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• Author: Annabelle Varrot
• Responsible Curator: Annabelle Varrot

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 recent support from the crystal structure of the Arb93A enzyme from Fusarium graminearum in complex with arabinobiose, the degradation product of alpha-methyl-arabinotetraose. [2]

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]

Three-dimensional structures

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

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]

References

1. Sakamoto T and Thibault JF. Exo-arabinanase of Penicillium chrysogenum able to release arabinobiose from alpha-1,5-L-arabinan. Appl Environ Microbiol 2001 Jul; 67(7) 3319-21. doi:10.1128/AEM.67.7.3319-3321.2001 pmid:11425761. PubMed HubMed [1]
2. Carapito R, Imberty A, Jeltsch JM, Byrns SC, Tam PH, Lowary TL, Varrot A, and Phalip V. 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 2009 May 1; 284(18) 12285-96. doi:10.1074/jbc.M900439200 pmid:19269961. PubMed HubMed [2]
3. Sakamoto T, Fujita T, and Kawasaki H. Transglycosylation catalyzed by a Penicillium chrysogenum exo-1,5-alpha-L-arabinanase. Biochim Biophys Acta 2004 Sep 6; 1674(1) 85-90. doi:10.1016/j.bbagen.2004.06.001 pmid:15342117. PubMed HubMed [3]
4. Gaskell A, Crennell S, and Taylor G. The three domains of a bacterial sialidase: a beta-propeller, an immunoglobulin module and a galactose-binding jelly-roll. Structure 1995 Nov 15; 3(11) 1197-205. pmid:8591030. PubMed HubMed [4]