Design and directed evolution of a dideoxy purine nucleoside phosphorylase

Protein Engineering, Design and Selection

Volumn 23, Issue 8, 2010, Pages 607-616

  Nannemann, David P ^a   Kaufmann, Kristian W ^a   Meiler, Jens ^a   Bachmann, Brian O ^a  

^a VANDERBILT UNIVERSITY   (United States)

Author keywords

directed evolution; enzyme design; nucleoside analog; purine nucleoside phosphorylase; Rosetta

Indexed keywords

AMINO ACIDS; BINDING ENERGY; BIOCHEMISTRY; CATALYSTS; COMPLEXATION; DESIGN; ENZYME ACTIVITY; ENZYMES; ESCHERICHIA COLI; MUTAGENESIS; ORGANIC ACIDS; PHOSPHATASES; PHOSPHORYLATION;

CATALYTIC ACTIVITY; DIRECTED EVOLUTION; ESCHERICHIA COLI CELLS; KINETIC CHARACTERIZATION; PHOSPHOROLYSIS; PURINE NUCLEOSIDE PHOSPHORYLASE; ROSETTA; SINGLE MUTANT; SITE DIRECTED MUTAGENESIS; TRANSITION STATE COMPLEX;

BIOMOLECULES;

DIDANOSINE; DIDEOXYNUCLEOTIDE; NUCLEOSIDE ANALOG; PHENYLALANINE; PURINE NUCLEOSIDE PHOSPHORYLASE; TYROSINE; PROTEIN BINDING;

AMINO ACID ANALYSIS; AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; ARTICLE; BINDING AFFINITY; CATALYSIS; ENZYME ACTIVITY; ENZYME BINDING; ENZYME ENGINEERING; ENZYME KINETICS; ENZYME PURIFICATION; ENZYME SUBSTRATE COMPLEX; ESCHERICHIA COLI; HUMAN; NONHUMAN; NUCLEIC ACID SYNTHESIS; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEIN FOLDING; SITE DIRECTED MUTAGENESIS; CHEMISTRY; COMPUTER PROGRAM; DIRECTED MOLECULAR EVOLUTION; GENETICS; METABOLISM; PROCEDURES; PROTEIN ENGINEERING; THERMODYNAMICS;

AMINO ACID SUBSTITUTION; DIDANOSINE; DIRECTED MOLECULAR EVOLUTION; HUMANS; MUTAGENESIS, SITE-DIRECTED; PROTEIN BINDING; PROTEIN ENGINEERING; PURINE-NUCLEOSIDE PHOSPHORYLASE; SOFTWARE; THERMODYNAMICS;

EID: 77954990456     PISSN: 17410126     EISSN: 17410134     Source Type: Journal    
DOI: 10.1093/protein/gzq033     Document Type: Article

References (46)

1. Bennett,E.M., Li,C.L., Allan,P.W., Parker,W.B. and Ealick,S.E. (2003) J. Biol. Chem., 278, 47110-47118.
2. Bernhardt,P., Mccoy,E. and O'Connor,S.E. (2007) Chem. Biol., 14, 888-897.
3. Bower,M.J., Cohen,F.E. and Dunbrack,R.L. (1997) J. Mol. Biol., 267, 1268-1282.
4. Canduri,F., dos Santos,D.M., Silva,R.G., Mendes,M.A., Basso,L.A., Palma,M.S., de Azevedo,W.F. and Santos,D.S. (2004) Biochem. Biophys. Res. Commun., 313, 907-914.
5. Clerq,E.D. (2009) Int. J. Antimicrob. Agents, 33, 307-320.
6. Crooks,G.E., Hon,G., Chandonia,J.M. and Brenner,S.E. (2004) Genome Res., 14, 1188-1190.
7. Damborsky,J. and Brezovsky,J. (2009) Curr. Opin. Chem. Biol., 13, 26-34.
8. Davis,I.W. and Baker,D. (2009) J. Mol. Biol., 385, 381-392.
9. de Azevedo,W.F., Canduri,F., dos Santos,D.M., Pereira,J.H., Dias,M.V.B., Silva,R.G., Mendes,M.A., Basso,L.A., Palma,M.S. and Santosce,D.S. (2003) Biochem. Biophys. Res. Commun., 309, 917-922.
10. Degroot,H., Degroot,H. and Noll,T. (1985) Biochem. J., 230, 255-260.
11. Deng,H., Lewandowicz,A., Schramm,V.L. and Callender,R. (2004) J. Am. Chem. Soc., 126, 9516-9517.
12. Dunbrack,R.L. and Karplus,M. (1993) J. Mol. Biol., 230, 543-574.
13. Erion,M.D., Takabayashi,K., Smith,H.B., Kessi,J., Wagner,S., Honger,S., Shames,S.L. and Ealick,S.E. (1997) Biochemistry, 36, 11725-11734.
14. Fazelinia,H., Cirino,P.C. and Maranas,C.D. (2007) Biophys. J., 92, 2120-2130.
15. Fedorov,A., et al. (2001) Biochemistry, 40, 853-860.
16. Fersht,A.R. (1974) Proc. R. Soc. London Ser. B, 187, 397-407.
17. Hsu,C.C., Hong,Z., Wada,M., Franke,D. and Wong,C.H. (2005) Proc. Natl Acad. Sci. USA, 102, 9122-9126.
18. Jackel,C., Kast,P. and Hilvert,D. (2008) Annu. Rev. Biophys., 37, 153-173.
19. Jiang,L., et al. (2008) Science, 319, 1387-1391.
20. Kaminski,P.A., Dacher,P., Dugue,L. and Pochet,S. (2008) J. Biol. Chem., 283, 20053-20059.
21. Kaufmann,K.W., Dawson,E.S., Henry,L.K., Field,J.R., Blakely,R.D. and Meiler,J. (2009) Proteins, 74, 630-642.
22. Komatsu,H., Awano,H., Ishibashi,H., Oikawa,T., Ikeda,I. and Araki,T. (2003) Nucleic Acids Res. Suppl., 3, 101-102.
23. Kortemme,T. and Baker,D. (2002) Proc. Natl Acad. Sci. USA, 99, 14116-14121.
24. Kuhlman,B., Dantas,G., Ireton,G.C., Varani,G., Stoddard,B.L. and Baker,D. (2003) Science, 302, 1364-1368.
25. Lewandowicz,A. and Schramm,V.L. (2004) Biochemistry, 43, 1458-1468.
26. Li,F., Maag,H. and Alfredson,T. (2008) J. Pharm. Sci., 97, 1109-1134.
27. Medici,R., Lewkowicz,E.S. and Iribarren,A.M. (2008) FEMS Microbiol. Lett., 289, 20-26.
28. Meiler,J. and Baker,D. (2006) Proteins, 65, 538-548.
29. Morley,K.L. and Kazlauskas,R.J. (2005) Trends Biotechnol., 23, 231-237.
30. Morozov,A.V., Havranek,J.J., Baker,D. and Siggia,E.D. (2005) Nucleic Acids Res., 33, 5781-5798.
31. Murphy,P.M., Bolduc,J.M., Gallaher,J.L., Stoddard,B.L. and Baker,D. (2009) Proc. Natl Acad. Sci. USA, 106, 9215-9220.
32. Pinheiro,E., Vasan,A., Kim,J.Y., Lee,E., Guimier,J.M. and Perriens,J. (2006) AIDS, 20, 1745-1752.
33. Popov,V.M., Yee,W.A. and Anderson,A.C. (2007) Proteins, 66, 375-387.
34. Pugmire,M.J. and Ealick,S.E. (2002) Biochem. J., 361, 1-25.
35. Qian,B., Raman,S., Das,R., Bradley,P., McCoy,A.J., Read,R.J. and Baker,D. (2007) Nature, 450, 259-264.
36. Reetz,M.T., Bocola,M., Carballeira,J.D., Zha,D. and Vogel,A. (2005) Angew. Chem. Int. Ed. Engl., 44, 4192-4196.
37. Ringia,E.A.T., Tyler,P.C., Evans,G.B., Furneaux,R.H., Murkin,A.S. and Schramm,V.L. (2006) J. Am. Chem. Soc., 128, 7126-7127.
38. Rogert,M.C., Trelles,J.A., Porro,S., Lewkowicz,E.S. and Iribarren,A.M. (2002) Biocatal. Biotransform., 20, 347-351.
39. Rothlisberger,D., et al. (2008) Nature, 453, 190-194.
40. Sammond,D.W., Eletr,Z.M., Purbeck,C., Kimple,R.J., Siderovski,D.P. and Kuhlman,B. (2007) J. Mol. Biol., 371, 1392-1404.
41. Schramm,V.L. (2005) Arch. Biochem. Biophys., 433, 13-26.
42. Shirae,H., Kobayashi,K., Shiragami,H., Irie,Y., Yasuda,N. and Yokozeki,K. (1989) Appl. Environ. Microbiol., 55, 419-424.
43. Soriano,V., Peters,M.G. and Zeuzem,S. (2009) Clin. Infect. Dis., 48, 313-320.
44. Stoeckler,J.D., Cambor,C. and Parks,R.E., Jr (1980) Biochemistry, 19, 102-107.
45. Voigt,C.A., Mayo,S.L., Arnold,F.H. and Wang,Z.G. (2001) Proc. Natl Acad. Sci. USA, 98, 3778-3783.
46. Zanghellini,A., Jiang,L., Wollacott,A.M., Cheng,G., Meiler,J., Althoff,E.A., Rothlisberger,D. and Baker,D. (2006) Protein Sci., 15, 2785-2794.