Beta-galactosidase

β-galactosidase

β-galactosidase from Penicillum sp.
Identifiers
EC number 3.2.1.23
CAS number 9031-11-2
Databases
IntEnz IntEnz view
BRENDA BRENDA entry
ExPASy NiceZyme view
KEGG KEGG entry
MetaCyc metabolic pathway
PRIAM profile
PDB structures RCSB PDB PDBe PDBsum
Gene Ontology AmiGO / EGO
galactosidase, beta 1
Identifiers
Symbol GLB1
Alt. symbols ELNR1
Entrez 2720
HUGO 4298
OMIM 230500
RefSeq NM_000404
UniProt P16278
Other data
Locus Chr. 3 p22.3

β-galactosidase, also called beta-gal or β-gal, is a glycoside hydrolase enzyme that catalyzes the hydrolysis of β-galactosides into monosaccharides through the breaking of a glycosidic bond. β-galactosides include carbohydrates containing galactose where the glycosidic bond lies above the galactose molecule. Substrates of different β-galactosidases include ganglioside GM1, lactosylceramides, lactose, and various glycoproteins.[1]

Properties and functions

β-galactosidase is an exoglycosidase which hydrolyzes the β-glycosidic bond formed between a galactose and its organic moiety. It may also cleave fucosides and arabinosides but with much lower efficiency. It is an essential enzyme in the human body. Deficiencies in the protein can result in galactosialidosis or Morquio B syndrome. In E. coli, the gene of β-galactosidase, the lacZ gene, is present as part of the inducible system lac operon which is activated in the presence of lactose when glucose level is low.

Beta-gal has many homologues based on similar sequences. A few are evolved beta-galactosidase (EBG), beta-glucosidase, 6-phospho-beta-galactosidase, beta-mannosidase, and lactase-phlorizin hydrolase. Although they may be structurally similar, they all have different functions.[2] Beta-gal is inhibited by L-ribose, non-competitive inhibitor iodine, and competitive inhibitors phenylthyl thio-beta-D-galactoside (PETG), D-galactonolactone, isopropyl thio-beta-D-galactoside (IPTG), and galactose.[3]

β-galactosidase is important for organisms as it is a key provider in the production of energy and a source of carbons through the break down of lactose to galactose and glucose. It is also important for the lactose intolerant community as it is responsible for making lactose-free milk and other dairy products. Many adult humans lack the lactase enzyme, which has the same function of beta-gal, so they are not able to properly digest dairy products. Beta-galactose is used in such dairy products as yogurt, sour cream, and some cheeses which are treated with the enzyme to break down any lactose before human consumption. In recent years, beta-galactosidase has been researched as a potential treatment for lactose intolerance through gene replacement therapy where it could be placed into the human DNA so individuals can break down lactose on their own.[4][5]

Structure

The 1,024 amino acids of E. coli β-galactosidase were first sequenced in 1970,[6] and its structure determined twenty-four years later in 1994. The protein is a 464-kDa homotetramer with 2,2,2-point symmetry.[7] Each unit of β-galactosidase consists of five domains; domain 1 is a jelly-roll type barrel, domain 2 and 4 are fibronectin type III-like barrels, domain 5 a β-sandwich, while the central domain 3 is a TIM-type barrel.

The third domain contains the active site.[8] 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 reaction

β-galactosidase can catalyze two 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-gal. It can also hydrolyze lactose into galactose and glucose which will proceed into glycolysis.[9] 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".[3]

The enzymatic reaction consists of two chemical steps, galactosylation (k2) and degalactosylation (k3). 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 .[3] It has been kinetically measured that single tetramers of the protein catalyze reactions at a rate of 38,500 ± 900 reactions per minute.[9] Monovalent potassium ions (K+) as well as divalent magnesium ions (Mg2+) are required for the enzyme's optimal activity. The beta-linkage of the substrate is cleaved by a terminal carboxyl group on the side chain of a glutamic acid.

The image on the left is a ribbon diagram of beta-galactosidase displaying the location of Glu 461, Glu 537, and Gly 794. The image on the right is a zoomed in version showing the interaction between the amino acids.

In E. coli, Glu-461 was thought to be the nucleophile in the substitution reaction.[10] However, it is now known that Glu-461 is an acid catalyst. Instead, Glu-537 is the actual nucleophile,[11] binding to a galactosyl intermediate. In humans, the nucleophile of the hydrolysis reaction is Glu-268.[12] Gly794 is important for β-gal activity. It is responsible for putting the enzyme in an "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.[3]

Uses

The β-galactosidase assay is used frequently in genetics, molecular biology, and other life sciences. An active enzyme may be detected using X-gal, which forms an intense blue product after cleavage by β-galactosidase, and is easy to identify and quantify. It is used for example in blue white screen.[13] 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,[14] exploiting β-galactosidase's tendency to oligomerise to suggest a potential role for oligomericity in MLL fusion protein function.[15]

In 1995, Dimri et al. proposed a new isoform for beta-galactosidase with optimum activity at pH 6.0 (Senescence Associated beta-gal or SA-beta-gal)[16] which would be specifically expressed in senescence (the irreversible growth arrest of cells). Specific quantitative assays were even developed for its detection.[17][18][19] However, it is now known that this is due to an overexpression and accumulation of the lysosomal endogenous beta-galactosidase,[20] 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.

Evolved beta-galactosidase

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.[21][22] and, as a result, the mutant enzyme is able to replace the lacZ β-galactosidase.[23] EbgA and LacZ are 50% identical on the DNA level and 33% identical on the amino acid level.[24] 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.[25]

References

  1. ↑ Dorland's Illustrated Medical Dictionary. Retrieved 2006-10-22.
  2. ↑ "Glycoside hydrolase, family 1, beta-glucosidase (IPR017736) < InterPro < EMBL-EBI". www.ebi.ac.uk. Retrieved 2015-12-11.
  3. 1 2 3 4 Juers, Douglas H.; Hakda, Shamina; Matthews, Brian W.; Huber, Reuben E. (2003-11-01). "Structural Basis for the Altered Activity of Gly794 Variants of Escherichia coli β-Galactosidase†". Biochemistry 42 (46): 13505–13511. doi:10.1021/bi035506j. ISSN 0006-2960.
  4. ↑ Salehi, Siamak; Eckley, Lorna; Sawyer, Greta J.; Zhang, Xiaohong; Dong, Xuebin; Freund, Jean-Noel; Fabre, John W. (2009-01-01). "Intestinal lactase as an autologous beta-galactosidase reporter gene for in vivo gene expression studies". Human Gene Therapy 20 (1): 21–30. doi:10.1089/hum.2008.101. ISSN 1557-7422. PMID 20377368.
  5. ↑ Ishikawa, Kazuhiko; Kataoka, Misumi; Yanamoto, Toshiaki; Nakabayashi, Makoto; Watanabe, Masahiro; Ishihara, Satoru; Yamaguchi, Shotaro (2015-07-01). "Crystal structure of β-galactosidase from Bacillus circulans ATCC 31382 (BgaD) and the construction of the thermophilic mutants". FEBS Journal 282 (13): 2540–2552. doi:10.1111/febs.13298. ISSN 1742-4658.
  6. ↑ Fowler AV, Zabin I (October 1970). "The amino acid sequence of beta galactosidase. I. Isolation and composition of tryptic peptides". J. Biol. Chem. 245 (19): 5032–41. PMID 4918568.
  7. ↑ Jacobson, R. H.; Zhang, X. -J.; Dubose, R. F.; Matthews, B. W. (1994). "Three-dimensional structure of β-galactosidase from E. Coli". Nature 369 (6483): 761–766. doi:10.1038/369761a0. PMID 8008071.
  8. ↑ Matthews BW (June 2005). "The structure of E. coli beta-galactosidase". C. R. Biol. 328 (6): 549–56. doi:10.1016/j.crvi.2005.03.006. PMID 15950161.
  9. 1 2 Juers, Douglas H.; Matthews, Brian W.; Huber, Reuben E. (2012-12-01). "LacZ β-galactosidase: Structure and function of an enzyme of historical and molecular biological importance". Protein Science 21 (12): 1792–1807. doi:10.1002/pro.2165. ISSN 1469-896X. PMC 3575911. PMID 23011886.
  10. ↑ Gebler JC, Aebersold R, Withers SG (June 1992). "Glu-537, not Glu-461, is the nucleophile in the active site of (lac Z) beta-galactosidase from Escherichia coli". J. Biol. Chem. 267 (16): 11126–30. PMID 1350782.
  11. ↑ Yuan J, Martinez-Bilbao M, Huber RE (April 1994). "Substitutions for Glu-537 of beta-galactosidase from Escherichia coli cause large decreases in catalytic activity". Biochem. J. 299 (Pt 2): 527–31. PMC 1138303. PMID 7909660.
  12. ↑ McCarter JD, Burgoyne DL, Miao S, Zhang S, Callahan JW, Withers SG (January 1997). "Identification of Glu-268 as the catalytic nucleophile of human lysosomal beta-galactosidase precursor by mass spectrometry". J. Biol. Chem. 272 (1): 396–400. doi:10.1074/jbc.272.1.396. PMID 8995274.
  13. ↑ Beta-Galactosidase Assay (A better Miller) - OpenWetWare
  14. ↑ Dobson, C. L.; Warren, A. J.; Pannell, R.; Forster, A.; Rabbitts, T. H. (2000). "Tumorigenesis in mice with a fusion of the leukaemia oncogene Mll and the bacterial lacZ gene". EMBO J 19: 843–851.
  15. ↑ Krivtsov, A. V.; Armstrong, S. A. (2007). "MLL translocations, histone modifications and leukaemia stem-cell development". Nature Reviews Cancer 7 (11): 823–833.
  16. ↑ Dimri GP, Lee X, Basile G, Acosta M, Scott G, Roskelley C, Medrano EE, Linskens M, Rubelj I, Pereira-Smith O (September 1995). "A biomarker that identifies senescent human cells in culture and in aging skin in vivo". Proc. Natl. Acad. Sci. U.S.A. 92 (20): 9363–7. doi:10.1073/pnas.92.20.9363. PMC 40985. PMID 7568133.
  17. ↑ Bassaneze V, Miyakawa AA, Krieger JE (January 2008). "A quantitative chemiluminescent method for studying replicative and stress-induced premature senescence in cell cultures". Anal. Biochem. 372 (2): 198–203. doi:10.1016/j.ab.2007.08.016. PMID 17920029.
  18. ↑ Gary RK, Kindell SM (August 2005). "Quantitative assay of senescence-associated beta-galactosidase activity in mammalian cell extracts". Anal. Biochem. 343 (2): 329–34. doi:10.1016/j.ab.2005.06.003. PMID 16004951.
  19. ↑ Itahana K, Campisi J, Dimri GP (2007). "Methods to detect biomarkers of cellular senescence: the senescence-associated beta-galactosidase assay". Methods Mol. Biol. Methods in Molecular Biology 371: 21–31. doi:10.1007/978-1-59745-361-5_3. ISBN 978-1-58829-658-0. PMID 17634571.
  20. ↑ Lee BY, Han JA, Im JS, Morrone A, Johung K, Goodwin EC, Kleijer WJ, DiMaio D, Hwang ES (April 2006). "Senescence-associated beta-galactosidase is lysosomal beta-galactosidase". Aging Cell 5 (2): 187–95. doi:10.1111/j.1474-9726.2006.00199.x. PMID 16626397.
  21. ↑ Hall, B. G. (1977). "Number of mutations required to evolve a new lactase function in Escherichia coli". Journal of Bacteriology 129 (1): 540–3. PMC 234956. PMID 318653.
  22. ↑ Hall, B. G. (1981). "Changes in the substrate specificities of an enzyme during directed evolution of new functions". Biochemistry 20 (14): 4042–9. doi:10.1021/bi00517a015. PMID 6793063.
  23. ↑ Hall, B. G. (1976). "Experimental evolution of a new enzymatic function. Kinetic analysis of the ancestral (ebg) and evolved (ebg) enzymes". Journal of Molecular Biology 107 (1): 71–84. doi:10.1016/s0022-2836(76)80018-6. PMID 794482.
  24. ↑ Stokes, H. W.; Betts, P. W.; Hall, B. G. (1985). "Sequence of the ebgA gene of Escherichia coli: Comparison with the lacZ gene". Molecular Biology and Evolution 2 (6): 469–77. PMID 3939707.
  25. ↑ Elliott, A. C.; k, S; Sinnott, M. L.; Smith, P. J.; Bommuswamy, J; Guo, Z; Hall, B. G.; Zhang, Y (1992). "The catalytic consequences of experimental evolution. Studies on the subunit structure of the second (ebg) beta-galactosidase of Escherichia coli, and on catalysis by ebgab, an experimental evolvant containing two amino acid substitutions". The Biochemical Journal 282 (1): 155–64. doi:10.1042/bj2820155. PMC 1130902. PMID 1540130.

External links

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