum Arb93A by Carapito and co-workers [2]


  1. Sakamoto T and Thibault JF. (2001) Exo-arabinanase of Penicillium chrysogenum able to release arabinobiose from alpha-1,5-L-arabinan. Appl Environ Microbiol. 67, 3319-21. DOI:10.1128/AEM.67.7.3319-3321.2001 | PubMed ID:11425761 | HubMed [Sakamoto2001]
  2. Carapito R, Imberty A, Jeltsch JM, Byrns SC, Tam PH, Lowary TL, Varrot A, and Phalip V. (2009) Molecular basis of arabinobio-hydrolase activity in phytopathogenic fungi: crystal structure and catalytic mechanism of Fusarium graminearum GH93 exo-alpha-L-arabinanase. J Biol Chem. 284, 12285-96. DOI:10.1074/jbc.M900439200 | PubMed ID:19269961 | HubMed [Carapito2009]
  3. Sakamoto T, Fujita T, and Kawasaki H. (2004) Transglycosylation catalyzed by a Penicillium chrysogenum exo-1,5-alpha-L-arabinanase. Biochim Biophys Acta. 1674, 85-90. DOI:10.1016/j.bbagen.2004.06.001 | PubMed ID:15342117 | HubMed [Sakamoto2004]
  4. Sogabe Y, Kitatani T, Yamaguchi A, Kinoshita T, Adachi H, Takano K, Inoue T, Mori Y, Matsumura H, Sakamoto T, and Tada T. (2011) High-resolution structure of exo-arabinanase from Penicillium chrysogenum. Acta Crystallogr D Biol Crystallogr. 67, 415-22. DOI:10.1107/S0907444911006299 | PubMed ID:21543843 | HubMed [Sogabe2011]
  5. Goddard-Borger ED, Carapito R, Jeltsch JM, Phalip V, Stick RV, Varrot A. α-L-Arabinofuranosylated pyrrolidines as arabinanase inhibitors. Chem Commun 2011 Sep 14;47(34):9684-9686.
    Note: Due to a problem with PubMed data, this reference is not automatically formatted. Please see these links out: DOI:10.1039/C1CC13675E PMID: 21773614
  6. Gaskell A, Crennell S, and Taylor G. (1995) The three domains of a bacterial sialidase: a beta-propeller, an immunoglobulin module and a galactose-binding jelly-roll. Structure. 3, 1197-205. PubMed ID:8591030 | HubMed [Gaskell1995]
All Medline abstracts: PubMed | HubMed