Three-dimensional structure of the R115E mutant of T4-bacteriophage 2′-deoxycytidylate deaminase

Biochemistry

Volumn 43, Issue 43, 2004, Pages 13715-13723

  Almog, Rami ^a   Maley, Frank ^a   Maley, Gladys F ^a   MacColl, Robert ^a   Van Roey, Patrick ^a  

^a WADSWORTH CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA; BINDING ENERGY; CHEMOTHERAPY; CRYSTAL STRUCTURE; DNA; METABOLISM; MOLECULES; SUBSTRATES; TUMORS;

CYTIDINE DEAMINASE (CDA); DEOXYCYTIDYLATE DEAMINASE (DCD);

ENZYMES;

2' DEOXYCYTIDINE PHOSPHATE DEAMINASE; CYTIDINE DEAMINASE; DEOXYCYTIDINE PHOSPHATE DEAMINASE; DIMER; DNA; PHOSPHATE; THYMIDYLATE SYNTHASE; UNCLASSIFIED DRUG; ZINC ION;

ARTICLE; BACTERIOPHAGE T4; BINDING SITE; CONTROLLED STUDY; CRYSTAL STRUCTURE; CRYSTALLIZATION; DNA SYNTHESIS; MOLECULAR INTERACTION; MOLECULE; NONHUMAN; PRIORITY JOURNAL; PROTEIN BINDING; WILD TYPE;

ALLOSTERIC REGULATION; AMINO ACID SUBSTITUTION; ARGININE; BACTERIOPHAGE T4; BINDING SITES; CRYSTALLIZATION; CRYSTALLOGRAPHY, X-RAY; CYTIDINE; CYTIDINE DEAMINASE; DCMP DEAMINASE; GLUTAMIC ACID; MODELS, MOLECULAR; MUTAGENESIS, SITE-DIRECTED; NUCLEOSIDE DEAMINASES; PROTEIN STRUCTURE, QUATERNARY; PROTEIN SUBUNITS; PYRIMIDINE NUCLEOSIDES; SUBSTRATE SPECIFICITY; VIRAL PROTEINS; ZINC;

BACTERIA (MICROORGANISMS); MAMMALIA;

EID: 7244249940     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi048928h     Document Type: Article

References (45)

1. Maley, F., and Maley, G. F. (1999) Structure, function analysis of T4-phage dexoycytidylate deaminase and its role in the phage metabolic pathway, Paths Pyrimidines 7, 1-7.
2. Nicander, B., and Reichard, P. (1985) Evidence for the involvement of substrate cycles in the regulation of deoxyribonucleoside triphosphate pools in 3T6 cells, J. Biol. Chem. 260, 9216-9222.
3. Carreras, C. W., and Santi, D. V. (1995) The catalytic mechanism and structure of thymidylate synthase, Annu. Rev. Biochem. 64, 721-762.
4. Rose, M. G., Farrell, M. P., and Schmitz, J. C. (2002) Thymidylate synthase: a critical target for cancer chemotherapy, Clin. Colorectal Cancer 1, 220-229.
5. Maley, F., and Maley, G. F. (1972) in Current Topics in Cellular Regulation (Horecker, B. L., and Stadtman, E. R., Eds.) pp 177-228, Academic Press, New York.
6. Hernandez-Santiago, B., Placidi, L., Cretton-Scott, E., Faraj, A., Bridges, E. G., Bryant, M. L., Rodriguez-Orengo, J., Imbach, J. L., Gosselin, G., Pierra, C., Dukhan, D., and Sommadossi, J. P. (2002) Pharmacology of β-L-thymidine and β-L-2′-deoxycytidine in HepG2 cells and primary human hepatocytes: relevance to chemotherapeutic efficacy against hepatitis B virus, Antimicrob. Agents Chemother. 46, 1728-1733.
7. Liou, J.-Y., Krishnan, P., Hsieh, C.-C., Dutschman, G. E., and Cheng, Y.-C. (2003) Assessment of the effect of phosphorylated metabolites of anti-human immunodeficiency virus and anti-hepatitis B virus pyrimidine analogs on the behavior of human deoxycytidylate deaminase, Mol. Pharmacol. 63, 105-110.
8. Maley, F. (1962) Nucleotide interconversions. VII. The effect of halogenated and N-methyl derivatives of deoxycytidylic acid on deoxycytidylate deaminase and thymidylate synthetase, Biochim. Biophys. Acta 60, 135-138.
9. Neuhard, J., and Nygaard, P. (1987) in Purines and pyrimidines (Neidhardt, F. C., Ingraham, J. L., Low, K. B., Magasanik, B., Schaechter, M., and Umbarger, H. E., Eds.) pp 445-473, American Society for Microbiology, Washington, DC.
10. Maley, G. F., and Maley, F. (1982) Allosteric transitions associated with the binding of substrate and effector ligands to T2 phage induced deoxycytidylate deaminase, Biochemistry 21, 3780-3785.
11. Anderson, A. C., O'Neil, R. H., DeLano, W. L., and Stroud, R. M. (1999) The structural mechanism for half-the-sites reactivity in an enzyme, thymidylate synthase, involves a relay of changes between subunits, Biochemistry 38, 13829-13836.
12. Maley, F., Pederson-Lane, J., and Changchien, L. M. (1995) Complete restoration of activity to inactive mutants of Escherichia coli thymidylate synthase: evidence that E. coli thymidylate synthase is a half-the-sites activity enzyme, Biochemistry 34, 1469-1474.
13. McGaughey, K. M., Wheeler, L. J., Moore, J. T., Maley, G. F., Maley, F., and Mathews, C. K. (1996) Protein-protein interactions involving T4 phage-coded deoxycytidylate deaminase and thymidylate synthase, J. Biol. Chem. 271, 23037-23042.
14. Maley, G. F., Lobo, A. P., and Maley, F. (1993) Properties of an affinity-column-purified human deoxycytidylate deaminase, Biochim. Biophys. Acta 1162, 161-170.
15. Moore, J. T., Ciesla, J. M., Changchien, L. M., Maley, G. F., and Maley, F. (1994) Identification of a site necessary for allosteric regulation in T4-phage deoxycytidylate deaminase, Biochemistry 33, 2104-2112.
16. Keefe, R. G., Maley, G. F., Saxl, R. L., and Maley, F. (2000) A T4-phage deoxycytidylate deaminase mutant that no longer requires deoxycytidine 5′-triphosphate for activation, J. Biol. Chem. 275, 12598-12602.
17. Betts, L., Xiang, S., Short, S. A., Wolfenden, R., and Carter, C. W. J. (1994) Cytidine deaminase. The 2.3 Å crystal structure of an enzyme: transition-state analog complex, J. Mol. Biol. 235, 635-656.
18. Carlow, D. C., Carter, C. W. J., Mejlhede, N., Neuhard, J., and Wolfenden, R. (1999) Cytidine deaminases from B. subtilis and E. coli: compensating effects of changing zinc coordination and quaternary structure, Biochemistry 38, 12258-12265.
19. Snider, M. J., Gaunitz, S., Ridgway, C., Short, S. A., and Wolfenden, R. (2000) Temperature effects on the catalytic efficiency, rate enhancement, and transition state affinity of cytidine deaminase, and the thermodynamic consequences for catalysis of removing a substrate "anchor", Biochemistry 39, 9746-9753.
20. Reizer, J., Buskirk, S., Bairoch, A., Reizer, A., and Saier, M. H., Jr. (1994) A novel zinc-binding motif found in two ubiquitous deaminase families, Protein Sci 3, 853-856.
21. Johansson, E., Mejlhede, N., Neuhard, J., and Larsen, S. (2002) Crystal structure of the tetrameric cytidine deaminase from Bacillus subtllls at 2.0 Å resolution, Biochemistry 41, 2563-2570.
22. Johansson, E., Neuhard, J., Willemoes, M., and Larsen, S. (2004) Structural, kinetic and mutational studies of the zinc ion environment in tetrameric cytidine deaminase, Biochemistry 43, 6020-6029.
23. Moore, J. T., Uppal, A., Maley, F., and Maley, G. F. (1993) Overcoming inclusion body formation in a high-level expression system, Protein Expression Purif. 4, 160-163.
24. Lebowitz, J., Lewis, M. S., and Schuck, P. (2002) Modern analytical ultracentrifugation in protein science: A tutorial review, Protein Sci. 11, 2067-2079.
25. Schuck, P., Perugini, M. A., Gonzalez, N. R., Howlett, G. J., and Schubert, D. (2002) Size-distribution analysis of proteins by analytical ultracentrifugation: strategies and application to model systems, Biophys. J. 82, 1096-1111.
26. Terwilliger, T. C., and Berendzen, J. (1999) Automated structure solution for MIR and MAD, Acta Crystallogr. D55, 849-861.
27. Cowtan, K. D., and Main, P. (1996) Phase combination and cross validation in iterated density-modification calculations, Acta Crystallogr. D52, 43-48.
28. Roussel, A., and Cambillau, C. (1989) in Silicon Graphics Geometry Partners Directory (Graphics, S., Ed.) pp 77-78, Silicon Graphics, Mountain View, CA.
29. Jones, T. A., Zou, J. Y., Cowan, S. W., and Kjeldgaard, M. (1991) Improved methods for the building of protein models in electron-density maps and the location of errors in these maps, Acta Crystallogr. A47, 110-119.
30. 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. (1998) Crystallography and NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr. D54, 905-921.
31. Laskowski, R. A., McArthur, M. W., Moss, D. S., and Thornton, J. M. (1993) PROCHECK: a program to check the stereochemical quality of protein structures, J. Appl. Crystallogr. 26, 282-291.
32. Maley, G. F., MacColl, R., and Maley, F. (1972) T2r+ bacteriophage- induced enzymes. II. The subunit structure of deoxycytidylate deaminase, J. Biol. Chem. 247, 940-945.
33. Maley, G. F., and Maley, F. (1966) The significance of the substrate specificity of T2r+-induced deoxycytidylate deaminase, J. Biol. Chem. 241, 2176-2177.
34. Ireton, G. C., McDermott, G., Black, M. E., and Stoddard, B. L. (2002) The structure of Escherichia coli cytosine deaminase, J. Mol. Biol. 315, 687-697.
35. Johansson, E., Bjornberg, O., Nyman, P. O., and Larsen, S. (2003) Structure of the bifunctional dCTP deaminase-dUTPase from Methanocaldococcus jannaschii and its relation to other homotrimeric dUTPases, J. Biol. Chem. 278, 27916-27922.
36. Carlow, D. C., Short, S. A., and Wolfenden, R. (1998) Complementary truncations of a hydrogen bond to ribose involved in transition-state stabilization by cytidine deaminase, Biochemistry 37, 1199-1203.
37. Xiang, S., Short, S. A., Wolfenden, R., and Carter, C. W. J. (1995) Transition-state selectivity for a single hydroxyl group during catalysis by cytidine deaminase, Biochemistry 34, 4516-4523.
38. Xiang, S., Short, S. A., Wolfenden, R., and Carter, C. W. J. (1997) The structure of the cytidine deaminase-product complex provides evidence for efficient proton transfer and ground-state destabilization, Biochemistry 36, 4768-4774.
39. Xiang, S., Short, S. A., Wolfenden, R., and Carter, C. W. J. (1996) Cytidine deaminase complexed to 3-deazacytidine: a "valence buffer" in zinc enzyme catalysis, Biochemistry 35, 1335-1341.
40. Helmstaedt, K., Krappmann, S., and Braus, G. H. (2001) Allosteric regulation of catalytic activity: Escherichia coli aspartate transcarbamoylase versus yeast chorismate mutase, Microbiol. Mol. Biol. Rev. 65, 404-421.
41. Koshland, D. E. J. (1969) in Current Topics in Cellular Regulation (Horecker, B. L., and Stadtman, E. R., Eds.) pp 1-27, Academic Press, New York.
42. Esnouf, R. M. (1999) Further additions to MolScript version 1.4, including reading and contouring of electron-density maps, Acta Crystallogr. D55, 938-940.
43. Kraulis, P. J. (1991) MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures, J. Appl. Crystallogr. 24, 946-950.
44. Merritt, E. A., and Bacon, D. J. (1997) Raster3D: photorealistic molecular graphics, Methods Enzymol. 277, 505-524.
45. DINO (2001) http://www.dino3d.org.