Active-site motifs of lysosomal acid hydrolases: Invariant features of clan GH-A glycosyl hydrolases deduced from hydrophobic cluster analysis

Glycobiology

Volumn 7, Issue 2, 1997, Pages 277-284

  Durand, Patrick ^a   Lehn, Pierre ^b   Callebaut, Isabelle ^a   Fabrega, Sylvie ^b   Henrissat, Bernard ^c   Mornon, Jean Paul ^a  

^a UNIVERSITÉ PIERRE ET MARIE CURIE   (France)

^b HÔPITAL ROBERT DEBRÉ   (France)

^c CENTRE DE RECHERCHES SUR LES MACROMOLÉCULES VÉGÉTALES CERMAV CNRS   (France)

Author keywords

Glycosyl hydrolases; Hydrophobic cluster analysis; Lysosomal storage diseases

Indexed keywords

BETA GALACTOSIDASE; BETA GLUCURONIDASE; BETA MANNOSIDASE; GLUCOSYLCERAMIDASE; GLYCOSIDASE; LEVO IDURONIDASE;

AMINO ACID SEQUENCE; ARTICLE; CLUSTER ANALYSIS; CONTROLLED STUDY; ENZYME ACTIVE SITE; ENZYME ANALYSIS; HUMAN; LYSOSOME STORAGE DISEASE; MUTATION; PRIORITY JOURNAL; PROTEIN FAMILY; SEQUENCE HOMOLOGY;

AMINO ACID SEQUENCE; ANIMALS; BINDING SITES; CLUSTER ANALYSIS; CONSERVED SEQUENCE; GLYCOSIDE HYDROLASES; HUMANS; LYSOSOMES; MOLECULAR SEQUENCE DATA; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY, AMINO ACID;

EID: 0030937787     PISSN: 09596658     EISSN: None     Source Type: Journal    
DOI: 10.1093/glycob/7.2.277     Document Type: Article

References (45)

1. Alzari, P.M., Souchon, H. and Dominguez, R. (1996) The crystal structure of endoglucanase CelA, a family 8 glycosyl hydrolase from Clostridium thermocellum. Structure, 4, 265-275.
2. Barrett, T., Surech, C.G., Tolley, S.P., Dodson, E.J. and Hughes, M.A. (1995) The crystal structure of a cyanogenic β-glucosidase from white clover, a family 1 glycosyl hydrolase. Structure, 3, 951-960.
3. Belaich, A., Fierobe, H.-P., Baty, D., Busetta, B., Bagnara-Tardif, C., Gaudin, C. and Belaich, J.-P. (1992) The catalytic domain of endoglucanase A from Clostridium cellulolyticum: effects of arginine 79 and histidine 122 mutations on catalysis. J. Bacteriol., 174, 4677-4682.
4. Beutler, E., Demina, A. and Gelbart, T. (1994) Glucocerebrosidase mutations in Gaucher disease. Mol. Med., 1, 82-92
5. Bunge, S., Keijer, W.J., Steglich, C., Beck, M., Zuther, C., Morris, C.P., Schwinger, E., Hopwood, J., Scott, H.S. and Gal, A. (1994) Mucopolysaccharidosis type I: identification of 8 novel mutations and determination of the frequency of the two common α-L-iduronidase mutations (W402X and Q70X) among European patients. Hum. Mol. Genet., 3, 861-866.
6. Chen, L., Fincher, G.B. and Høj, P.B. (1993) Evolution of polysaccharide hydrolase substrate specificity. J. Biol. Chem., 268, 13318-13326.
7. Chen, H., Leipprandt, J.R., Traviss, C.E., Sopher, B.L., Jones, M.Z., Cavanagh, K.T. and Friderici, K.H. (1995) Molecular cloning and characterization of bovine β-mannosidase. J. Biol. Chem., 270, 3841-3848.
8. Cupples, C.G., Miller, J.H and Huber, R.E. (1990) Determination of the roles of Glu-461 in β-galactosidase (Escherichia coli) using site-specific mutagenesis. J. Biol. Chem., 265, 5512-5518.
9. Davies, G. and Henrissat, B. (1995) Structures and mechanisms of glycosyl hydrolases. Structure, 3, 853-859.
10. Dominguez, R., Souchon, H., Spinelli S., Dauter, Z., Wilson, K.S., Chauvaux, S., Béguin, P. and Alzari, P.M. (1995) A common protein fold and similar active site in two distinct families of β-glycanases. Nature Struct. Biol., 2, 569-576.
11. Dominguez, R., Souchon, H., Lascombe, M.B. and Alzari, P.M. (1996) The crystal structure of a family 5 endoglucanase mutant in complexed and uncomplexed forms reveals an induced fit activation mechanism. J. Mol. Biol., 257, 1042-1051.
12. Ducros, V., Czjzek, M., Belaich, A., Gaudin, C., Fierobe, H.P., Belaich, J.P., Davies, G.J. and Haser, R. (1995) Crystal structure of the catalytic domain of a bacterial cellulase belonging to family 5. Structure, 3, 939-949.
13. Gaboriaud, C., Bissery, V., Benchetrit, T. and Mornon, J.P. (1987) Hydrophobic cluster analysis. An efficient new way to compare and analyse amino-acid sequences. FEBS Lett., 224, 149-155.
14. Gebler, J.C., Aebersold, R. and Withers, S.G. (1992) Glu-537, not Glu-461, is the nucleophile in the active site of (Lac Z) β-galactosidase from Escherichia coli. J. Biol. Chem., 267, 11126-11130.
15. Gieselmann, V. (1995) Lysosomal storage diseases. Biochem. Biophys. Acta, 1270, 103-136.
16. Ginns, E.I., Choudary, P.V., Martin, B.M., Winfield, S., Stubblefield, B., Mayor, J., Merkle-Lehman, D., Murray, G.J., Bowers, L.A. and Barranger, J. (1984) Isolation of c-DNA clones for human beta-glucocerebrosidase using the lambda-gt11 expression system. Biochem. Biophys. Res. Commun., 123, 574-580.
17. Graves, P.N., Grabowski, G.A., Eisner, R., Palese, P. and Smith, F.I. (1988) Gaucher disease type I: cloning and characterization of a cDNA encoding acid beta-glucosidase from an Ashkenazi Jewish patient. DNA, 7, 521-528.
18. Henrissat, B. (1991) A classification of glycosyl hydrolases based on amino acid sequence similarities. Biochem. J., 280, 309-316.
19. Henrissat, B. and Bairoch, A. (1993) New families in the classification of glycosyl hydrolases based on amino acid sequence similarities. Biochem. J., 293, 781-788.
20. Henrissat, B. and Bairoch, A. (1996) Updating the sequence-based classification of glycosyl hydrolases. Biochem. J., in press.
21. Henrissat, B., Callebaut, I., Fabrega, S., Lehn, P., Mornon, J.P. and Davies, G (1995) Conserved catalytic machinery and the prediction of a common fold for several families of glycosyl hydrolases. Proc. Natl. Acad. Sci. USA, 92, 7090-7094.
22. Horowitz, M., Wilder, S., Horowitz, Z., Reiner, O., Gelbart, T. and Beutler, E. (1989) The human glucocerebrosidase gene and pseudogene: structure and evolution. Genomics, 4, 87-96.
23. Imai, K., Nakamura, M., Yamada, M., Asano, A., Yokoyama, S., Tsuji, S. and Ginns, E. (1993) A novel transcript from a pseudogene for human glucocerebrosidase in non-Gaucher cells. Gene, 136, 365-368.
24. Ishii, N., Oohira, T., Oshima, A., Sakuraba, H., Endo, F., Matsuda, I., Sukegawa, K., Orii, T. and Suzuki, Y. (1995) Clinical and molecular analysis of a Japanese boy with Morquio B disease. Clin. Genet., 48, 103-108.
25. Jacobson, R.H., Zhang, X.J., DuBose, R.F. and Matthews, B.W. (1994) Three-dimensional structure of β-galactosidase from Escherichia coli. Nature, 369, 761-766.
26. Jain, S., Drendel, W.B., Chen, Z.-W., Mathews, F.S, Sly, W.S. and Grubb, J.H. (1996) Structure of human β-glucuronidase reveals candidate lysosomal targeting and active-site motifs. Nature Struct. Biol., 3, 375-381.
27. Jenkins, J., Lo Leggio, L., Harris, G. and Pickersgill, R.W. (1995) β-Glucosidase, β-galactosidase, family A cellulases, family F xylanases and two barley glycanases form a superfamily of enzymes with 8-fold β/α architecture and with two conserved glutamates near the carboxy-terminal ends of two β-strands four and seven. FEBS Lett., 362, 281-285.
28. Kraulis, P.J. (1991) MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Cryst., 24, 946-950.
29. Lemesle-Varloot, L., Henrissat, B, Gaboriaud, C., Bissery, V., Morgat, A. and Mornon, J.P. (1990) Hydrophobic cluster analysis: procedures to derive structural and functional information from 2D representation of protein sequences. Biochimie, 72, 555-574.
30. McCarter, J.D. and Withers, S.G. (1994) Mechanisms of enzymatic glycoside hydrolysis. Curr. Opinion Struct. Biol., 4, 885-892.
31. Miao, S., McCarter, J.D., Grace, M.E., Grabowski, G.A., Aebersold, R. and Withers, S.G. (1994) Identification of Glu340 as the active-site nucleophile in human glucocerebrosidase by use of electrospray tandem mass spectrometry. J. Biol. Chem., 269, 10975-10978.
32. Morreau, H., Galjart, N.J., Gillemans, N., Willemsen, R., van der Horst, G.T.J. and d'Azzo, A. (1989) Alternative splicing of β-galactosidase mRNA generates the classic lysosomal enzyme and a β-galactosidase-related protein. J. Biol. Chem., 264, 20655-20663.
33. Oshima, A., Kyle, J.W., Miller, R.D., Hoffmann, J.W., Powell, P.P., Grubb, J.H., Sly, W.S., Tropak, M., Guise, K.S. and Gravel, R.A. (1987) Cloning, sequencing and expression of cDNA for β-glucuronidase. Proc. Natl. Acad. Sci. USA, 84, 685-689.
34. Ring, M. and Huber, R.E. (1990) Multiple replacements establish the importance of tyrosine-503 in β-galactosidase (Escherichia coli). Arch. Biochem. Biophys., 283, 342-350.
35. Scott, H.S., Anson, D.S, Orsborn, A.M., Nelson, P.V., Clements P.R., Morris, C.P. and Hopwood, J.J. (1991) Human α-L-iduronidase: cDNA isolation and expression. Proc. Natl. Acad. Sci. USA, 88, 9695-9699.
36. Scott, H.S., Litjens, T., Nelson, P.V., Thompson, P.R., Brooks, D.A., Hopwood, J.J. and Morris, C. P. (1993) Identification of mutations in the alpha-L-iduronidase gene (IDUA) that cause Hurler and Scheie syndromes. Am. J. Hum. Genet., 53, 973-986.
37. Sorge, J., Gross, E., West, C. and Beutler, E. (1990) High level transcription of the glucocerebrosidase pseudogene in normal subjects and patients with Gaucher disease. J. Clin. Invest., 86, 1137-1141.
38. Tomatsu, S., Fukuda, S., Sukegawa, K., Ikedo, Y., Yamada, S., Yamada, Y., Sasaki, T., Okamoto, H., Kuwahara, T., Yamaguchi, S., Kiman, T., Shintaku, H., Isshiki, G. and Orii, T. (1991) Mucopolysaccharidosis type VII: characterization of mutations and molecular heterogeneity. Am. J. Hum. Genet., 48, 89-96.
39. Varghese, J.N., Garett, T.P., Colman, P.M., Chen, L., Høj, P.B. and Fincher, G.B. (1994) Three-dimensional structures of two plant β-glucan endohydrolases with distinct substrate specificities. Proc. Natl. Acad. Sci. USA, 91, 2785-2789.
40. White, A., Withers, S.G, Gilkes, N.R. and Rose, D.R. (1994) Crystal structure of the catalytic domain of the β-1,4-glycanase Cex from Cellulomonas fimi. Biochemistry, 33, 12546-12552.
41. White, A., Tull, D., Jones, K., Withers, S.G and Rose, D.R. (1996) Crystallographic observation of a covalent catalytic intermediate in a β-glycosidase. Nature Struct. Biol., 3, 149-154.
42. Woodcock, S., Mornon, J.P. and Henrissat, B. (1992) Detection of secondary structure elements in proteins by hydrophobic cluster analysis. Protein Eng., 5, 629-635.
43. Yamada, S., Tomatsu, S., Sly, W.S., Islam, R., Wenger, D.A., Fukuda, S., Sukegawa, K. and Orii, T. (1995) Four novel mutations in mucopolysaccharidosis type VII including a unique base substitution in exon 10 of the β-glucuronidase gene that creates a novel 5′-splice site. Hum. Mol. Genet., 4, 651-655.
44. Yamagishi, A., Tomatsu, S., Fukuda, S., Uchiyama, A., Shimozawa, N., Suzuki, Y., Kondo, N., Sukegawa, K. and Orii, T. (1996) Mucopolysaccharidosis type I: identification of common mutations that cause Hurler and Scheie syndromes in Japanese populations. Hum. Mutat., 7, 23-29.
45. Zhang, X.J. and Matthews, B.W. (1995) EDPDB: a multifunctional tool for protein structure analysis. J. Appl. Cryst. 28, 624-630.