Glycoside Hydrolase Family 2

• Author: Stephen Withers
• Responsible Editor: Stephen Withers

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Glycoside Hydrolase Family GH2
Clan	GH-A
Mechanism	retaining
Active site residues	known
CAZy DB link
http://www.cazy.org/fam/GH2.html

Substrate specificities

This family contains beta-galactosidases, beta-glucuronidases, beta-mannosidases, exo-beta-glucosaminidases and, in plants, a mannosylglycoprotein endo-beta-mannosidase. The enzymes are found across a broad spectrum of life forms, but are concentrated in bacteria. The most famous enzyme in this family is the E. coli (lacZ) beta-galactosidase of lac operon fame. Not only did this enzyme play a key role in developing the understanding of operon structure and control of gene expression, but also it continues to play a key role as a cell biological probe. Another matter of note is that this remains the largest protein monomer to be sequenced entirely at the peptide level [1]. E. coli also contains a second, vestigial beta-galactosidase (ebg) whose activity has been shown to evolve in lacZ^- strains of E. coli grown under selective pressure with lactose as sole carbon source [2]. Another reasonably well-studied GH2 enzyme is the E. coli beta-glucuronidase, whose activity is used to detect the presence of E. coli (http://www.cfsan.fda.gov/~ebam/bam-4.html), though interestingly not the nasty 0157 strain. The principal enzyme of medical interest in GH2 is the lysosomal beta-glucuronidase whose deficiency leads to Sly syndrome [3]. The only other human GH2 enzyme is the lysosomal beta-mannosidase.

Kinetics and Mechanism

Family 1 beta-glycosidases are retaining enzymes, as first shown by XXXXX [4] and follow a classical Koshland double-displacement mechanism. The best studied enzyme kinetically must be the E. coli (lacZ) beta-galactosidase, for which a key set of studies defining the two- step mechanism and elucidating rate-limiting steps was published by the groups of Yon and Sinnott in the early 1970’s [5], [6], [7]. Indeed the approaches developed on that system laid the foundations for many subsequent studies on other glycosidases. An analysis of the roles of each substrate hydroxyl in catalysis, based upon kinetic studies with modified sugars has also been published [8]. Some GH2 glycosidases require Mg2+ for activity and in E. coli beta-galactosidase this Mg2+ requirement is associated with the binding of the cation in the active site such that it places the acid/base catalyst appropriately. Others, such as the human beta-glucuronidase, have no such metal ion requirement.

Catalytic Residues

The catalytic nucleophile in GH2 was first correctly identified in the E. coli (lacZ) beta-galactosidase as Glu537 in the sequence ILCEYAH through trapping of the 2-deoxy-2-fluorogalactosyl-enzyme intermediate and subsequent peptide mapping via HPLC techniques using radiolabeled tracers [9]. Earlier studies, carefully done using conduritol C cis-epoxide as affinity label, had identified Glu461 as the labeled residue, [10] on which basis a series of beautifully executed kinetic studies on mutants modified at this position that appeared initially to support this conclusion were performed [11]. However doubts were when similar kinetic analysis of nucleophile mutants of the GH1 Agrobacterium sp. b-glucosidase yielded quite different results, leading to the above labeling study [9]. The acid/base catalyst was then identified as Glu461 by re-interpretation [9] of the published kinetic results on mutants at that position [11], which had included azide rescue experiments. These conclusions were fully supported by subsequent 3-dimensional structural analyses (below).

Three-dimensional structures

Three-dimensional structures are available for five Family GH2 enzymes currently, the first solved being that of the E. coli (lacZ) beta-galactosidase in a tour de force of X-ray crystallography at that time, given its huge size (4 x 125,000 Da)[12]. The enzyme is multidomain, but as members of Clan GHA the catalytic domains a classical (a/b)8 TIM barrel fold with the two key active site glutamic acids being approximately 200 residues apart in sequence and located at the C-terminal ends of b-strands 4 (acid/base) and 7 (nucleophile).

Family Firsts

First sterochemistry determination

(pmid=TBA)

First catalytic nucleophile identification

E. coli (lacZ) beta-galactosidase by 2-fluorogalactose labeling [9]

First general acid/base residue identification

E. coli (lacZ) beta-galactosidase by re-interpretation of kinetic studies with mutants [9, 11]

First 3-D structure

E. coli (lacZ) beta-galactosidase [12]

References

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4. pmid=TBA