Phosphodeoxyribosyltransferases, designed enzymes for deoxyribonucleotides synthesis

Journal of Biological Chemistry

Volumn 288, Issue 9, 2013, Pages 6534-6541

  Kaminski, Pierre Alexandre ^a,b   Labesse, Gilles ^c,d  

^a INSTITUT PASTEUR   (France)

^b CNRS   (France)

^c CENTRE DE BIOCHIMIE STRUCTURALE   (France)

^d UNIV MONTPELLIER   (France)

Author keywords

[No Author keywords available]

Indexed keywords

DEOXYRIBONUCLEOTIDES; DNA METABOLISM; IN-VITRO; IN-VIVO; MONOPHOSPHATES; NUCLEOBASES; NUCLEOSIDE ANALOGUES; TRIPHOSPHATE;

BACILLI; BIOCHEMISTRY; BIOMOLECULES; PHOSPHORYLATION;

ENZYMES;

5' MONOPHOSPHATE 2' DEOXYRIBONUCLEOSIDE HYDROLASE; DEOXYRIBONUCLEOTIDE; DEOXYRIBOSE MONOPHOSPHATE; DEOXYRIBOSE TRIPHOSPHATE; HYDROLASE; NUCLEIC ACID BASE; NUCLEOTIDE DERIVATIVE; PHOSPHODEOXYRIBOSYLTRANSFERASE; RIBONUCLEOTIDE; TRANSFERASE; UNCLASSIFIED DRUG;

ARTICLE; CONTROLLED STUDY; ENZYME ACTIVITY; ENZYME ANALYSIS; ENZYME ASSAY; ENZYME ENGINEERING; IN VITRO STUDY; LACTOBACILLUS LEICHMANNII; LIGAND BINDING; MOLECULAR DOCKING; MOLECULAR MODEL; NONHUMAN; NUCLEOTIDE METABOLISM; PRIORITY JOURNAL; PROTEIN EXPRESSION; RAT; SIGNAL TRANSDUCTION;

ANIMALS; BACTERIAL PROTEINS; DEOXYRIBONUCLEOTIDES; LACTOBACILLUS; PENTOSYLTRANSFERASES; RATS; RECOMBINANT FUSION PROTEINS;

EID: 84874767570     PISSN: 00219258     EISSN: 1083351X     Source Type: Journal    
DOI: 10.1074/jbc.M112.446492     Document Type: Article

References (47)

1. Kirnos, M. D., Khudyakov, I. Y., Alexandrushkina, N. I., and Vanyushin, B. F. (1977) 2-Aminoadenine is an adenine substituting for a base in S-2L cyanophage DNA. Nature 270, 369-370
2. Warren, R. A. (1980) Modified bases in bacteriophage DNAs. Annu Rev. Microbiol. 34, 137-158
3. Benner, S. A. (2004) Understanding nucleic acids using synthetic chemistry. Acc. Chem. Res. 37, 784-797
4. Khakshoor, O., and Kool, E. T. (2011) Chemistry of nucleic acids. Impacts in multiple fields. Chem. Commun. (Camb.) 47, 7018-7024
5. Gibson, D. G., Glass, J. I., Lartigue, C., Noskov, V. N., Chuang, R. Y., Algire, M. A., Benders, G. A., Montague, M. G., Ma, L., Moodie, M. M., Merryman, C., Vashee, S., Krishnakumar, R., Assad-Garcia, N., Andrews- Pfannkoch, C., Denisova, E. A., Young, L., Qi, Z. Q., Segall-Shapiro, T. H., Calvey, C. H., Parmar, P. P., Hutchison, C. A., 3rd, Smith, H. O., and Venter, J. C. (2010) Creation of a bacterial cell controlled by a chemically synthesized genome. Science 329, 52-56
6. Gibson, D. G., Smith, H. O., Hutchison, C. A., 3rd, Venter, J. C., and Merryman, C. (2010) Chemical synthesis of the mouse mitochondrial genome. Nat. Methods 7, 901-903
7. Burgess, K., and Cook, D. (2000) Syntheses of nucleoside triphosphates. Chem. Rev. 100, 2047-2060
8. Mikhailopulo, I. A., and Miroshnikov, A. I. (2011) Biologically important nucloesides. Modern trends in biotechnology and application. Mendeleev Commun. 21, 57-68
9. Nordlund, P., and Reichard, P. (2006) Ribonucleotide reductases. Annu. Rev. Biochem. 75, 681-706
10. Doddapaneni, K., Zahurancik, W., Haushalter, A., Yuan, C., Jackman, J., and Wu, Z. (2011) RCL hydrolyzes 2'-deoxyribonucleoside 5'-monophosphate via formation of a reaction intermediate. Biochemistry 50, 4712-4719
11. Porter, D. J., Merrill, B. M., and Short, S. A. (1995) Identification of the active site nucleophile in nucleoside 2-deoxyribosyltransferase as glutamic acid 98. J. Biol. Chem. 270, 15551-15556
12. Ghiorghi, Y. K., Zeller, K. I., Dang, C. V., and Kaminski, P. A. (2007) The c-Myc target gene Rcl (C6orf108) encodes a novel enzyme, deoxynucleoside 5'-monophosphate N-glycosidase. J. Biol. Chem. 282, 8150-8156
13. Leslie, A. G. (2006) The integration of macromolecular diffraction data. Acta Crystallogr. D Biol. Crystallogr. 62, 48-57
14. Bailey, S., and Collaborative Computational Project, Number 4 (1994) The CCP4 Suite. Programs for protein crystallography. Acta. Crystallogr.D50, 760-763
15. Vagin, A., and Teplyakov, A. (2010) Molecular replacement with MOLREP. Acta Crystallogr. D 66, 22-25
16. Armstrong, S. R., Cook, W. J., Short, S. A., and Ealick, S. E. (1996) Crystal structures of nucleoside 2-deoxyribosyltransferase in native and ligandbound forms reveal architecture of the active site. Structure 4, 97-107
17. Emsley, P., and Cowtan, K. (2004) COOT. Model-building tools for molecular graphics. Acta Crystallogr. D 60, 2126-2132
18. Murshudov, G. N., Vagin, A. A., and Dodson, E. J. (1997) Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D 53, 240-255
19. Winn, M. D., Isupov, M. N., and Murshudov, G. N. (2001) Use of TLS parameters to model anisotropic displacements in macromolecular refinement. Acta Crystallogr. D 57, 122-133
20. Pons, J. L., and Labesse, G. (2009) @TOME-2. A new pipeline for comparative modeling of protein-ligand complexes. Nucleic Acids Res. 37, W485-W491
21. Wang, Y., Xiao, J., Suzek, T. O., Zhang, J., Wang, J., and Bryant, S. H. (2009) PubChem.Apublic information system for analyzing bioactivities of small molecules. Nucleic Acids Res. 37, W623-W633
22. Korb, O., Stützle, T., and Exner, T. E. (2009) Empirical scoring functions for advanced protein-ligand docking with PLANTS. J. Chem. Inf. Model 49, 84-96
23. Kaminski, P. A. (2002) Functional cloning, heterologous expression, and purification of two different N-deoxyribosyltransferases from Lactobacillus helveticus. J. Biol. Chem. 277, 14400-14407
24. Yang, Y., Padilla, A., Zhang, C., Labesse, G., and Kaminski, P. A. (2009) Structural characterization of the mammalian deoxynucleotide N-hydrolase Rcl and its stabilizing interactions with two inhibitors. J. Mol. Biol. 394, 435-447
25. Cardinaud, R., and Holguin, J. (1979) Nucleoside deoxyribosyltransferase- II from Lactobacillus helveticus substrate specificity studied. Pyrimidine bases as acceptors. Biochim. Biophys. Acta 568, 339-347
26. Huang, M. C., Montgomery, J. A., Thorpe, M. C., Stewart, E. L., Secrist, J. A., 3rd, and Blakley, R. L. (1983) Formation of 3-(2'-deoxyribofuranosyl) and 9-(2'-deoxyribofuranosyl) nucleosides of 8-substituted purines by nucleoside deoxyribosyltransferase. Arch. Biochem. Biophys. 222, 133-144
27. Müller, M., Hutchinson, L. K., and Guengerich, F. P. (1996) Addition of deoxyribose to guanine and modified DNA based by Lactobacillus helveticus trans-N-deoxyribosylase. Chem. Res. Toxicol. 9, 1140-1144
28. Schnetz-Boutaud, N. C., Mao, H., Stone, M. P., and Marnett, L. J. (2000) Synthesis of oligonucleotides containing the alkali-labile pyrimidopurinone adduct, M(1)G. Chem. Res. Toxicol. 13, 90-95
29. Holguin, J., Cardinaud, R., and Salemink, C. A. (1975) Trans-N-deoxyribosylase. Substrate specificity studies. Purine bases as acceptors. Eur. J. Biochem. 54, 515-520
30. Huang, M. C., Hatfield, K., Roetker, A. W., Montgomery, J. A., and Blakley, R. L. (1981) Analogs of 2'-deoxyadenosine. Facile enzymatic preparation and growth inhibitory effects on human cell lines. Biochem. Pharmacol. 30, 2663-2671
31. Freeman, G. A., Shaver, S. R., Rideout, J. L., and Short, S. A. (1995) 2- Amino-9-(3-azido-2,3-dideoxy-beta-D-erythro-pentofuranosyl)-6-substitute d-9H-purines. Synthesis and anti-HIV activity. Bioorg. Med. Chem. 3, 447-458
32. Kaminski, P. A., Dacher, P., Dugué, L., and Pochet, S. (2008) In vivo reshaping the catalytic site of nucleoside 2'-deoxyribosyltransferase for dideoxy- and didehydronucleosides via a single amino acid substitution. J. Biol. Chem. 283, 20053-20059
33. Gerlt, J. A., and Babbitt, P. C. (2009) Enzyme (re)design. Lessons from natural evolution and computation. Curr. Opin. Chem. Biol. 13, 10-18
34. Höhne, M., Schätzle, S., Jochens, H., Robins, K., and Bornscheuer, U. T. (2010) Rational assignment of key motifs for function guides in silico enzyme identification. Nat. Chem. Biol. 6, 807-813
35. Jochens, H., and Bornscheuer, U. T. (2010) Natural diversity to guide focused directed evolution. ChemBioChem 11, 1861-1866
36. Johnson, D. C., 2nd, and Widlanski, T. S. (2004) Overview of the synthesis of nucleoside phosphates and polyphosphates. Current Protocols in Nucleic Acid Chemistry, Chapter 13, Unit 13.11, Wiley, New York
37. Caton-Williams, J., Smith, M., Carrasco, N., and Huang, Z. (2011) Protection- free one-pot synthesis of 2'-deoxynucleoside 5'-triphosphates and DNA polymerization. Org. Lett. 13, 4156-4159
38. Bao, J., and Ryu, D. D. (2007) Total biosynthesis of deoxynucleoside triphosphates using deoxynucleoside monophosphate kinases for PCR application. Biotechnol. Bioeng. 98, 1-11
39. Ladner, W. E., and Whitesides, G. M. (1985) Enzymatic synthesis of Deoxy- ATP using DNA as starting material. J. Org. Chem. 50, 1076-1079
40. Eriksson, S., Munch-Petersen, B., Johansson, K., and Eklund, H. (2002) Structure and function of cellular deoxyribonucleoside kinases. Cell Mol. Life Sci. 59, 1327-1346
41. Johansson, M., van Rompay, A. R., Degrève, B., Balzarini, J., and Karlsson, A. (1999) Cloning and characterization of the multisubstrate deoxyribonucleoside kinase of Drosophila melanogaster. J. Biol. Chem. 274, 23814-23819
42. Munch-Petersen, B., Piskur, J., and Sondergaard, L. (1998) Four deoxynucleoside kinase activities from Drosophila melanogaster are contained within a single monomeric enzyme, a new multifunctional deoxynucleoside kinase. J. Biol. Chem. 273, 3926-3931
43. Hébrard, C., Dumontet, C., and Jordheim, L. P. (2009) Development of gene therapy in association with clinically used cytotoxic deoxynucleoside analogues. Cancer Gene Ther. 16, 541-550
44. Chen, M. S., Summers, W. P., Walker, J., Summers, W. C., and Prusoff, W. H. (1979) Characterization of pyrimidine deoxyribonucleoside kinase (thymidine kinase) and thymidylate kinase as a multifunctional enzyme in cells transformed by herpes simplex virus type 1 and in cells infected with mutant strains of herpes simplex virus. J. Virol. 30, 942-945
45. Chen, M. S., Walker, J., and Prusoff, W. H. (1979) Kinetic studies of herpes simplex virus type 1-encoded thymidine and thymidylate kinase, a multifunctional enzyme. J. Biol. Chem. 254, 10747-10753
46. Marlière, P., Patrouix, J., Döring, V., Herdewijn, P., Tricot, S., Cruveiller, S., Bouzon, M., and Mutzel, R. (2011) Chemical evolution of a bacterium's genome. Angew. Chem. Int. Ed. Engl. 50, 7109-7114
47. Padilla, A., Amiable, D., Pochet, S., Kaminski, P.-A., and Labesse, G. (2013) Structure of the oncoprotein Rcl bound to three nucleotide analogues. Acta Cryst. D69, 247-255