α/β hydrolase fold enzymes: The family keeps growing

Current Opinion in Structural Biology

Volumn 9, Issue 6, 1999, Pages 732-737

  Nardini, Marco ^a   Dijkstra, Bauke W ^a  

^a UNIVERSITY OF GRONINGEN   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

HYDROLASE;

ENZYME CONFORMATION; ENZYME SPECIFICITY; EVOLUTION; NONHUMAN; PRIORITY JOURNAL; PROTEIN FAMILY; PROTEIN FOLDING; REVIEW;

EID: 0032784276     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0959-440X(99)00037-8     Document Type: Review

References (37)

1. Ollis D.L., Cheah E., Cygler M., Dijkstra B., Frolow F., Franken S.M., Harel M., Remington S.J., Silman I., Schrag J.et al. The α/β hydrolase fold. Protein Eng. 5:1992;197-211.
2. Heikinheimo P., Goldman A., Jeffries C., Ollis D.L. Of barn owls and bankers: a lush variety of α/β hydrolases. Structure. 7:1999;R141-R146. Following on from the first paper to define the α/β hydrolase fold [1], this review gives an original family-like classification and interesting considerations about future research developments.
3. Hubbard T.J.P., Ailey B., Brenner S.E., Murzin A.G., Chothia C. SCOP, structural classification of proteins database: applications to evaluation of the effectiveness of sequence alignment methods and statistics of protein structural data. Acta Crystallogr D. 54:1998;1147-1154.
4. Orengo C.A., Martin A.M., Hutchinson G., Jones S., Jones D.T., Michie A.D., Swindells M.B., Thornton J.M. Classifying a protein in the CATH database of domain structures. Acta Crystallogr D. 54:1998;1155-1167.
5. Cousin X., Hotelier T., Giles K., Toutant J.P., Chatonnet A. aCHEdb: the database system for ESTHER, the α/β fold family of proteins and the cholinesterase gene server. Nucleic Acids Res. 26:1998;226-228.
6. Schrag J.D., Cygler M. Lipases and α/β hydrolase fold. Methods Enzymol. 284:1997;85-107.
7. Jaeger K.-E., Reetz M.T. Microbial lipases form versatile tools for biotechnology. Trends Biotechnol. 16:1998;396-403.
8. Alberghina L., Lotti M. Lipases and lipids: structure, specificity and applications in biocatalysis. Chem Phys Lipids. 93:1998;1-216.
9. Jaeger K.-E., Dijkstra B.W., Reetz M.T. Bacterial biocatalysts: molecular biology, three-dimensional structures, and biotechnological applications of lipases. Annu Rev Microbiol. 53:1999;315-351. A paper that offers a thorough overview of current knowledge on bacterial lipases.
10. Schmid R.D., Verger R. Lipases: interfacial enzymes with attractive applications. Angew Chem Int Ed. 37:1998;1608-1633.
11. Verger R. 'Interfacial activation' of lipases: facts and artifacts. Trends Biotechnol. 15:1997;32-38.
12. Roussel A., Canaan S., Egloff M.-P., Rivière M., Dupuis L., Verger R., Cambillau C. Crystal structure of human gastric lipase and model of lysosomal acid lipase, two lipolytic enzymes of medical interest. J Biol Chem. 274:1999;16995-17002.
13. Chen J.C.-H., Miercke L.J.W., Krucinski J., Starr J.R., Saenz G., Wang X., Spilburg C.A., Lange L.G., Ellsworth J.L., Stroud R.M. Structure of bovine pancreatic cholesterol esterase at 1.6 Å: novel structural features involved in lipase activation. Biochemistry. 37:1998;5107-5117.
14. Ghosh D., Erman M., Sawicki M., Lala P., Weeks D.R., Li N., Pangborn W., Thiel D.J., Jörnvall H., Gutierrez R., Eyzaguirre J. Determination of a protein structure by iodination: the structure of iodinated acetylxylan esterase. Acta Crystallogr D. 55:1999;779-784.
15. Wei Y., Swenson L., Castro C., Derewenda U., Minor W., Arai H., Aoki J., Inoue K., Servin-Gonzalez L., Derewenda Z.S. Structure of a microbial homologue of mammalian platelet-activating factor acetylhydrolases: Streptomyces exfoliatus lipase at 1.9 Å resolution. Structure. 6:1998;511-519.
16. Longhi S., Czjzek M., Lamzin V., Nicolas A., Cambillau C. Atomic resolution (1.0 Å) crystal structure of Fusarium solani cutinase: stereochemical analysis. J Mol Biol. 268:1997;779-799.
17. Fülöp V., Böcskei Z., Polgár L. Prolyl oligopeptidase: an unusual β-propeller domain regulates proteolysis. Cell. 94:1998;161-170. This article shows the peculiar structure of the two-domain prolyl oligopeptidase enzyme, with an unusual β-propeller domain covering the catalytic triad of the α/β hydrolase fold domain, thus protecting large peptides and proteins from proteolysis in the cytosol.
18. Wei Y., Contreras J.A., Sheffield P., Osterlund T., Derewenda U., Kneusel R.E., Matern U., Holm C., Derewenda Z.S. Crystal structure of brefeldin A esterase, a bacterial homolog of the mammalian hormone-sensitive lipase. Nat Struct Biol. 6:1999;340-345. The crystal structure described in this paper revealed that the previously reported amino acid sequence was wrong, as a result of frame shifts in the cDNA sequence. Most importantly, the homology of brefeldin A esterase and mammalian hormone sensitive lipase (HSL) gives the first direct structural information regarding the HSL enzyme family.
19. Krooshof G.H., Kwant E.M., Damborsky J., Koca J., Janssen D.B. Repositioning the catalytic triad aspartic acid of haloalkane dehalogenase: effects on stability, kinetics, and structure. Biochemistry. 36:1997;9571-9580.
20. Copley S.D. Microbial dehalogenases: enzymes recruited to convert xenobiotic substrates. Curr Opin Chem Biol. 2:1998;613-617.
21. Liu J.-Q., Kurihara T., Ichiyama S., Miyagi M., Tsunasawa S., Kawasaki H., Soda K., Esaki N. Reaction mechanism of fluoroacetate dehalogenase from Moraxella sp. B. J Biol Chem. 273:1998;30897-30902.
22. Hynková K., Nagata Y., Takagi M., Damborsky J. Identification of the catalytic triad in the haloalkane dehalogenase from Sphingomonas paucimobilis UT26. FEBS Lett. 446:1999;177-181.
23. Bourne P.C., Isupov M.N., Littlechild J.A. Crystallization and preliminary X-ray diffraction studies of a novel bacterial esterase. Acta Crystallogr D. 55:1999;915-917.
24. Rink R., Fennema M., Smids M., Dehmel U., Janssen D.B. Primary structure and catalytic mechanism of the epoxide hydrolase from Agrobacterium radiobacter AD1. J Biol Chem. 272:1997;14650-14657.
25. Rink R., Janssen D.B. Kinetic mechanism of the enantioselective conversion of styrene oxide by epoxide hydrolase from Agrobacterium radiobacter AD1. Biochemistry. 37:1998;18119-18127.
26. Nardini M., Ridder I.S., Rozeboom H.J., Kalk K.H., Rink R., Janssen D.B., Dijkstra B.W. The X-ray structure of epoxide hydrolase from Agrobacterium radiobacter AD1: an enzyme to detoxify harmful epoxides. J Biol Chem. 274:1999;14579-14586. This paper describes, for the first time, an epoxide hydrolase structure, providing novel, detailed information on the residues involved in the enzymatic mechanism.
27. Rink R., Lutje Spelberg J.H., Pieters R.J., Kingma J., Nardini M., Kellogg R.M., Dijkstra B.W., Janssen D.B. Mutation of tyrosine residues involved in the alkylation half reaction of epoxide hydrolase from Agrobacterium radiobacter AD1 results in improved enantioselectivity. J Am Chem Soc. 121:1999;7417-7418. Mutation of two active site tyrosine residues resulted in a significant increase in the enantioselectivity of epoxide hydrolase from A. radiobacter. As at least one of these tyrosines is conserved among all epoxide hydrolases, a role in catalysis for this residue is suggested for other epoxide hydrolases as well.
28. Archelas A., Furstoss R. Epoxide hydrolases: new tools for the synthesis of fine organic chemicals. Trends Biotechnol. 16:1998;108-116. An interesting review about epoxide hydrolases, focusing on their enzymatic mechanism and biotechnological application.
29. Ridder I.S., Rozeboom H.J., Dijkstra B.W. Haloalkane dehalogenase from Xanthobacter autotrophicus GJ10 refined at 1.15 Å resolution. Acta Crystallogr D. 55:1999;1273-1290.
30. Hofmann B., Tölzer S., Pelletier I., Altenbuchner J., van Pée K.H., Hecht H.J. Structural investigation of the cofactor-free chloroperoxidases. J Mol Biol. 279:1998;889-900.
31. Kirk O., Conrad L.S. Metal-free haloperoxidases: fact or artifact? Angew Chem Int Ed. 38:1999;977-979.
32. Argiriadi M.A., Morisseau C., Hammock B.D., Christianson D.W. Detoxification of environmental mutagens and carcinogens: structure-based mechanism and evolution of liver epoxide hydrolase. Proc Natl Acad Sci USA. 96:1999;10637-10642. In this article, a structure-based mechanism is proposed for epoxide hydrolysis. Furthermore, evolutionary considerations are used to explain the peculiar presence of an additional, inactive N-terminal domain with the fold of an haloacid dehalogenase.
33. Kim K.K., Song H.K., Shin D.H., Hwang K.Y., Choe S., Yoo O.J., Suh S.W. Crystal structure of carboxylesterase from Pseudomonas fluorescens, an α/β hydrolase with broad substrate specificity. Structure. 5:1997;1571-1584.
34. Lang D., Hofmann B., Haalck L., Hecht H.-J., Spener F., Schmid R.D., Schomburg D. Crystal structure of a bacterial lipase from Chromobacterium viscosum ATCC refined at 1.6 Å resolution. J Mol Biol 1996. 259:6918;704-717.
35. Kim K.K., Song H.K., Shin D.H., Hwang K.Y., Suh S.W. The crystal structure of a triacylglycerol lipase from Pseudomonas cepacia reveals a highly open conformation in the absence of a bound inhibitor. Structure. 5:1997;173-185.
36. Schrag J.D., Li Y., Cygler M., Lang D., Burgdorf T., Hecht H.-J., Schmid R., Schomburg D., Rydel T.J., Oliver J.D.et al. The open conformation of a Pseudomonas lipase. Structure. 5:1997;187-202.
37. Lang D.A., Mannesse M.L.M., De Haas G.H., Verheij H.M., Dijkstra B.W. Structural basis of the chiral selectivity of Pseudomonas cepacia lipase. Eur J Biochem. 254:1998;333-340.