Glycoside Hydrolase Family 53

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• Author: ^^^Leila Lo Leggio^^^
• Responsible Curator: ^^^Leila Lo Leggio^^^

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

Substrate specificities

The only known specificity for this family is beta-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.

Kinetics and Mechanism

GH53 beta-1,4-galactanases follow a classical retaining mechanism as first demonstrated by following thestereochemical course of rection for the endo-beta-1,4-galactanase of the bacterium Cellvibrio japonicus (at that time referred to as Pseudomonas fluorescens subspecies cellulosa) (Braithwaite et al, 1997). Most characterized members have been reported to have an endo-mode of action, although processivity has been suggested in one case (Ref).

Catalytic Residues

The catalytic residues were first identified by Braithwaite et al,1997, for the endo-beta-1,4-galactanase of the bacterium Cellvibrio japonicus (at that time referred to as Pseudomonas fluorescens subspecies cellulosa). As expected for a member for clan GH-A, the two catalytic residues were, by a combination of mutagenesis and kinetic analysis, identified to be two glutamates, one acting as an acid-base (E161) and the other as a nucleophile (E270).

Three-dimensional structures

As for all members of Clan GH-A (ref), GH53 displays a (beta/alpha)8 barrel structure for the catalytic domain, usually with fairly compact loop structure (ref) and a size range... A disulphide bridging two loops in 3 known fungal structures, is replaced functionally by a calcium ion in one bacterial structure (refs). In most cases the catalytic domain is found in isolation, and not accompanied by accessory domains, but some exceptions exist (refs). For one bacterial member of the family ligand complexes with products have been obtained crystallographically, occupying subsites -4 to -2 and +1 to +2 (refs). Based on these crystal structures, binding of a galactononaose fragment has also been computationally modelled (ref).

Family Firsts

First sterochemistry determination

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

First catalytic nucleophile identification

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

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. 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 |

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

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.