Glycoside Hydrolase Family 53

This page has been approved by the Responsible Curator as essentially complete. CAZypedia is a living document, so further improvement of this page is still possible. If you would like to suggest an addition or correction, please contact the page's Responsible Curator directly by e-mail.

Glycoside Hydrolase Family GH53
Clan	GH-A
Mechanism	retaining
Active site residues	known
CAZy DB link
https://www.cazy.org/GH53.html

Function and Substrate specificities

The only known specificity for glycoside hydrolases of this family is β-1,4-galactanase (EC 3.2.1.89) and the only reported function is the microbial degradation of galactans and arabinogalactans in the pectic component of plant cell walls. A number of patents on industrial applications of GH53 have been filed. In a number of bacteria, GH53 β-1,4-galactanases genes have been found as part of gene clusters devoted to galactan utilization and additionally comprising genes encoding for a GH42 β-1,4-galactosidase, a galactooligosaccharide transport system and a transcriptional regulator.

Kinetics and Mechanism

GH53 β-1,4-galactanases follow a retaining mechanism as first demonstrated by following the stereochemical course of rection for the endo-β-1,4-galactanase of the bacterium Cellvibrio japonicus (at that time referred to as Pseudomonas fluorescens subspecies cellulosa) [1]. Most characterized members have been reported to be endo-acting, although processivity has been suggested in one case [2].

Catalytic Residues

The catalytic residues were first identified for the endo-β-1,4-galactanase of the bacterium Cellvibrio japonicus [1] (previously known as Pseudomonas fluorescens subspecies cellulosa). Prior to structure determination Henrissat used hydrophobic cluster analysis and sequence alignments to predict that the family belonged to clan GH-A, and the two proposed catalytic residues, which were confirmed by a combination of mutagenesis and kinetic analysis; one acting as a general acid/base (E161) and the other as a catalytic nucleophile (E270).

Three-dimensional structures

As for all members of Clan GH-A [3, 4], structurally characterized GH53 enzymes [5, 6, 7] display a (β/α)₈ barrel structure for the catalytic domain, usually with fairly compact loop structure and a sequence under 400 residues in length. The catalytic residues are typically positioned at the C-terminal ends of βstrands 4 and 7 in the barrel. Somewhat unusually, none of the four structurally characterized GH53 catalytic domains was accompanied by other catalytic domains or accessory modules, but modularity can be inferred by sequence in other members of the family. A disulphide bridging two loops (β/α loops 7 and 8) in 3 known fungal structures [5, 6], is replaced functionally by a calcium ion in one bacterial structure [7]. For one bacterial member of the family ligand complexes with products have been obtained crystallographically, occupying subsites -4 to -2 and +1 to +2 [7, 8]. Based on these crystal structures, binding of a galactononaose fragment has also been computationally modelled [8].

Family Firsts

First stereochemistry determination: Cellvibrio japonicus endo-β-1,4-galactanase [1].
First catalytic nucleophile identification: Cellvibrio japonicus endo-β-1,4-galactanase [1].
First general acid/base residue identification: Cellvibrio japonicus endo-β-1,4-galactanase [1].
First 3-D structure: Aspergillus aculeatus endo-β-1,4-galactanase [5].

References

All Medline abstracts: PubMed