Glycoside Hydrolase Family 86

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• Author: Mirjam Czjzek
• Responsible Curator: Mirjam Czjzek

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Glycoside Hydrolase Family GH86
Clan	GH-A
Mechanism	probably retaining
Active site residues	inferred from clan GH-A as two Glu
CAZy DB link
https://www.cazy.org/GH86.html

Substrate specificities

Glycoside hydrolases of family 86 have first been identified to be β-agarases (EC 3.2.1.81) that cleave β-1,4 glycosidic bonds of agarose. This polysaccharide chain is ideally made of alternating 1,3-linked β-D-galactose (G) and 1,4-linked 3,6-anhydro-α-L-galactose (LA) residues forming a parallel double helix. Four agarolytic enzymes have been characterized: AgrA from Pseudoalteromonas atlantica, AgaO from Microbulbifer thermotolerans JAMB-A94, Aga86E from Saccharophagus degradans 2-40 [1, 2, 3] and more recently a GH86 β-agarase from a non marine Vibrio species (sp. OA-2007)[4]. AgaO from M. thermotolerans was reported to be an endo-hydrolytic enzyme, releasing neoagaro-hexaose as main product [2], while the recombinant Aga86E from S. degradans released only neoagarobiose in an exo-acting manner [3]. In june 2012, a first GH86 enzyme was identified in the human gut Bacteroidetes B. plebeius that was active on porphyran, an agarocolloïd in which the 3,6-anhydro-L-galactose unit (LA) of neutral agarose is replaced by L-galactose-6-sulfate (L6S). The endo-acting enzyme, BpGH86A, is inactive on agarose and the main products released by cleavage of β-1,4 glycosidic bonds of porphyran, are tetrasaccharides having the sequence L6S-G-L6S-G∼ [5].

Kinetics and Mechanism

A potential retaining mechanism of this glycoside hydrolase family can be inferred from analogy to clan GH-A enzymes, and is confirmed by structural analyses of a product complex showing an arrangement of the putative catalytic residues that is in agreement with the double displacement mechanism [5]. However, no mechanistic or kinetic analysis demonstrating the stereochemical outcome of the reaction have been reported for this family to date.

Catalytic Residues

The catalytic residues can be inferred from the crystal structure and by analogy to clan GH-A enzymes as two glutamate residues, which are Glu152 (acid/base) and Glu279 (nucleophile) in BpGH86A from B. plebeius [5].

Three-dimensional structures

The first 3D structure was determined in 2012 by [5] et al. In agreement with distant sequence homology to clan GH-A enzymes, the overall topology contains an N-terminal (β/α)₈ barrel. However the enzyme architecture is more complex and contains two additional Cterminal β-sandwich domains, which align via their convex faces to the exterior of the (β/α)₈ barrel and connect with two N-terminal β-strands that become part of these C-terminal β-sandwich domains.

Family Firsts

Identification of first family member

The first member of this family, AgrA, was identified in Pseudoalteromonas atlantica [1].

First stereochemistry determination

the retaining mechanism is inferred from the arrangement of the most probable catalytic residues in the crystal structure of a product complex [5].

First catalytic nucleophile identification

Glu279 in BpGH86A from B.plebeius.

First general acid/base residue identification

Glu152 in BpGH86A from B.plebeius.

First 3-D structure

The crystal structure of BpGH86A from B.plebeius, (PDB 4aw7).

References

1. Belas R (1989). Sequence analysis of the agrA gene encoding beta-agarase from Pseudomonas atlantica. J Bacteriol. 1989;171(1):602-5. DOI:10.1128/jb.171.1.602-605.1989 |
2. Ohta Y, Hatada Y, Nogi Y, Li Z, Ito S, and Horikoshi K. (2004). Cloning, expression, and characterization of a glycoside hydrolase family 86 beta-agarase from a deep-sea Microbulbifer-like isolate. Appl Microbiol Biotechnol. 2004;66(3):266-75. DOI:10.1007/s00253-004-1757-5 |
3. Ekborg NA, Taylor LE, Longmire AG, Henrissat B, Weiner RM, and Hutcheson SW. (2006). Genomic and proteomic analyses of the agarolytic system expressed by Saccharophagus degradans 2-40. Appl Environ Microbiol. 2006;72(5):3396-405. DOI:10.1128/AEM.72.5.3396-3405.2006 |
4. Ariga O, Inoue T, Kubo H, Minami K, Nakamura M, Iwai M, Moriyama H, Yanagisawa M, and Nakasaki K. (2012). Cloning of agarase gene from non-marine agarolytic bacterium Cellvibrio sp. J Microbiol Biotechnol. 2012;22(9):1237-44. DOI:10.4014/jmb.1202.02020 |
5. Hehemann JH, Kelly AG, Pudlo NA, Martens EC, and Boraston AB. (2012). Bacteria of the human gut microbiome catabolize red seaweed glycans with carbohydrate-active enzyme updates from extrinsic microbes. Proc Natl Acad Sci U S A. 2012;109(48):19786-91. DOI:10.1073/pnas.1211002109 |