Structural basis for the specificity, catalysis, and regulation of human uridine-cytidine kinase

Structure

Volumn 12, Issue 5, 2004, Pages 751-764

  Suzuki, Nobuo N ^a,b   Koizumi, Katsuhisa ^c   Fukushima, Masanori ^c   Matsuda, Akira ^a   Inagaki, Fuyuhiko ^a,b  

^a HOKKAIDO UNIVERSITY   (Japan)

^b JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

^c TAIHO PHARMACEUTICAL CO LTD   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE DIPHOSPHATE; CYTIDINE; CYTIDINE PHOSPHATE; CYTIDINE TRIPHOSPHATE; RIBONUCLEOSIDE; URIDINE KINASE; URIDINE TRIPHOSPHATE;

ARTICLE; CATALYSIS; CRYSTAL STRUCTURE; ENZYME REGULATION; ENZYME SPECIFICITY; ENZYME STRUCTURE; ENZYME SUBSTRATE COMPLEX; NUCLEOTIDE BINDING SITE; PRIORITY JOURNAL; RNA SYNTHESIS;

ADENOSINE TRIPHOSPHATE; AMINO ACID SEQUENCE; BINDING SITES; FEEDBACK, BIOCHEMICAL; HUMANS; LIGANDS; MOLECULAR SEQUENCE DATA; PROTEIN STRUCTURE, QUATERNARY; PROTEIN STRUCTURE, TERTIARY; SUBSTRATE SPECIFICITY; ULTRACENTRIFUGATION; URIDINE KINASE;

EID: 2342600247     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.str.2004.02.038     Document Type: Article

References (47)

1. 1 ATPase. Acta Crystallogr. D Biol. Crystallogr. 52:1996;30-42
2. Anderson E.P. Nucleoside and nucleotide kinases. Third Edition, Volume 9 P.D., Boyer The Enzymes. 1973;49-96 Academic Press, New York
3. Berry M.B., Phillips G.N. Jr. Crystal structures of Bacillus stearothermophilus adenylate kinase with bound Ap5A, Mg2+ Ap5A, and Mn2+ Ap5A reveal an intermediate lid position and six coordinate octahedral geometry for bound Mg2+ and Mn2+. Proteins. 32:1998;276-288
4. Briozzo P., Golinelli-Pimpaneau B., Gilles A.-M., Gaucher J.-F., Burlacu-Miron S., Sakamoto H., Janin J., Barzu O. Structures of escherichia coli CMP kinase alone and in complex with CDP. a new fold of the nucleoside monophosphate binding domain and insights into cytosine nucleotide specificity Structure. 6:1998;1517-1527
5. Brünger A.T., Adams P.D., Clore G.M., DeLano W.L., Gros P., Grosse-Kunstleve R.W., Jiang J.S., Kuszewski J., Nilges M., Pannu N.S., et al. Crystallography & NMR system. a new software suite for macromolecular structure determination Acta Crystallogr. D Biol. Crystallogr. 54:1998;905-921
6. Cambillau, C., and Roussel, A. (1997). Turbo-Frodo, Version OpenGL 1, Université Aix-Marseille II, Marseille, France.
7. Charlier H.A., Runquist J.A., Miziorko H.M. Evidence supporting catalytic roles for aspartate residues in phosphoribulokinase. Biochemistry. 33:1994;9343-9350
8. Cheng N., Payne R.C., Traut T.W. Regulation of uridine kinase. Evidence for a regulatory site. J. Biol. Chem. 261:1986;13006-13012
9. Cihak A., Rada B. Uridine kinase. properties, biological significance and chemotherapeutic aspects (a review) Neoplasma. 23:1976;233-257
10. Deng Q.-I., Ives D.H. Non-allosteric regulation of the uridine kinase from seeds of Zea mays. Biochim. Biophys. Acta. 377:1975;84-94
11. Greenberg N., Schumm D.E., Webb T.E. Uridine kinase activities and pyrimidine nucleoside phosphorylation in fluoropyrimidine-sensitive and -resistant cell lines of the Novikoff hepatoma. Biochem. J. 164:1977;379-387
12. Harrison D.H., Runquist J.A., Holub A., Miziorko H.M. The crystal structure of phosphoribulokinase from Rhodobacter sphaeroides reveals a fold similar to that of adenylate kinase. Biochemistry. 37:1998;5074-5085
13. Hattori H., Tanaka M., Fukushima M., Sasaki T., Matsuda A. Nucleosides and nucleotides. 158. 1-(3-C-Ethynyl-beta-D-ribo-pentofuranosyl)cytosine, 1-(3-C-ethynyl-beta-D-ribo-pentofuranosyl)uracil, and their nucleobase analogues as new potential multifunctional antitumor nucleosides with a broad spectrum of activity. J. Med. Chem. 39:1996;5005-5011
14. Holm L., Sander C. Mapping the protein universe. Science. 273:1996;595-603
15. Iltzsch M.H., Uber S.S., Tankersley K.O., el Kouni M.H. Structure-activity relationship for the binding of nucleoside ligands to adenosine kinase from Toxoplasma gondii. Biochem. Pharmacol. 49:1995;1501-1512
16. Izard T., Ellis J. The crystal structures of chloramphenicol phosphotransferase reveal a novel inactivation mechanism. EMBO J. 19:2000;2690-2700
17. Johansson K., Ramaswamy S., Ljungcrantz C., Knecht W., Piskur J., Munch-Petersen B., Eriksson S., Eklund H. Structural basis for substrate specificities of cellular deoxyribonucleoside kinases. Nat. Struct. Biol. 8:2001;616-620
18. Jones T.A., Zou J.Y., Cowan S.W., Kjeldgaard M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A. 47:1991;110-119
19. Kang G.J., Cooney D.A., Moyer J.D., Kelley J.A., Kim H.Y., Marquez V.E., Johns D.G. Cyclopentenylcytosine triphosphate. Formation and inhibition of CTP synthetase. J. Biol. Chem. 264:1989;713-718
20. Koizumi K., Shimamoto Y., Azuma A., Wataya Y., Matsuda A., Sasaki T., Fukushima M. Cloning and expression of uridine/cytidine kinase cDNA from human fibrosarcoma cells. Int. J. Mol. Med. 8:2001;273-278
21. Koshland D.E. Jr. The key-lock theory and the induced fit theory. Angew. Chem. Int. Ed. Engl. 33:1994;2375-2378
22. Kraulis P.J. Molscript. a program to produce both detailed and schematic plots of protein structures J. Appl. Crystallogr. 24:1991;946-950
23. Krystal G., Scholefield P. The partial purification and properties of uridine kinase from Ehrlich ascites tumor cells. Can. J. Biochem. 51:1973;379-389
24. LeMaster D.M., Richards F.M. 1H-15N heteronuclear NMR studies of Escherichia coli thioredoxin in samples isotopically labeled by residue type. Biochemistry. 24:1985;7263-7268
25. Matsuda A., Fukushima M., Wataya Y., Sasaki T. A new antitumor nucleoside, 1-(3-C-ethynyl-beta-D-ribo-pentofuranosyl)cytosine (ECyd), is a potent inhibitor of RNA synthesis. Nucleosides Nucleotides. 18:1999;811-814
26. Merrit E.A., Murphy M.E.P. Raster3D Version 2.0. A program for photorealistic molecular graphics. Acta Crystallogr. D Biol. Crystallogr. 50:1994;869-873
27. Mikkelsen N.E., Johansson K., Karlsson A., Knecht W., Andersen G., Piškur J., Munch-Petersen B., Eklund H. Structural basis for feedback inhibition of the deoxyribonucleoside salvage pathway. studies of the drosophila deoxyribonucleoside kinase Biochemistry. 42:2003;5706-5712
28. Miziorko H.M. Phosphoribulokinase. current perspectives on the structure/function basis for regulation and catalysis Adv. Enzymol. Relat. Areas Mol. Biol. 74:2000;95-127
29. Müller C.W., Schlauderer G.J., Reinstein J., Schulz G.E. Adenylate kinase motions during catalysis. an energetic counterweight balancing substrate binding Structure. 4:1996;147-156
30. Munch-Petersen B., Knecht W., Lenz C., Sondergaard L., Piskur J. Functional expression of a multisubstrate deoxyribonucleoside kinase from Drosophila melanogaster and its C-terminal deletion mutants. J. Biol. Chem. 275:2000;6673-6679
31. Nicholls A., Sharp K., Honig B. Protein folding and association. insights from the interfacial and thermodynamic properties of hydrocarbons Proteins. 11:1991;281-296
32. Orengo A. Regulation of enzymic activity by metabolites. I. Uridine-cytidine kinase of Novikoff ascites rat tumor. J. Biol. Chem. 244:1969;2204-2209
33. Otwinowski Z., Minor W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276:1997;307-326
34. Parks R.E., Agarwal R.P. Nucleoside diphosphokinases. Boyer P.D. The Enzymes. 1973;307-334 Academic Press, New York
35. Pflugrath J.W. The finer things in X-ray diffraction data collection. Acta Crystallogr. D Biol. Crystallogr. 55:1999;1718-1725
36. Read R.J., Schierbeek A.J.J. A phased translation function. J. Appl. Crystallogr. 21:1988;490-495
37. Ropp P.A., Traut T.W. Uridine kinase. altered enzyme with decreased affinities for uridine and CTP Arch. Biochem. Biophys. 359:1998;63-68
38. Schumacher M.A., Scott D.M., Mathews I.I., Ealick S.E., Roos D.S., Ullman B., Brennan R.G. Crystal structures of Toxoplasma gondii adenosine kinase reveal a novel catalytic mechanism and prodrug binding. J. Mol. Biol. 298:2000;875-893
39. Sekulic N., Shuvalova L., Spangenberg O., Konrad M., Lavie A. Structural characterization of the closed conformation of mouse guanylate kinase. J. Biol. Chem. 33:2002;30236-30243
40. Suzuki N.N., Koizumi K., Fukushima M., Matsuda A., Inagaki F. Crystallization and preliminary X-ray analysis of human uridine-cytidine kinase 2. Acta Crystallogr. D Biol. Crystallogr. 59:2003;1477-1478
41. Tabata S., Tanaka M., Endo Y., Obata T., Matsuda A., Sasaki T. Anti-tumor mechanisms of 3′-ethynyluridine and 3′-ethynylcytidine as RNA synthesis inhibitors. development and characterization of 3′- ethynyluridine-resistant cells Cancer Lett. 116:1997;225-231
42. Van Rompay A.R., Johansson M., Karlsson A. Phosphorylation of deoxycytidine analog monophosphates by UMP-CMP kinase. molecular characterization of the human enzyme Mol. Pharmacol. 56:1999;562-569
43. Van Rompay A.R., Norda A., Linden K., Johansson M., Karlsson A. Phosphorylation of uridine and cytidine nucleoside analogs by two human uridine-cytidine kinases. Mol. Pharmacol. 59:2001;1181-1186
44. Vonrhein C., Schlauderer G.J., Schulz G.E. Movie of the structural changes during a catalytic cycle of nucleoside monophosphate kinases. Structure. 3:1995;483-490
45. Walker J.E., Saraste M., Runswick M.J., Gay N.J. Distantly related sequences in the alpha- and beta-subunits of ATP synthase, myosin, kinases and other ATP-requiring enzymes and a common nucleotide binding fold. EMBO J. 1:1982;945-951
46. Yan H., Tsai M.-D. Nucleoside monophosphate kinases. structure, mechanism, and substrate specificity Adv. Enzymol. Relat. Areas Mol. Biol. 73:1999;103-134
47. Yun M., Park C.-G., Kim J.-Y., Rock C.O., Jackowski S., Park H.-W. Structural basis for the feedback regulation of Escherichia coli pantothenate kinase by coenzyme A. J. Biol. Chem. 275:2000;28093-28099