Glycoside Hydrolase Family 35

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• Authors: ^^^Alexander Golubev^^^ and ^^^Anna Kulminskaya^^^
• Responsible Curator: ^^^Anna Kulminskaya^^^

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Glycoside Hydrolase Family GH35
Clan	GH-A
Mechanism	retaining
Active site residues	known
CAZy DB link
https://www.cazy.org/GH35.html

Substrate specificities

The major activity of enzymes of this GH family is β-galactosidase (EC 3.2.1.23). Reported enzymes were isolated from microorganisms such as fungi, bacteria and yeasts; plants, animals and human cells, and from recombinant sources and act in acidic conditions. The β-galactosidase (EC 3.2.1.23) catalyses the hydrolysis of terminal non-reducing β-D-galactose residues in β-D-galactosides as, for example, lactose (1,4-O-β-D-galactopyranosyl-D-glucose) and structurally related compounds. GH35 includes multiple genes in various plant species [1, 2, 3, 4, 5] suggesting ubiquity of GH35 gene multiplicity in plants. Family 35 β-galactosidases demonstrate specificity towards β1,3-, β1,6- or β1,4-galactosidic linkages. Plant β-galactosidases can be divided into two classes: members of the first are capable of hydrolyzing pectic β-1,4-galactans; another ones can specifically cleave β-1,3- and β1,6-galactosyl linkages of arabinogalactan proteins.

Besides β-galactosidases, GHF35 contains two exo-β-glucosaminidases (EC 3.2.1.165) [6], [7]. This enzyme hydrolyze chitosan or chitosan oligosaccharides to remove successive D-glucosamine residues from the non-reducing termini.

Kinetics and Mechanism

Beta-galactosidases of GH35 family catalyze hydrolysis of β-galactosyl linkages between terminal galactosyl residues of oligosaccharides, glycolipids, and glycoproteins acting via a double-displacement mechanism and retaining β-anomeric configuration of the released galactose molecule. The stereochemistry of the reaction has been first shown by NMR for human β-galactosidase precursor [8] and then confirmed by other investigators for microbial and plant enzymes.

Catalytic Residues

The catalytic residues for family 35 were first predicted on the basis of hydrophobic cluster analysis of proteins of similar protein fold [9]. Experimentally, the glutamic acid residue 268 was first identified as the catalytic nucleophile in human lysosomal β-galactosidase precursor using the slow substrate 2,4-dinitrophenyl-2-deoxy-2-fluoro- β-D-galactopyranoside that trapped a glycosyl enzyme intermediate. It allowed subsequent peptide mapping and exact nulceophile ID [10]. Further, the same work was done for two bacterial β-galactosidases, from Xanthomonas manihotis and Bacillus circulans [11]. The general acid/base catalyst was inferred by structural studies of Penicillium β-galactosidase as Glu200 [12]. Recent structural studies of Maksimainen et al. [13] revealed two different conformations of the general acid/base catalyst Glu200 in the β-galactosidase of Trichoderma reeesei, which influence the catalytic machinery of the enzyme.

Three-dimensional structures

Content is to be added here.

Family Firsts

First stereochemistry determination

Human β-galactosidase precursor by NMR [8]

First catalytic nucleophile identification

Human β-galactosidase precursor by 2-fluorogalactose labeling [14].

First general acid/base residue identification

Penicillium sp. β-galactosidase by structural identification [12].

First 3-D structure

Penicillium β-galactosidase [12].

References

1. Ahn YO, Zheng M, Bevan DR, Esen A, Shiu SH, Benson J, Peng HP, Miller JT, Cheng CL, Poulton JE, and Shih MC. (2007). Functional genomic analysis of Arabidopsis thaliana glycoside hydrolase family 35. Phytochemistry. 2007;68(11):1510-20. DOI:10.1016/j.phytochem.2007.03.021 |
2. Smith DL and Gross KC. (2000). A family of at least seven beta-galactosidase genes is expressed during tomato fruit development. Plant Physiol. 2000;123(3):1173-83. DOI:10.1104/pp.123.3.1173 |
3. Lazan H, Ng SY, Goh LY, and Ali ZM. (2004). Papaya beta-galactosidase/galactanase isoforms in differential cell wall hydrolysis and fruit softening during ripening. Plant Physiol Biochem. 2004;42(11):847-53. DOI:10.1016/j.plaphy.2004.10.007 |
4. Ross GS, Wegrzyn T, MacRae EA, and Redgwell RJ. (1994). Apple beta-galactosidase. Activity against cell wall polysaccharides and characterization of a related cDNA clone. Plant Physiol. 1994;106(2):521-8. DOI:10.1104/pp.106.2.521 |
5. Tanthanuch W, Chantarangsee M, Maneesan J, and Ketudat-Cairns J. (2008). Genomic and expression analysis of glycosyl hydrolase family 35 genes from rice (Oryza sativa L.). BMC Plant Biol. 2008;8:84. DOI:10.1186/1471-2229-8-84 |

6. Fukui T, Atomi H, Kanai T, Matsumi R, Fujiwara S, and Imanaka T. (2005). Complete genome sequence of the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1 and comparison with Pyrococcus genomes. Genome Res. 2005;15(3):352-63. DOI:10.1101/gr.3003105 |
7. Kawarabayasi Y, Sawada M, Horikawa H, Haikawa Y, Hino Y, Yamamoto S, Sekine M, Baba S, Kosugi H, Hosoyama A, Nagai Y, Sakai M, Ogura K, Otsuka R, Nakazawa H, Takamiya M, Ohfuku Y, Funahashi T, Tanaka T, Kudoh Y, Yamazaki J, Kushida N, Oguchi A, Aoki K, and Kikuchi H. (1998). Complete sequence and gene organization of the genome of a hyper-thermophilic archaebacterium, Pyrococcus horikoshii OT3 (supplement). DNA Res. 1998;5(2):147-55. DOI:10.1093/dnares/5.2.147 |

8. Zhang S, McCarter JD, Okamura-Oho Y, Yaghi F, Hinek A, Withers SG, and Callahan JW. (1994). Kinetic mechanism and characterization of human beta-galactosidase precursor secreted by permanently transfected Chinese hamster ovary cells. Biochem J. 1994;304 ( Pt 1)(Pt 1):281-8. DOI:10.1042/bj3040281 |

11. Blanchard JE, Gal L, He S, Foisy J, Warren RA, and Withers SG. (2001). The identification of the catalytic nucleophiles of two beta-galactosidases from glycoside hydrolase family 35. Carbohydr Res. 2001;333(1):7-17. DOI:10.1016/s0008-6215(01)00108-2 |
12. Rojas AL, Nagem RA, Neustroev KN, Arand M, Adamska M, Eneyskaya EV, Kulminskaya AA, Garratt RC, Golubev AM, and Polikarpov I. (2004). Crystal structures of beta-galactosidase from Penicillium sp. and its complex with galactose. J Mol Biol. 2004;343(5):1281-92. DOI:10.1016/j.jmb.2004.09.012 |
13. Maksimainen M, Hakulinen N, Kallio JM, Timoharju T, Turunen O, and Rouvinen J. (2011). Crystal structures of Trichoderma reesei β-galactosidase reveal conformational changes in the active site. J Struct Biol. 2011;174(1):156-63. DOI:10.1016/j.jsb.2010.11.024 |
15. Henrissat B, Callebaut I, Fabrega S, Lehn P, Mornon JP, and Davies G. (1995). Conserved catalytic machinery and the prediction of a common fold for several families of glycosyl hydrolases. Proc Natl Acad Sci U S A. 1995;92(15):7090-4. DOI:10.1073/pnas.92.15.7090 |
16. McCarter JD, Burgoyne DL, Miao S, Zhang S, Callahan JW, and Withers SG. (1997). Identification of Glu-268 as the catalytic nucleophile of human lysosomal beta-galactosidase precursor by mass spectrometry. J Biol Chem. 1997;272(1):396-400. DOI:10.1074/jbc.272.1.396 |