Crystal structures of GMP kinase in complex with ganciclovir monophosphate and Ap5G

Biochimie

Volumn 88, Issue 9, 2006, Pages 1157-1164

  Hible, G ^a   Daalova, P ^a,b   Gilles, A M ^c   Cherfils, J ^a  

^a LABORATOIRE D ENZYMOLOGIE ET BIOCHIMIE STRUCTURALES   (France)

^b INSTITUTE OF ORGANIC CHEMISTRY   (Bulgaria)

^c INSTITUT PASTEUR   (France)

Author keywords

Crystal structure; Domain motion; Ganciclovir; GMP kinase; Interfacial inhibitor

Indexed keywords

BACTERIAL ENZYME; DEOXYGUANOSINE PHOSPHATE; ENZYME INHIBITOR; GANCICLOVIR; GUANOSINE DIPHOSPHATE; GUANYLATE KINASE; RIBOSE; ADENOSINE 5' (HEXAHYDROGEN PENTAPHOSPHATE) 5' 5' ESTER WITH GUANOSINE; ADENOSINE 5'-(HEXAHYDROGEN PENTAPHOSPHATE) 5'-5' ESTER WITH GUANOSINE; ANTIVIRUS AGENT; DINUCLEOSIDE PHOSPHATE; NUCLEOTIDE;

ARTICLE; BINDING SITE; CATALYSIS; COMPLEX FORMATION; CRYSTAL STRUCTURE; DRUG BINDING; DRUG STRUCTURE; ENZYME ACTIVITY; ENZYME CONFORMATION; ENZYME PHOSPHORYLATION; ENZYME STABILITY; ENZYME SUBSTRATE; ESCHERICHIA COLI; PROTEIN DOMAIN; CHEMICAL STRUCTURE; CHEMISTRY; DRUG ANTAGONISM; DRUG EFFECT; HUMAN; X RAY CRYSTALLOGRAPHY;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI;

ANTIVIRAL AGENTS; BINDING SITES; CRYSTALLOGRAPHY, X-RAY; DINUCLEOSIDE PHOSPHATES; GANCICLOVIR; GUANYLATE KINASE; HUMANS; MODELS, MOLECULAR; MOLECULAR STRUCTURE; NUCLEOTIDES;

EID: 33748801478     PISSN: 03009084     EISSN: 61831638     Source Type: Journal    
DOI: 10.1016/j.biochi.2006.04.002     Document Type: Article

References (42)

1. Schaeffer H.J., Beauchamp L., de Miranda P., Elion G.B., Bauer D.J., and Collins P. 9-(2-hydroxyethoxymethyl) guanine activity against viruses of the herpes group. Nature 272 (1978) 583-585
2. Elion G.B. The purine path to chemotherapy. Science 244 (1989) 41-47
3. Coen D.M., and Schaffer P.A. Antiherpesvirus drugs: a promising spectrum of new drugs and drug targets. Nat. Rev. Drug Discov. 2 (2003) 278-288
4. Cheng Y.C., Huang E.S., Lin J.C., Mar E.C., Pagano J.S., Dutschman G.E., and Grill S.P. Unique spectrum of activity of 9-[(1,3-dihydroxy-2-propoxy)methyl]-guanine against herpesviruses in vitro and its mode of action against herpes simplex virus type 1. Proc. Natl. Acad. Sci. USA 80 (1983) 2767-2770
5. Field A.K., Davies M.E., DeWitt C., Perry H.C., Liou R., Germershausen J., Karkas J.D., Ashton W.T., Johnston D.B., and Tolman R.L. 9-([2-hydroxy-1-(hydroxymethyl)ethoxy]methyl)guanine: a selective inhibitor of herpes group virus replication. Proc. Natl. Acad. Sci. USA 80 (1983) 4139-4143
6. Crumpacker C.S., and Ganciclovir N. Engl. J. Med. 335 (1996) 721-729
7. Frank K.B., Chiou J.F., and Cheng Y.C. Interaction of herpes simplex virus-induced DNA polymerase with 9-(1,3-dihydroxy-2-propoxymethyl)guanine triphosphate. J. Biol. Chem. 259 (1984) 1566-1569
8. Fyfe J.A., Keller P.M., Furman P.A., Miller R.L., and Elion G.B. Thymidine kinase from herpes simplex virus phosphorylates the new antiviral compound, 9-(2-hydroxyethoxymethyl)guanine. J. Biol. Chem. 253 (1978) 8721-8727
9. Culver K.W., Ram Z., Wallbridge S., Ishii H., Oldfield E.H., and Blaese R.M. In vivo gene transfer with retroviral vector-producer cells for treatment of experimental brain tumors. Science 256 (1992) 1550-1552
10. Champness J.N., Bennett M.S., Wien F., Visse R., Summers W.C., Herdewijn P., de Clerq E., Ostrowski T., Jarvest R.L., and Sanderson M.R. Exploring the active site of herpes simplex virus type-1 thymidine kinase by X-ray crystallography of complexes with aciclovir and other ligands. Proteins 32 (1998) 350-361
11. Boehme R.E. Phosphorylation of the antiviral precursor 9-(1,3-dihydroxy-2-propoxymethyl)guanine monophosphate by guanylate kinase isozymes. J. Biol. Chem. 259 (1984) 12346-12349
12. Karkas J.D., Germershausen J., Tolman R.L., MacCoss M., Wagner A.F., Liou R., and Bostedor R. Stereochemical considerations in the enzymatic phosphorylation and antiviral activity of acyclonucleosides. I. Phosphorylation of 2'-nor-2'-deoxyguanosine. Biochim. Biophys. Acta 911 (1987) 127-135
13. Akyurek L.M., Nallamshetty S., Aoki K., San H., Yang Z.Y., Nabel G.J., and Nabel E.G. Coexpression of guanylate kinase with thymidine kinase enhances prodrug cell killing in vitro and suppresses vascular smooth muscle cell proliferation in vivo. Mol. Ther. 3 (2001) 779-786
14. Gallois-Montbrun S., Faraj A., Seclaman E., Sommadossi J.P., Deville-Bonne D., and Veron M. Broad specificity of human phosphoglycerate kinase for antiviral nucleoside analogs. Biochem. Pharmacol. 68 (2004) 1749-1756
15. Hible G., Christova P., Renault L., Seclaman E., Thompson A., Girard E., Munier-Lehmann H., and Cherfils J. Unique GMP-binding site in Mycobacterium tuberculosis guanosine monophosphate kinase. Proteins 62 (2005) 489-500
16. Hible G., Renault L., Schaeffer F., Christova P., Zoe Radulescu A., Evrin C., Gilles A.M., and Cherfils J. Calorimetric and crystallographic analysis of the oligomeric structure of Escherichia coli GMP kinase. J. Mol. Biol. 352 (2005) 1044-1059
17. Fioravanti E., Haouz A., Ursby T., Munier-Lehmann H., Delarue M., and Bourgeois D. Mycobacterium tuberculosis thymidylate kinase: structural studies of intermediates along the reaction pathway. J. Mol. Biol. 327 (2003) 1077-1092
18. Sekulic N., Shuvalova L., Spangenberg O., Konrad M., and Lavie A. Structural characterization of the closed conformation of mouse guanylate kinase. J. Biol. Chem. 277 (2002) 30236-30243
19. Stehle T., and Schulz G.E. Refined structure of the complex between guanylate kinase and its substrate GMP at 2.0 A resolution. J. Mol. Biol. 224 (1992) 1127-1141
20. Blaszczyk J., Li Y., Yan H., and Ji X. Crystal structure of unligated guanylate kinase from yeast reveals GMP-induced conformational changes. J. Mol. Biol. 307 (2001) 247-257
21. Kabsch W. Automatic processing of rotation diffraction data from crystals of initially unknown symmetry and cell constants. J. Appl. Crystallogr. 26 (1993) 795-800
22. Brunger 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., Read R.J., Rice L.M., Simonson T., and Warren G.L. Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr. D Biol. Crystallogr. 54 Pt 5 (1998) 905-921
23. Roussel A., and Cambillau C. Silicon Graphics, Mountain View (1989), TURBO-FRODO.l, California, USA (Vol. l, Page 1)
24. Schuttelkopf A.W., and van Aalten D.M. PRODRG: a tool for high-throughput crystallography of protein-ligand complexes. Acta Crystallogr. D Biol. Crystallogr. 60 (2004) 1355-1363
25. Abele U., and Schulz G.E. High-resolution structures of adenylate kinase from yeast ligated with inhibitor Ap5A, showing the pathway of phosphoryl transfer. Protein Sci. 4 (1995) 1262-1271
26. 2+. Proteins 32 (1998) 276-288
27. Gardberg A., Shuvalova L., Monnerjahn C., Konrad M., and Lavie A. Structural basis for the dual thymidine and thymidylate kinase activity of herpes thymidine kinases. Structure (Camb) 11 (2003) 1265-1277
28. Lavie A., Konrad M., Brundiers R., Goody R.S., Schlichting I., and Reinstein J. Crystal structure of yeast thymidylate kinase complexed with the bisubstrate inhibitor P1-(5'-adenosyl) P5-(5'-thymidyl) pentaphosphate (TP5A) at 2.0 A resolution: implications for catalysis and AZT activation. Biochemistry 37 (1998) 3677-3686
29. Muller C.W., and Schulz G.E. Structure of the complex between adenylate kinase from Escherichia coli and the inhibitor Ap5A refined at 1.9 A resolution. A model for a catalytic transition state. J. Mol. Biol. 224 (1992) 159-177
30. 2+ at 2.2 A: implications for water-mediated specificity. Biochemistry 35 (1996) 9716-9727
31. Haouz A., Vanheusden V., Munier-Lehmann H., Froeyen M., Herdewijn P., Van Calenbergh S., and Delarue M. Enzymatic and structural analysis of inhibitors designed against Mycobacterium tuberculosis thymidylate kinase. New insights into the phosphoryl transfer mechanism. J. Biol. Chem. 278 (2003) 4963-4971
32. Brown D.G., Visse R., Sandhu G., Davies A., Rizkallah P.J., Melitz C., Summers W.C., and Sanderson M.R. Crystal structures of the thymidine kinase from herpes simplex virus type-1 in complex with deoxythymidine and ganciclovir. Nat. Struct. Biol. 2 (1995) 876-881
33. Johansson K., Ramaswamy S., Ljungcrantz C., Knecht W., Piskur J., Munch-Petersen B., Eriksson S., and Eklund H. Structural basis for substrate specificities of cellular deoxyribonucleoside kinases. Nat. Struct. Biol. 8 (2001) 616-620
34. Sabini E., Ort S., Monnerjahn C., Konrad M., and Lavie A. Structure of human dCK suggests strategies to improve anticancer and antiviral therapy. Nat. Struct. Biol. 10 (2003) 513-519
35. Sandrini M.P., and Piskur J. Deoxyribonucleoside kinases: two enzyme families catalyze the same reaction. Trends Biochem. Sci. 30 (2005) 225-228
36. 2+ at 2-A resolution. Biochemistry 33 (1994) 9062-9069
37. Xu Y.W., Morera S., Janin J., and Cherfils J. AlF3 mimics the transition state of protein phosphorylation in the crystal structure of nucleoside diphosphate kinase and MgADP. Proc. Natl. Acad. Sci. USA 94 (1997) 3579-3583
38. Endrizzi J.A., Kim H., Anderson P.M., and Baldwin E.P. Mechanisms of Product Feedback Regulation and Drug Resistance in Cytidine Triphosphate Synthetases from the Structure of a CTP-Inhibited Complex(,). Biochemistry 44 (2005) 13491-13499
39. Yan H., and Tsai M.D. Nucleoside monophosphate kinases: structure, mechanism, and substrate specificity. Adv. Enzymol. Relat. Areas Mol. Biol. 73 (1999) 103-134 (x)
40. Wolf-Watz M., Thai V., Henzler-Wildman K., Hadjipavlou G., Eisenmesser E.Z., and Kern D. Linkage between dynamics and catalysis in a thermophilic-mesophilic enzyme pair. Nat. Struct. Mol. Biol. 11 (2004) 945-949
41. Choi B., Zocchi G., Wu Y., Chan S., and Jeanne Perry L. Allosteric control through mechanical tension. Phys. Rev. Lett. 95 (2005) (078102)
42. Pommier Y., and Cherfils J. Interfacial inhibition of macromolecular interactions: nature's paradigm for drug discovery. Trends Pharmacol. Sci. 26 (2005) 138-145