Β-Galactosidase

Structure

The 1,023 amino acids of E. coli β-galactosidase were sequenced in 1983, and its structure determined eleven years later in 1994. The protein is a 464-kDa homotetramer with 2,2,2-point symmetry. Each unit of β-galactosidase consists of five domains; domain 1 is a jelly-roll type β-barrel, domain 2 and 4 are fibronectin type III-like barrels, domain 5 a novel β-sandwich, while the central domain 3 is a distorted TIM-type barrel, lacking the fifth helix with a distortion in the sixth strand.

The third domain contains the active site. The active site is made up of elements from two subunits of the tetramer, and disassociation of the tetramer into dimers removes critical elements of the active site. The amino-terminal sequence of β-galactosidase, the α-peptide involved in α-complementation, participates in a subunit interface. Its residues 22–31 help to stabilize a four-helix bundle which forms the major part of that interface, and residue 13 and 15 also contributing to the activating interface. These structural features provide a rationale for the phenomenon of α-complementation, where the deletion of the amino-terminal segment results in the formation of an inactive dimer.

Reaction

β-Galactosidase can catalyze three different reactions in organisms. In one, it can go through a process called transgalactosylation to make allolactose, creating a positive feedback loop for the production of β-galactose. Allolactose can also be cleaved to form monosaccharides. It can also hydrolyze lactose into galactose and glucose which will proceed into glycolysis. The active site of β-galactosidase catalyzes the hydrolysis of its disaccharide substrate via "shallow" (nonproductive site) and "deep" (productive site) binding. Galactosides such as PETG and IPTG will bind in the shallow site when the enzyme is in "open" conformation while transition state analogs such as L-ribose and D-galactonolactone will bind in the deep site when the conformation is "closed".

The enzymatic reaction consists of two chemical steps, galactosylation and degalactosylation. Galactosylation is the first chemical step in the reaction where Glu461 donates a proton to a glycosidic oxygen, resulting in galactose covalently bonding with Glu537. In the second step, degalactosylation, the covalent bond is broken when Glu461 accepts a proton, replacing the galactose with water. Two transition states occur in the deep site of the enzyme during the reaction, once after each step. When water participates in the reaction, galactose is formed, otherwise, when D-glucose acts as the acceptor in the second step, transgalactosylation occurs . It has been kinetically measured that single tetramers of the protein catalyze reactions at a rate of 38,500 ± 900 reactions per minute. Monovalent potassium ions (K⁺) as well as divalent magnesium ions (Mg²⁺) are required for the enzyme's optimal activity. The β-linkage of the substrate is cleaved by a terminal carboxyl group on the side chain of a glutamic acid.

In E. coli, Glu-461 was thought to be the nucleophile in the substitution reaction. However, it is now known that Glu-461 is an acid catalyst. Instead, Glu-537 is the actual nucleophile, binding to a galactosyl intermediate. In humans, the nucleophile of the hydrolysis reaction is Glu-268. Gly794 is important for β-galactosidase activity. It is responsible for putting the enzyme in a "closed", ligand bounded, conformation or "open" conformation, acting like a "hinge" for the active site loop. The different conformations ensure that only preferential binding occurs in the active site. In the presence of a slow substrate, Gly794 activity increased as well as an increase in galactosylation and decrease in degalactosylation.

Applications

The β-galactosidase assay is used frequently in genetics, molecular biology, and other life sciences. An active enzyme may be detected using artificial chromogenic substrate 5-bromo-4-chloro-3-indolyl-β-D-galactopyranoside, X-gal. β-galactosidase will cleave the glycosidic bond in X-gal and form galactose and 5-bromo-4-chloro-3-hydroxyindole which dimerizes and oxidizes to 5,5'-dibromo-4,4'-dichloro-indigo, an intense blue product that is easy to identify and quantify. It is used for example in blue white screen. Its production may be induced by a non-hydrolyzable analog of allolactose, IPTG, which binds and releases the lac repressor from the lac operator, thereby allowing the initiation of transcription to proceed.

It is commonly used in molecular biology as a reporter marker to monitor gene expression. It also exhibits a phenomenon called α-complementation which forms the basis for the blue/white screening of recombinant clones. This enzyme can be split in two peptides, LacZα and LacZΩ, neither of which is active by itself but when both are present together, spontaneously reassemble into a functional enzyme. This property is exploited in many cloning vectors where the presence of the lacZα gene in a plasmid can complement in trans another mutant gene encoding the LacZΩ in specific laboratory strains of E. coli. However, when DNA fragments are inserted in the vector, the production of LacZα is disrupted, the cells therefore show no β-galactosidase activity. The presence or absence of an active β-galactosidase may be detected by X-gal, which produces a characteristic blue dye when cleaved by β-galactosidase, thereby providing an easy means of distinguishing the presence or absence of cloned product in a plasmid. In studies of leukaemia chromosomal translocations, Dobson and colleagues used a fusion protein of LacZ in mice, exploiting β-galactosidase's tendency to oligomerise to suggest a potential role for oligomericity in MLL fusion protein function.

A recent study conducted in 2020–2021 determined that Beta-Galactosidase activity correlates with senescence of the cells. Senescence of the cells can be interpreted as cells that do not divide, but cells that do not die. Beta-Galactosidase activity can be overexpressed, and this can lead to various diseases afflicting a wide range of body systems. These systems include the cardiovascular system, skeletal system, and many more. Detecting senescence cells can be achieved by measuring the lysosomal Beta-Galactosidase activity.

A new isoform for beta-galactosidase with optimum activity at pH 6.0 (Senescence Associated beta-gal or SA-beta-gal) which is specifically expressed in senescence (the irreversible growth arrest of cells). Specific quantitative assays were even developed for its detection. However, it is now known that this is due to an overexpression and accumulation of the lysosomal endogenous beta-galactosidase, and its expression is not required for senescence. Nevertheless, it remains the most widely used biomarker for senescent and aging cells, because it is reliable and easy to detect.

Evolution

Some species of bacteria, including E. coli, have additional β-galactosidase genes. A second gene, called evolved β-galactosidase (ebgA) gene was discovered when strains with the lacZ gene deleted (but still containing the gene for galactoside permease, lacY), were plated on medium containing lactose (or other 3-galactosides) as sole carbon source. After a time, certain colonies began to grow. However, the EbgA protein is an ineffective lactase and does not allow growth on lactose. Two classes of single point mutations dramatically improve the activity of ebg enzyme toward lactose. and, as a result, the mutant enzyme is able to replace the lacZ β-galactosidase. EbgA and LacZ are 50% identical on the DNA level and 33% identical on the amino acid level. The active ebg enzyme is an aggregate of ebgA -gene and ebgC-gene products in a 1:1 ratio with the active form of ebg enzymes being an α4 β4 hetero-octamer.

Species distribution

Much of the work done on β-galactosidase is derived from E. coli. However the enzyme can be found in many plants (especially fruits), mammals, yeast, bacteria, and fungi. β-galactosidase genes can differ in the length of their coding sequence and the length of proteins formed by amino acids. This separates the β-galactosidases into four families: GHF-1, GHF-2, GHF-35, and GHF- 42. E. Coli belongs to GHF-2, all plants belong to GHF-35, and Thermus thermophilus belongs to GHF-42. Various fruits can express multiple β-galactosidase genes. There are at least seven β-galactosidase genes expressed in tomato fruit development, that have amino acid similarity between 33% and 79%. A study targeted at identifying fruit softening of peaches found 17 different gene expressions of β-galactosidases. The only other known crystal structure of β-galactosidase is from Thermus thermophilus.