Review Article | Published:

Modular enzymes

Nature volume 409, pages 247252 (11 January 2001) | Download Citation

Subjects

Abstract

Although modular macromolecular devices are encountered frequently in a variety of biological situations, their occurrence in biocatalysis has not been widely appreciated. Three general classes of modular biocatalysts can be identified: enzymes in which catalysis and substrate specificity are separable, multisubstrate enzymes in which binding sites for individual substrates are modular, and multienzyme systems that can catalyse programmable metabolic pathways. In the postgenomic era, the discovery of such systems can be expected to have a significant impact on the role of enzymes in synthetic and process chemistry.

Access optionsAccess options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

References

  1. 1.

    , , & General nature of the genetic code for proteins. Nature 192, 1227–1232 (1961).

  2. 2.

    , & Modular binding proteins in signal transduction proteins . Cell 80, 237–248 (1995).

  3. 3.

    From Src homology domains to other signaling modules: proposal of the protein recognition code. Oncogene 17, 1469– 1474 (1998).

  4. 4.

    & Modular structure of transcription factors: implications for gene regulation. Cell 65, 717–719 (1991).

  5. 5.

    & Imposing specificity by localization: mechanism and evolvability. Curr. Biol. 8, R897–R904 (1998).

  6. 6.

    Location of domains in globular proteins. Nature 291 , 85–87 (1981).

  7. 7.

    , & Protein superfamilies and domain superfolds. Nature 372, 631–634 ( 1994).

  8. 8.

    et al. Gene families: the taxonomy of protein paralogs and chimeras . Science 278, 609–614 (1997).

  9. 9.

    & Protein evolution viewed through Escherichia coli protein sequences: introducing the notion of a structural segment of homology, the module. J. Mol. Biol. 268, 857–868 (1997).

  10. 10.

    , & Protein alchemy: changing β-sheet into α-helix . Nature Struct. Biol. 4, 548– 552 (1997).

  11. 11.

    Catalysis in Chemistry and Enzymology 615–806 (Dover, New York, 1987).

  12. 12.

    , & Functional domains in Fok-I restriction endonuclease . Proc. Natl Acad. Sci. USA 89, 4275– 4279 (1992).

  13. 13.

    , & Hybrid restriction enzymes—zinc finger fusions to Fok I cleavage domain. Proc. Natl Acad. Sci. USA 93, 1156–1160 (1996).

  14. 14.

    , , & Splase—a new class I zinc-finger restriction endonuclease with specificity for Sp1 binding sites. J. Protein Chem. 15, 481–489 (1996).

  15. 15.

    & Novel site-specific DNA endonucleases. Curr. Opin. Struct. Biol. 8, 19–25 (1998).

  16. 16.

    et al. Homologous xylanases from Clostridium thermocellum: evidence for bi-functional activity, synergism between xylanase catalytic modules and the presence of xylan-binding domains in enzyme complexes. Biochem. J. 342, 105–110 (1999).

  17. 17.

    et al. Pseudomonas cellulose-binding domains mediate their effects by increasing enzyme substrate proximity. Biochem. J. 331, 775–781 (1998).

  18. 18.

    et al. Detecting protein function and protein-protein interactions from genome sequences. Science 285, 751– 753 (1999).

  19. 19.

    On the attribution and additivity of binding energies. Proc. Natl Acad. Sci. USA 78, 4046–4050 (1981).

  20. 20.

    & Alteration of substrate specificity for the endoribonucleolytic cleavage of RNA by the Tetrahymena ribozyme . Proc. Natl Acad. Sci. USA 86, 9218– 9222 (1989).

  21. 21.

    , , , & Engineering Src family protein kinases with unnatural nucleotide specificity. Chem. Biol. 5, 91 –101 (1998).

  22. 22.

    , , & Converting trypsin to chymotrypsin—ground-state binding does not determine substrate specificity. Biochemistry 33, 8764–8769 (1994).

  23. 23.

    Rapid evolution of a protein in vitro by DNA shuffling. Nature 370, 389–391 ( 1994).

  24. 24.

    , & Bacterial biocatalysts: molecular biology, three-dimensional structures, and biotechnological applications of lipases. Annu. Rev. Microbiol. 53, 327–351 (1999).

  25. 25.

    & Enzymes and protecting group chemistry . Curr. Opin. Chem. Biol. 2, 112– 120 (1998).

  26. 26.

    , & Selective deprotection of phthalyl protected amines . Tetrahedron Lett. 37, 7469– 7472 (1996).

  27. 27.

    , & A structure-activity study with aryl acylamidases. Appl. Env. Microbiol. 60, 3939–3944 (1994).

  28. 28.

    Preparative biotransformations: the employment of enzymes and whole-cells in synthetic organic chemistry. J. Chem. Soc. Perkin Trans. 1, 157–169 (1998).

  29. 29.

    Preparative biotransformations. J. Chem. Soc. Perkin Trans. 1, 1–21 (1999).

  30. 30.

    Preparative biotransformations. J. Chem. Soc. Perkin Trans. 1, 611–633 (2000).

  31. 31.

    et al. Penicillin acylase has a single amino-acid catalytic centre . Nature 373, 264–268 (1995).

  32. 32.

    , , & Ligand-induced conformational change in penicillin acylase. J. Mol. Biol. 284, 463–475 (1998).

  33. 33.

    , , , & Structural basis of the chiral selectivity of Pseudomonas cepacia lipase. Eur. J. Biochem. 254, 333–340 ( 1998).

  34. 34.

    Enzyme Structure and Mechanism (Freeman, 1985).

  35. 35.

    , & Cobalamin-dependent methionine synthase is a modular protein with distinct regions for binding homocysteine, methyltetrahydrofolate, cobalamin, and adenosylmethionine. Biochemistry 36, 8082–8091 (1997).

  36. 36.

    , , & The 1.9 A crystal structure of Escherichia coli MurG, a membrane-associated glycosyltransferase involved in peptidoglycan biosynthesis. Protein Sci. 9, 1045–1052 (2000).

  37. 37.

    , , , & The first structure of UDP-glucose dehydrogenase reveals the catalytic residues necessary for the two-fold oxidation . Biochemistry 39, 7012– 7023 (2000).

  38. 38.

    , , & Biosynthesis of desosamine: construction of a new macrolide carrying a genetically designed sugar moiety. Org. Lett. 1, 133– 136 (1999).

  39. 39.

    , , , & A two-plasmid system for the glycosylation of polyketide antibiotics: bioconversion of epsilon-rhodomycinone to rhodomycin D. Chem. Biol. 6, 845– 855 (1999).

  40. 40.

    & Conserved domains of glycosyltransferases . Glycobiology 9, 961–978 (1999).

  41. 41.

    , & Harnessing the biosynthetic code. Combinations, permutations, mutations. Science 282, 63– 68 (1998).

  42. 42.

    , , & Tolerance and specificity of polyketide synthases. Annu. Rev. Biochem. 68, 219–253 ( 1999).

  43. 43.

    & Design and application of multimodular peptide synthetases. Curr. Opin. Biotechnol. 10, 341–348 (1999).

  44. 44.

    , & Aminoacyl-CoAs as probes of condensation domain selectivity in nonribosomal peptide synthesis. Science 284, 486–489 (1999).

  45. 45.

    , , & Analysis of the molecular recognition features of individual modules derived from the erythromycin polyketide synthase. J. Am. Chem. Soc. 122, 4847–4852 (2000).

  46. 46.

    et al. Multiple genetic modifications of the erythromycin polyketide synthase to produce a library of novel “unnatural” natural products . Proc. Natl Acad. Sci. USA 96, 1846– 1851 (1999).

  47. 47.

    & A novel, definitive test for substrate channeling illustrated with the aspartate aminotransferase/malate dehydrogenase system. Biochemistry 38, 8032– 8037 (1999).

  48. 48.

    , , , & Three-dimensional structure of the tryptophan synthase alpha 2 beta 2 multienzyme complex from Salmonella typhimurium. J. Biol. Chem. 263, 17857 –17871 (1988).

  49. 49.

    et al. Coupled formation of an amidotransferase interdomain ammonia channel and a phosphoribosyltransferase active site. Biochemistry 36, 11061–11068 ( 1997).

  50. 50.

    , , , & Structure of carbamoyl phosphate synthetase: a journey of 96 Å from substrate to product. Biochemistry 36, 6305–6316 (1997).

  51. 51.

    & Swinging arms in multifunctional enzymes and the specificity of post-translational modification. Biochem. Soc. Trans. 26, 299–303 (1998).

  52. 52.

    , , & Preferential heterodimer formation by isolated leucine zippers from Fos and Jun. Science 245, 646 –648 (1989).

  53. 53.

    Molscript—a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr. 24, 946–950 (1991).

  54. 54.

    et al. Gain of function mutagenesis of a modular polyketide synthase II. Engineered biosynthesis of an eight-membered ring tetraketide lactone . J. Am. Chem. Soc. 119, 11339– 11340 (1997).

  55. 55.

    , , , & An unusually large multifunctional polypeptide in the erythromycin-producing polyketide synthase of Saccharopolyspora erythraea. Nature 348, 176– 178 (1990).

  56. 56.

    , , , & Modular organization of genes required for complex polyketide biosynthesis. Science 252, 675–679 (1991).

Download references

Acknowledgements

Research on modular enzymes in C.K.'s laboratory is supported by grants from the National Science Foundation and the National Institutes of Health. P.B.H. is a Terman Fellow, a Searle Scholar and a Burroughs–Wellcome Young Investigator in the Pharmacological Sciences. We thank S. Walker for helpful discussions regarding glycosyltransferases.

Author information

Affiliations

  1. Departments of Chemistry, Chemical Engineering and Biochemistry, Stanford University, Stanford, California 94305, USA

    • Chaitan Khosla
    •  & Pehr B. Harbury

Authors

  1. Search for Chaitan Khosla in:

  2. Search for Pehr B. Harbury in:

Corresponding author

Correspondence to Chaitan Khosla.

About this article

Publication history

Published

DOI

https://doi.org/10.1038/35051723

Further reading

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.

Newsletter Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing