Crystal structures of adenine phosphoribosyltransferase from Leishmania donovani

EMBO Journal

Volumn 18, Issue 13, 1999, Pages 3533-3545

  Phillips, Cynthia L ^a   Ullman, Buddy ^b   Brennan, Richard G ^b   Hill, Christopher P ^a  

^a UNIVERSITY OF UTAH SCHOOL OF MEDICINE   (United States)

^b OREGON HEALTH AND SCIENCE UNIVERSITY   (United States)

Author keywords

Adenine phosphoribosyltransferase; Crystal structure; Leishmania donovani; Purines

Indexed keywords

ADENINE; ADENINE PHOSPHORIBOSYLTRANSFERASE; ADENOSINE PHOSPHATE; CITRIC ACID; DIMER; LIGAND; PHOSPHORIBOSYLTRANSFERASE; PURINE; SULFATE;

ARTICLE; CARBOXY TERMINAL SEQUENCE; CATALYSIS; CRYSTAL STRUCTURE; DIMERIZATION; HYDROGEN BOND; INBORN ERROR OF METABOLISM; LEISHMANIA DONOVANI; NONHUMAN; PARASITE; PRIORITY JOURNAL; PURINE SYNTHESIS;

ADENINE; ADENINE PHOSPHORIBOSYLTRANSFERASE; ADENOSINE MONOPHOSPHATE; AMINO ACID SEQUENCE; ANIMALS; ANIONS; BINDING SITES; CRYSTALLIZATION; CRYSTALLOGRAPHY, X-RAY; DIMERIZATION; HUMANS; HYDROGEN BONDING; LEISHMANIA DONOVANI; LIGANDS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MUTATION; PROTEIN STRUCTURE, SECONDARY; SEQUENCE ALIGNMENT; STRUCTURE-ACTIVITY RELATIONSHIP;

LEISHMANIA DONOVANI; PROTOZOA;

EID: 0033168676     PISSN: 02614189     EISSN: None     Source Type: Journal    
DOI: 10.1093/emboj/18.13.3533     Document Type: Article

References (52)

1. Allen, T., Hwang, H.-Y., Wilson, K., Hanson, S., Jardim, A. and Ullman, B. (1995) Cloning and expression of the adenine phosphoribosyltransferase gene from Leishmania donovani. Mol. Biochem. Parasitol., 74, 99-103.
2. Argos, P., Hanei, M., Wilson, J.M. and Kelley, W.N. (1983) A possible nucleotide-binding domain in the tertiary fold of phosphoribosyltransferases. J. Biol. Chem., 258, 6450-6457.
3. Berens, R.L., Krug, E.C. and Marr, J.J. (1995) Purine and Pyrimidine Metabolism. Academic Press, London, UK.
4. Bhatia, M.B., Vinitsky, A. and Grubmeyer, C. (1990) Kinetic mechanism of orotate phosphoribosyltransferase from Salmonella typhimurium. Biochemistry, 29, 10480-10487.
5. Brünger, A.T. (1996) X-PLOR version 3.843, a system for X-ray crystallography and NMR. Yale University, New Haven, CT.
6. Corpet, F. (1988) Multiple sequence alignment with hierarchical clustering. Nucleic Acids Res., 16, 10881-10890.
7. Crother, T.R. and Taylor, M.W. (1998) Site directed mutagenesis of the Saccharomyces cerevisiae APT1 gene. In Griesmacher, A., Chiba, P. and Müller, M.M. (eds) Purine and Pyrimidine Metabolism in Man IX. Plenum Press, New York, NY, Vol. 431, pp. 299-303.
8. de Boer, J.G. and Glickman, B.W. (1991) Mutational analysis of the structure and function of the adenine phosphoribosyltransferase enzyme of Chinese hamster. J. Mol. Biol., 221, 163-174.
9. Dodson, E.J., Winn, M. and Ralph, A. (1997) Collaborative computational project, number 4: Providing programs for protein crystallography. Methods Enzymol., 277, 620-633.
10. Eads, J.C., Scapin, G., Xu, Y, Grubmeyer, C. and Sacchettini, J.C. (1994) The crystal structure of human hypoxanthine-guanine phosphoribosyltransferase with bound GMP. Cell, 78, 325-334.
11. Eads, J.C., Ozturk, D., Wexler, T.B., Grubmeyer, C. and Saccettini, J.C. (1997) A new function for a common fold: the crystal structure of quinolinic acid phosphoribosyltransferase. Nature Struct. Biol., 5, 47-58.
12. Focia, P.J., Sydney, P.C., III, Nieves-Alicea, R., Fletterick, R.J. and Eakin, A.E. (1998a) A 1.4 Å crystal structure for the hypoxanthine phosphoribosyltransferase of Trypanosoma cruzi. Biochemistry, 37, 15066-15075.
13. Focia, P.J., Craig, S.P., III and Eakin, A.E. (1998b) Approaching the transition state in the crystal structure of a phosphoribosyltransferase. Biochemistry, 37, 17120-17127.
14. Fujimori, S., Akaoka, I., Sakamoto, K., Yamanaka, H., Nishioka, K. and Kamatani, N. (1985) Common characteristics of mutant adenine phosphoribosyltransferase from four separate Japanese families with, 2,8-dihydroxyadenine urolithiasis associated with partial enzyme deficiencies. Hum. Genet., 71, 171-176.
15. Fujimori, S., Akaoka, I., Takeuchi, F., Kanayama, H., Tatara, K., Nishioka, K. and Kamatani, N. (1986) Altered kinetic properties of a mutant adenine phosphoribosyltransferase. Metabolism, 35, 187.
16. Furey, W. and Swaminathan, S. (1997) PHASES-95: A program package for processing and analyzing diffraction data from macromolecules. Methods Enzymol., 277, 590-620.
17. Gill, S.C. and von Hippel, P.H. (1989) Calculation of extinction coefficients from amino acid sequence data. Anal. Biochem., 182, 319-326.
18. Henriksen, A., Aghajari, N., Jensen, K.F. and Galhede, M. (1996) A flexible loop at the dimer interface is a part of the active site of the adjacent monomer of Escherichia coli orotate phosphoribosyltransferase. Biochemistry, 35, 3803-3809.
19. Hershey, H.V. and Taylor, M.W. (1986) Nucleotide sequence and deduced amino acid sequence of Escherichia coli adenine phosphoribosyltransferase and comparison with other analogous enzymes. Gene, 43, 287-293.
20. Hove-Jensen, B., Harlow, K.W., King, C.J. and Switzer, R.L. (1986) Phosphoribosyl-pyrophosphate synthetase of Escherichia coli: properties of the purified enzyme and primary structure of the prs gene. J. Biol. Chem., 261, 6765-6771.
21. Hubbard, S.J. and Thornton, J.M. (1993) NACCESS. Department of Biochemistry and Molecular Biology, University College London.
22. Hutchinson, E.G. and Thornton, J.M. (1996) PROMOTIF - a program to identify and analyze structural motifs in proteins. Protein Sci., 5, 212-220.
23. Hwang, H. and Ullman, B. (1997) Genetic analysis of purine metabolism in Leishmania donovani. J. Biol. Chem., 272, 19488-19496.
24. Jardim, A. and Ullman, B. (1997) The conserved serine-tyrosine dipeptide in Leishmania donovani hypoxanthine-guanine phosphoribosyltransferase is essential for catalytic activity. J. Biol. Chem., 272, 8967-8973.
25. Jones, J.A., Zou, J.Y., Cowan, S.W. and Kjeldgaard, M. (1991) Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr., A47, 110-119.
26. Khattar, N.H., Jennings, C.D., Walker, K.A. and Turker, S.T. (1995) Isolation and characterization of mutations in the mouse APRT gene that encode functional enzymes with resistance to toxic adenine analogs. In Sahota, A. and Taylor, M.W. (eds) Purine and Pyrimidine Metabolism in Man VIII. Plenum Press, New York, NY, Vol. 370, pp. 665-670.
27. Krahn, J.M., Kim, J.H., Burns, M.R., Parry, R.J., Zalkin, H. and Smith, J. (1997) Coupled formation of an amidotransferase interdomain ammonia channel and a phosphoribosyltransferase active site. Biochemistry, 36, 11061-11068.
28. Kraulis, P.J. (1991) MOLSCRIPT: a program to produce both detailed and schematic plots of structures. J. Appl. Crystallogr., 24, 946-950.
29. Laskowski, R.A., MacArthur, M.W. and Thornton, J.M. (1993) PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Crystallogr., 26, 283-291.
30. Looker, D.L., Berens, R.L. and Marr, J.J. (1983) Purine metabolism in Leishmania donovani amastigotes and promastigotes. Mol. Biochem. Parasitol., 9, 15-23.
31. Matthews, B.W. (1968) Solvent content of protein crystals. J. Mol. Biol., 33, 491-497.
32. Muchmore, C.R., Krahn, J.M., Kim, J.H., Zalkin, H. and Smith, J.L. (1998) Crystal structure of glutamine phosphoribosylphosphate amidotransferase from Escherichia coli. Protein Sci., 7, 39-51.
33. Munagala, N.R. and Wang, C.C. (1998) Altering the purine specificity of hypoxanthine-guanine-xanthine phosphoribosyltransferase from Tritrichomonas foetus by structure-based point mutations in the enzyme protein. Biochemistry, 37, 16612-16619.
34. Musick, W.D.L. (1981) Structural features of the phosphoribosyltransferases and their relationship to the human deficiency disorders of purine and pyrimidine metabolism. CRC Crit. Rev. Biochem., 11, 1-34.
35. Otwinowski, Z. and Minor, W. (1997) Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol., 276, 307-326.
36. Daresbury Laboratory, Warrington, UK, pp. 56-62.
37. Ozturk, D.H., Dorfman, R.H., Scapin, G., Sacchettini, J.C. and Grubmeyer, C. (1995) Structure and function of Salmonella typhimurium orotate phosphoribosyltransferase: protein complementation reveals shared active sites. Biochemistry, 34, 10764-10770.
38. Phillips, C.L., Ullman, B. and Brennan, R.G. (1996) Crystallization of the purine salvage enzyme adenine phosphoribosyltransferase. Proteins Struct. Funct. Genet., 25, 510-513.
39. Pillwein, K. et al. (1990) Purine metabolism of human glioblastoma in vivo. Cancer Res., 50, 1576-1579.
40. Scapin, G., Grubmeyer, C. and Sacchettini, J.C. (1994) Crystal structure of orotate phosphoribosyltransferase. Biochemistry, 33, 1287-1294.
41. Scapin, G., Ozturk, D.H., Grubmeyer, C. and Sacchettini, J.C. (1995) The crystal structure of the orotate phosphoribosyltransferase complexed with orotate and α-D-5-phosphoribosyl-L-phosphate. Biochemistry, 34, 10744-10754.
42. Schumacher, M.A., Carter, D., Roos, D., Ullman, B. and Brennan, R.G. (1996) Crystal structures of Toxoplasma gondii HGXPRTase reveal the catalytic role of a long flexible loop. Nature Struct. Biol., 3, 881-887.
43. Schumacher, M.A., Carter, D., Scott, D.M., Roos, D., Ullman, B. and Brennan, R.G. (1998) Crystal structure of Toxoplasma gondii uracil phosphoribosyltransferase reveal the atomic basis of pyrimidine discrimination and prodrug binding. EMBO J., 17, 3219-3232.
44. Simmonds, H.A., Sahota, A.S. and Van Acker, K.J. (1995) Adenine phosphoribosyltransferase deficiency and 2,8-dihydroxyadenine lithiasis. In Scriver, C.R., Beaudet, W.S., Sly, W.S. and Valle, D. (eds), The Metabolic and Molecular Bases of Inherited Disease. McGraw-Hill, New York, NY, pp. 1707-1724.
45. Smith, J.L., Zaluzee, E.J., Wery, J.P., Niu, L., Switzer, R.L., Zalkin, H. and Satow, Y. (1994) The structure of the allosteric regulatory enzyme of purine biosynthesis. Science, 264, 1427-1433.
46. Somoza, J.R., Chin, M.S., Focia, P.J., Wang, C.C. and Fletterick, R.J. (1996) Crystal structure of the hypoxanthine-guanine-xanthine phosphoribosyltransferase from the protozoan parasite Tritrichomonas foetus. Biochemistry, 35, 7032-7040.
47. Vos, S., de Jersey, J. and Martin, J.L. (1997) Crystal structure of Escherichia coli xanthine phosphoribosyltransferase. Biochemistry, 36, 4125-4134.
48. Wang, G.P., Lundegaard, C., Jensen, K.F. and Grubmeyer, C. (1999a) Kinetic mechanism of OMP synthase: A slow physical step following group transfer limits catalytic rate. Biochemistry, 38, 275-283.
49. Wang, G.P., Cahill, S.M., Liu, X., Girvin, M.E. and Grubmeyer, C. (1999b) Motional dynamics of the catalytic loop in OMP synthase. Biochemistry, 38, 284-295.
50. Weber, G., Jayaram, H.M., Pillwein, K., Natsumeda, Y., Reardon, M.A. and Zhen, W.S. (1987) Salvage pathways as targets of chemotherapy. Adv. Enzyme Regul., 26, 335-352.
51. Xuong, N.H., Nielson, C., Hamlin, R. and Anderson, D.J. (1985) Strategy for data collection from protein crystals using a multiwire counter area detector diffractometer. J. Appl. Crystallogr., 18, 342-350.
52. Yuan, L., Craig, S.P., III, McKerrow, J.H. and Wang, C.C. (1992) Steady-state kinetics of the schistosomal hypoxanthine-guanine phosphoribosyltransferase. Biochemistry, 31, 806-810.