Evolutionary potential of (β/α)8-barrels: In vitro enhancement of a "new" reaction in the enolase superfamily

Biochemistry

Volumn 44, Issue 35, 2005, Pages 11722-11729

  Vick, Jacob E ^a   Schmidt, Dawn M Z ^a   Gerlt, John A ^a  

^a UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CATALYSIS; MUTAGENESIS; NEGATIVE IONS; SUBSTRATES;

O-SUCCINYLBENZOATE SYNTHASE (OSBS); PERMIT ANAEROBIC GROWTH; RANDOM MUTAGENESIS;

ENZYMES;

CARBOXYLIC ACID; DNA; ENOLASE; EPIMERASE; SYNTHETASE;

ARTICLE; CATALYSIS; CHEMICAL REACTION; DNA SEQUENCE; ENZYME ACTIVITY; ENZYME SPECIFICITY; ESCHERICHIA COLI; EVOLUTION; IN VITRO STUDY; KINETICS; NONHUMAN; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL;

AMINO ACID ISOMERASES; AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; BACILLUS SUBTILIS; BINDING SITES; CARBON-CARBON LYASES; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; EVOLUTION, MOLECULAR; GENE LIBRARY; INTRAMOLECULAR LYASES; MUTAGENESIS, SITE-DIRECTED; PHENYLBUTYRATES; PHOSPHOPYRUVATE HYDRATASE; PROTEIN STRUCTURE, SECONDARY; RACEMASES AND EPIMERASES; SUBSTRATE SPECIFICITY;

ESCHERICHIA COLI;

EID: 24344494387     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi050963g     Document Type: Article

References (26)

1. Babbitt, P. C., Hasson, M. S., Wedekind, J. E., Palmer, D. R., Barrett, W. C., Reed, G. H., Rayment, I., Ringe, D., Kenyon, G. L., and Gerlt, J. A. (1996) The enolase superfamily: a general strategy for enzyme-catalyzed abstraction of the alpha-protons of carboxylic acids, Biochemistry 35, 16489-501.
2. Gerlt, J. A., and Babbitt, P. C. (2001) Divergent Evolution Of Enzymatic Function: Mechanistically Diverse Superfamilies and Functionally Distinct Suprafamilies, Annu. Rev. Biochem. 70, 209-46.
3. Gerlt, J. A., and Raushel, F. M. (2003) Evolution of function in (beta/alpha)(8)-barrel enzymes, Curr. Opin. Chem. Biol. 7, 252-64.
4. Jensen, R. A. (1976) Enzyme recruitment in evolution of new function, Annu. Rev. Microbiol. 30, 409-25.
5. Ohno, S. (1970) Evolution by Gene Duplication, Springer-Verlag. New York.
6. Hughes, A. L. (1994) The evolution of functionally novel proteins after gene duplication, Proc. R. Soc. London, Ser. B 256, 119-24.
7. Lynch, M., and Katju, V. (2004) The altered evolutionary trajectories of gene duplicates, Trends Genet. 20, 544-9.
8. Schmidt, D. M., Mundorff, E. C., Dojka, M., Bermudez, E., Ness, J. E., Govindarajan, S., Babbitt, P. C., Minsbull, J., and Gerlt, J. A. (2003) Evolutionary potential of (beta/alpha)8-barrels: functional promiscuity produced by single substitutions in the enolase superfamily, Biochemistry 42, 8387-93.
9. Schmidt, D. M., Hubbard, B. K., and Gerlt, J. A. (2001) Evolution of Enzymatic Activities in the Enolase Superfamily: Functional Assignment of Unknown Proteins in Bacillus subtilis and Escherichia coli as L-Ala-D/L-Glu Epimerases, Biochemistry 40, 15707-15.
10. Klenchin, V. A., Taylor Ringia, E. A., Gerlt, J. A., and Rayment, I. (2003) Evolution of enzymatic activity in the enolase superfamily: structural and mutagenic studies of the mechanism of the reaction catalyzed by o-succinylbenzoate synthase from Escherichia coli, Biochemistry 42, 14427-33.
11. Klenchin, V. A., Schmidt, D. M., Gerlt, J. A., and Rayment, I. (2004) Evolution of enzymatic activities in the enolase superfamily: structure of a substrate-liganded complex of the L-Ala-D/ L-Glu epimerase from Bacillus subtilis, Biochemistry 43, 10370-8.
12. Meganathan, R. (1996) in Escherichia coli and Salmonella (Neidhart, F. C., Curtiss, R., Ingraham, J. L., Lin, E. C. C., Low, K. B., Magasanik, B., Reznikoff, W. S., Riley, M., Schaechter, M., and Umbarger, H. E., Eds.) pp 642-56. ASM Press, Washington, DC.
13. Taylor, E. A., Palmer, D. R., and Gerlt, J. A. (2001) The Lesser "Burden Borne" by o-Succinylbenzoate Synthase: An "Easy" Reaction Involving a Carboxylate Carbon Acid, J. Am. Chem. Soc. 123, 5824-5.
14. Thompson, T. B., Garrett, J. B., Taylor, E. A., Meganathan, R., Gerlt, J. A., and Rayment, I. (2000) Evolution of enzymatic activity in the enolase superfamily: Structure of o-succinylbenzoate synthase from Escherichia coli in complex with Mg(II) and o-succinylbenzoate, Biochemistry 39, 10662-76.
15. Spencer, M. E., and Guest, J. R. (1973) Isolation and properties of fumarate reductase mutants of Escherichia coli, J. Bacteriol. 114, 563-70.
16. Palmer, D. R., Garrett, J. B., Sharma, V., Meganathan, R., Babbitt, P. C., and Gerlt, J. A. (1999) Unexpected divergence of enzyme function and sequence: "N-acylamino acid racemase" is o-succinylbenzoate synthase, Biochemistry 38, 4252-8.
17. Cleland, W. W. (1979) Statistical analysis of enzyme kinetic data, Methods Enzymol. 63, 103-38.
18. O'Brien, P. J., and Herschlag, D. (1999) Catalytic promiscuity and the evolution of new enzymatic activities, Chem. Biol. 6, R91-R105.
19. James, L. C., and Tawfik, D. S. (2001) Catalytic and binding polyreactivities shared by two unrelated proteins: The potential role of promiscuity in enzyme evolution, Protein Sci. 10, 2600-7.
20. Copley, S. D. (2003) Enzymes with extra talents: moonlighting functions and catalytic promiscuity, Curr. Opin. Chem. Biol. 7, 265-72.
21. Kazlauskas, R. J. (2005) Enhancing catalytic promiscuity for biocatalysis, Curr. Opin. Chem. Biol. 9, 195-201.
22. Bornscheucr, U. T., and Kazlauskas, R. J. (2004) Catalytic promiscuity in biocatalysis: using old enzymes to form new bonds and follow new pathways, Angew. Chem., Int. Ed. 43, 6032-40.
23. Yew, W. S., Akana, J., Wise, E. L., Rayment, I., and Gerlt, J. A. (2005) Evolution of enzymatic activities in the orotidine 5′-monophosphate decarboxylase suprafamily: enhancing the promiscuous D-arabino-hex-3-ulose 6-phosphate synthase reaction catalyzed by 3-keto-L-gulonate 6-phosphate decarboxylase, Biochemistry 44, 1807-15.
24. Aharoni, A., Gaidukov, L., Khersonsky, O., McQ Gould, S., Roodveldt, C., and Tawfik, D. S. (2005) The 'evolvability' of promiscuous protein functions, Nat. Genet. 37, 73-6.
25. Kondrashov, F. A. (2005) In search of the limits of evolution, Nat. Genet. 37, 9-10.
26. Gould, S. M., and Tawfik, D. S. (2005) Directed evolution of the promiscuous esterase activity of carbonic anhydrase II, Biochemistry 44, 5444-52.