Crystal structures of nucleoside 2-deoxyribosyltransferase in native and ligand-bound forms reveal architecture of the active site

Structure

Volumn 4, Issue 1, 1996, Pages 97-107

  Armstrong, Shelly R ^a   Cook, William J ^b,d   Short, Steven A ^c   Ealick, Steven E ^a  

^a Department of Obstetrics Gynecology   (United States)

^b University of Alabama at Birmingham   (United States)

^c Burroughs Wellcome Co   (United States)

^d BIOCRYST PHARMACEUTICALS INC   (United States)

Author keywords

Active site; Alpha beta protein; Biocatalyst; Nucleoside; X ray crystallography

Indexed keywords

GLYCOSYLTRANSFERASE; NUCLEOSIDE DEOXYRIBOSYLTRANSFERASE; PURINE DERIVATIVE; PYRIMIDINE DERIVATIVE;

ARTICLE; BINDING SITE; CHEMISTRY; ENZYME SPECIFICITY; ENZYMOLOGY; LACTOBACILLUS; METABOLISM; PROTEIN BINDING; PROTEIN SECONDARY STRUCTURE; X RAY CRYSTALLOGRAPHY;

BINDING SITES; CRYSTALLOGRAPHY, X-RAY; LACTOBACILLUS; PENTOSYLTRANSFERASES; PROTEIN BINDING; PROTEIN STRUCTURE, SECONDARY; PURINES; PYRIMIDINES; SUBSTRATE SPECIFICITY;

LACTOBACILLUS;

EID: 0029643856     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0969-2126(96)00013-5     Document Type: Article

References (49)

1. Chawdhri, R.F., Hutchinson, D.W. & Richards, A. O'L. (1991). Nucleoside deoxyribosyltransferase activity and inosine phosphorylase activity in lactic acid bacteria. Arch. Microbiol. 155, 409-411.
2. MacNutt, W.S. (1952). The enzymically catalyzed transfer of the deoxyribosyl group from one purine or pyrimidine to another. Biochem. J. 50, 384-397.
3. Smar, M., Short, S. & Wertenden, R. (1991). Lyase activity of nucleoside-2′-deoxyribosyltransferase: transient generation of ribal and its use in the synthesis of 2′-deoxynucleosides. Biochemistry 30, 7908-7912.
4. Uerkvitz, W. (1971). Trans-N-deoxyribosylase from Lactobacillus helveticus. Eur. J. Biochem. 23, 387-395.
5. Steenkamp, D. (1991). The purine-2-deoxyribonucleosidase from Crithidia luculiae: purification and trans-N-deoxyribosylase activity. Eur. J. Biochem. 197, 431-439.
6. Steenkamp, D.J. & Halbich, J.F. (1992). Substrate specificity of the purine-2′-deoxyribonucleosidase of Crithidia luculiae. Biochem. J. 287, 125-129.
7. Porter, D.J., Merrill, B.M. & Short, S.A. (1995). Identification of the active site nucleophile in nucleoside 2′-deoxyribosyltransferase as glutamic acid 98. J. Biol. Chem. 270, 15551-15556.
8. Cook, W.J., Short, S.A. & Ealick, S.E. (1989). Crystallization and preliminary X-ray investigation of recombinant Lactobacillus leichmannii nucleoside deoxyribosyltransferase. J. Biol. Chem. 265, 2682-2683.
9. Beck, W.S. & Levin, M. (1963). Purification, kinetics, and repression control of bacterial trans-N-deoxyribosylase. J. Biol. Chem. 238, 702-709.
10. Danzin, C. & Cardinaud, R. (1974). Deoxyribosyl transfer catalysis with trans-N-deoxyribosylase. Eur. J. Biochem. 48, 255-262.
11. Mooser, G. (1992). Glycosidases and Glycosyltransferases. In The Enzymes, Vol. 20. (Sigman, D.S., ed), pp. 187-233, Academic Press, New York.
12. McCarter, J.D. & Withers, S.G. (1994). Mechanisms of enzymatic glycoside hydrolysis. Curr. Opin. Struct. Biol. 4, 885-892.
13. Carson, D. & Wasson, D. (1988). Synthesis of 2′,3′-dideoxynucleosides by enzymatic transglycosylation. Biochem. Biophys. Res. Commun. 155, 829-834.
14. Betbeder, D., Heath, C.M. & Hutchinson, D.W. (1991). Enzymatic synthesis of dideoxyribonucleosides. Nucleosides Nucleotides 10, 465-468.
15. Hutchinson, D.W. (1990), New approaches to the synthesis of antiviral nucleosides. Trends Biotechnol. 8, 348-353.
16. Hanrahan, J.R. & Hutchinson, D.W. (1992). The enzymatic synthesis of antiviral agents. J. Biotech. 23, 193-210.
17. Huang, M., Hatfield, K., Roetker, A., Montgomery, J. & Blakely, R. (1981). Analogs of 2′-deoxyadenosine: facile enzyme preparation and growth inhibitory effects on human cell lines. Biochem. Pharmacol. 30, 2663-2671.
18. Freeman, G.A., Shaver, S.R., Rideout, J.L. & Short, S.A. (1995). 2-amino-9-(3-azido-2,3-dideoxy-β-D-erythro-pentofuranosyl)-6-substituted- purines: synthesis and anti-HIV activity. Bioorg. Med. Chem. Lett. 3, in press.
19. Porter, D.J.T. & Short, S.A. (1995). Nucleoside 2-deoxyribosyltransferase. Pre-steady state kinetic analysis of native enzyme and mutant enzyme with an alanyl residue replacing Glu-98. J. Biol. Chem. 270, 15557-15562.
20. Watenpaugh, K.D., Sieker, L.C., Jensen, L.H., Legall, J. & Dubourdieu, M. (1972). Structure of the oxidized form of a flavodoxin at 2.5 Å resolution. Proc. Natl. Acad. Sci. USA 69, 3185-3188.
21. Stock, A.M., Mottonen, J.M., Stock, J.B. & Schutt, C.E. (1989). Three-dimensional structure of CheY, the response regulator of bacterial chemotaxis. Nature 337, 745-749.
22. Wilson, O.K., Rudolph, F.B. & Quiocho, F.A. (1991). Atomic structure of adenosine deaminase completed with a transition-state analog: understanding catalysis and immunodeficiency mutations. Science 252, 1278-1284.
23. Betts, L., Xiang, S., Short, S.A., Wolfenden, R. & Carter, C.W., Jr. (1994). Cytidine deaminase. The 2.3 å crystal structure of an enzyme:transition state complex. J. Mol. Biol. 235, 635-656.
24. Ealick, S.E., et al., & Bugg, O.E. (1990). Three-dimensional structure of human erythrocitic purine nucleoside phosphorylase at 3.2 Å resolution. J. Biol. Chem. 265, 1812-1820.
25. Walter, M.R., et al., & Ealick, S.E. (1990). Three-dimensional structure of thymidine phosphorylase from Escherichia coli at 2.8 Å resolution. J. Biol. Chem. 265, 14016-14022.
26. Morgunova, E.Y., et al., & Debabov, V.G. (1995). Atomic structure at 2.5 Å resolution of uridine phosphorylase from E. coli as refined in the monoclinic crystal lattice. FEBS Lett. 367, 183-187.
27. Scapin, G., Grubmeyer, C. & Sacchettini, J.C. (1994). Crystal structure of orotate phosphoribosyltransferase. Biochemistry 33, 1287-1294.
28. Eads, J.C., Scapin, G., Xu, Y., Grubmeyer, C. & Sacchettini, J.C. (1994). The crystal structure of human hypoxanthine-guanine phosphoribosyltransferase with bound GMP. Cell 78, 325-334.
29. Smith, J.L., et al., & Satow, Y. (1994). Structure of the allosteric regulatory enzyme of purine biosynthesis. Science 264, 1427-1433.
30. Dumas, C., et al., & Janin, J. (1992). X-ray structure of nucleoside diphosphate kinase. EMBO J. 11, 3202-3208.
31. Kabsch, W. & Sander, C. (1983). Dictionary of protein secondary structure: pattern recognition of hydrogen bonded and geometrical features. Biopolymers 22, 2577-2637.
32. Chothia, C. & Finkelstein, A. (1990). The classification and origins of protein folding patterns. Annu. Rev. Biochem. 59, 1007-1039.
33. Saenger, W. (1984). Structures and conformational properties of bases, furanose sugars, and phosphate groups. In Principles of Nucleic Acid Structure, (Cantor, C.R., ed), pp. 51-104, Springer-Verlag New York, Inc., New York.
34. Branden, C. (1980). Relation between structure and function of α/β proteins. Q. Rev. Biophys. 13, 317-338.
35. Huang, M., Montgomery, J.A., Thorpe, M.C., Stewart, E.L., Secrist, J.A. & Blakely, R.L. (1983). Formation of 3-(2′-deoxyribofuranosyl) and 9-(2′-deoxyribofuranosyl) nucleosides of 8-substituted purines by nucleoside deoxyribosyltransferase. Arch. Biochem. Biophys. 222, 183-144.
36. Howard, A.J., Nielsen, C. & Xuong, N.H. (1985). Software for a diffractometer with multiwire area detector. Methods Enzymol. 114, 452-472.
37. Xuong, N.B., Nielsen, C., Hamlin, R. & Anderson, D. (1985). Strategy for data collection from protein crystals using a multiwire counter area detector diffractometer, J. Appl. Cryst. 18, 342-350.
38. Matthews, B.W. (1968). Solvent content of protein crystals. J. Mol. Biol. 33, 491-497.
39. Wang, B.C. (1985). Resolution of phase ambiguity in macromolecular crystallography. Methods Enzymol. 155, 90-112.
40. Jones, T.A. (1985). Interactive computer graphics: FRODO. Methods Enzymol. 115, 157-171.
41. Finzel, B.C. (1987). Incorporation of fast Fourier transforms to speed least squares refinement of protein structures. J. Appl. Cryst. 20, 53-55.
42. Brünger, A.T. (1988). X-PLOR Manual, Version 3.1. Yale University, New Haven, CT.
43. Brünger, A.T. (1992). Free R value: a novel statistical quantity for assessing the accuracy of crystal structures. Nature 355, 472-475.
44. Mohamadi, F., et al., & Still, W.C. (1990). MacroModel V3.5X. J. Comput. Chem. 11, 440.
45. Sack, J. (1988). CHAIN - a crystallographic modeling program. J. Mol. Graph. 6, 244-245.
46. Berstein, F.C., et al., & Tasumi, M. (1977). The protein data bank: a computer-based archival file for macromolecular structures. J. Mol. Biol. 112, 535-542.
47. Kraulis, P.J. (1991). MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Cryst. 24, 946-950.
48. Carson, M. (1987). Ribbon models of macromolecules. J. Mol. Graphics 5, 103-106.
49. Laskowski, R.A., MacArthur, M.W., Moss, D.S. & Thornton, J.M. (1993). PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Cryst. 26, 283-291.