Reaction coupling through interdomain contacts in imidazole glycerol phosphate synthase

Biochemistry

Volumn 44, Issue 36, 2005, Pages 11974-11985

  Myers, Rebecca S ^a   Amaro, Rommie E ^b   Luthey Schulten, Zaida A ^b   Davisson, V Jo ^a  

^a PURDUE UNIVERSITY   (United States)

^b UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMMONIA; BIOSYNTHESIS; CATALYSIS; HYDROLYSIS; PHOSPHATES;

AMIDOTRANSFERASES; GLUTAMINE; IMIDAZOLE GLYCEROL PHOSPHATE (IGP); KINETIC ANALYSES;

GLYCEROL;

5 AMINO 4 IMIDAZOLECARBOXAMIDE DERIVATIVE; 5 AMINO 4 IMIDAZOLECARBOXAMIDE RIBOSIDE; AMMONIA; ASPARTIC ACID; GLUTAMIC ACID; GLUTAMINE; GLUTAMINE AMIDOTRANSFERASE; GLYCEROPHOSPHATE; HISTIDINE; IMIDAZOLE GLYCEROPHOSPHATE; IMIDAZOLE GLYCEROPHOSPHATE SYNTHASE; LYSINE; MUTANT PROTEIN; N1 [(5' PHOSPHORIBULOSYL)FORMIMINO] 5 AMINOIMIDAZOLE 4 CARBOXAMIDE RIBONUCLEOTIDE; RIBONUCLEOTIDE; SYNTHETASE; TRANSFERASE; UNCLASSIFIED DRUG;

AMINO ACID SYNTHESIS; ARTICLE; BINDING SITE; CATALYSIS; ENZYME ACTIVE SITE; ENZYME ACTIVITY; HYDROLYSIS; KINETICS; MOLECULAR DYNAMICS; NONHUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN; SACCHAROMYCES CEREVISIAE; SIMULATION;

AMINOHYDROLASES; BINDING SITES; CRYSTALLOGRAPHY, X-RAY; ENZYME STABILITY; GLUTAMINASE; GLUTAMINE; HYDROLYSIS; KINETICS; MODELS, MOLECULAR; MUTATION; PROTEIN BINDING; PROTEIN STRUCTURE, TERTIARY; SACCHAROMYCES CEREVISIAE; TRANSAMINASES;

EID: 23244441019     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi050706b     Document Type: Article

References (46)

1. Klem, T. J., and Davisson, V. J. (1993) Imidazole glycerol phosphate synthase: the glutamine amidotransferase in histidine biosynthesis, Biochemistry 32, 5177-86.
2. Zalkin, H., and Smith, J. (1998) Enzymes using glutamine as an amide donor, Adv. Enzymol. Relat. Areas Mol. Biol. 72, 87-144.
3. 8 barrel joins two active sites, Structure 9, 987-997.
4. 8 barrel of the imidazole glycerole phosphate synthase bienzyme complex, Structure 10, 185-193.
5. Omi, R., Mizuguchi, H., Goto, M., Miyahara, I., Hayashi, H., Kagamiyama, H., and Hirotsu, K. (2002) Structure of imidazole glycerol phosphate synthase from Thermus thermophilus HB8: open-closed conformational change and ammonia tunneling, J. Biochem. (Tokyo) 132, 759-765.
6. 8 barrel: ammonia conduction through HisF, Proc. Natl. Acad. Sci. U.S.A. 100, 7599-7605.
7. Amaro, R., and Luthey-Schulten, Z. (2004) Molecular dynamics simulations of substrate channeling through an α/β barrel protein, Chem. Phys. 307, 147-155.
8. Chaudhuri, B. N., Lange, S. C., Myers, R. S., Davisson, V. J., and Smith, J. L. (2003) Toward understanding the mechanism of the complex cyclization reaction catalyzed by imidazole glycerol phosphate synthase: crystal structures of a ternary complex and the free enzyme, Biochemistry 42, 7003-7012.
9. Morollo, A. A., and Eck, M. J. (2001) Structure of the cooperative allosteric anthranilate synthase from Salmonella typhimurium, Nat. Struct. Biol. 8, 243-247.
10. Tesmer, J. J. G., Klem, T. J., Deras, M. L., Davisson, V. J., and Smith, J. L. (1996) The crystal structure of GMP synthetase reveals a novel catalytic triad and is a structural paradigm for two enzyme families, Nat. Struct. Biol. 3, 74-86.
11. Thoden, J. B., Holden, H. M., Wesenberg, G., Raushel, F. M., and Rayment, I. (1997) Structure of carbamoyl phosphate synthetase: a journey of 96 Å from substrate to product, Biochemistry 36, 6305-6316.
12. Knochel, T., Ivens, A., Hester, G., Gonzalez, A., Bauerle, R., Wilmanns, M., Kirschner, K., and Jansonius, J. N. (1999) The crystal structure of anthranilate synthase from Sulfolobus solfataricus: functional implications, Proc. Natl. Acad. Sci. U.S.A. 96, 9479-9484.
13. Endrizzi, J. A., Kim, H., Anderson, P. M., and Baldwin, E. P. (2004) Crystal structure of Escherichia coli cytidine triphosphate synthetase, a nucleotide-regulated glutamine amidotransferase/ ATP-dependent amidoligase fusion protein and homologue of anticancer and antiparasitic drug targets, Biochemistry 43, 6447-6463.
14. Anand, R., Hoskins, A. A., Stubbe, J., and Ealick, S. E. (2004) Domain organization of Salmonella typhimurium formylglycinamide ribonucleotide amidotransferase revealed by X-ray crystallography, Biochemistry 43, 10328-10342.
15. Huang, X., Holden, H. M., and Raushel, F. M. (2001) Channeling of substrates and intermediates in enzyme-catalyzed reactions, Annu. Rev. Biochem. 70, 149-180.
16. Myers, R. S., Jensen, J. R., Deras, I. L., Smith, J. L., and Davisson, V. J. (2003) Substrate-induced changes in the ammonia channel for imidazole glycerol phosphate synthase, Biochemistry 42, 7013-7022.
17. Roux, B., and Walsh, C. T. (1992) p-Aminobenzoate synthesis in Escherichia coli: kinetic and mechanistic characterization of the amidotransferase PabA, Biochemistry 31, 6904-6910.
18. Chaparian, M. G., and Evans, D. R. (1991) The catalytic mechanism of the amidotransferase domain of the syrian hamster multifunctional protein CAD, J. Biol. Chem. 266, 3387-3395.
19. Willemoes, M. (2003) Thr-431 and Arg-433 are part of a conserved sequence motif of the glutamine amidotransferase domain of CTP synthases and are involved in GTP activation of the Lactococcus lactis enzyme, J. Biol. Chem. 278, 9407-9411.
20. Nakamura, J., Straub, K., Wu, J., and Lou, L. (1995) The glutamine hydrolysis function of human GMP synthetase, J. Biol. Chem. 270, 23450-23455.
21. Chittur, S. V., Klem, T. J., Shafer, C. M., and Davisson, V. J. (2001) Mechanism for acivicin inactivation of triad glutamine amidotransferases, Biochemistry 40, 876-887.
22. Chittur, S. V., Chen, Y., and Davisson, V. J. (2000) Expression and purification of imidazole glycerol phosphate synthase from Saccharomyces cerevisiae, Protein Expression Purifi. 18, 366-377.
23. Hirschbein, B. L., Mazenod, F. P., and Whitesides, G. M. (1982) Synthesis of phosphoenolpyruvate and its use in adenosine triphosphate cofactor regeneration, J. Org. Chem. 47, 3765-3766.
24. Kunkel, T. A. (1985) Rapid and efficient site-specific mutagenesis without phenotypic selection, Proc. Natl. Acad. Sci. U.S.A. 82, 488-492.
25. Gleitz, J., Tosch, C., and Peters, T. (1996) Continuous enzyme-linked fluorometric detection of L-(+)-lactate released from rat brain vesicles under anoxic conditions, J. Neurosci. Methods 67, 97-102.
26. Gray, P. J., and Duggleby, R. G. (1989) Analysis of kinetic data for irreversible enzyme inhibition, Biochem. J. 257, 419-424.
27. Humphrey, W., Dalke, A., and Schulten, K. (1996) VMD-visual molecular dynamics, J. Mol. Graph. 14, 33-38.
28. MacKerell, A. (2003), http://www.psc.edu/general/software/ packages/charmm/tutorial/index.html.
29. MacKerell, A. (2003), http://www.psc.edu/general/software/ packages/charmm/tutorial/mackerell/parameters.html.
30. Kale, L., Skeel, R., Bhandarkar, M., Brunner, R., Gursoy, A., Krawetz, N., Phillips, J., Shinozaki, A., Varadarajan, K., and Schulten, K. (1999) NAMD2: Greater Scalability for Parallel Molecular Dynamics, J. Comput. Phys. 151, 283-312.
31. Grubmuller, H. (1996) Theoretical Biophysics Group, Institute for Medical Optics, Ludwig-Maximilians University, Munich.
32. MacKerrell, A. D., Jr., Bashford, D., Bellott, M., Dunbrack, R. L., Jr., Evansecl, J. D., Field, M. J., Fischer, S., Gao, J., Guo, H., Ha, S., Joseph-McCarthy, D., Kuchnir, L., Kuczera, K., Lau, F. T. K., Mattos, C., Michnick, S., Ngo, T., Nguyen, D. T., Prodhom, B., Reiher, W. E., III, Roux, B., Schlenkrich, M., Smith, J. C., Stote, R., Straub, J., Watanabe, M., Wiorkiewicz-Kuczera, J., Yin, D., and Karplus, M. (1998) All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins, J. Phys. Chem. B 102, 3586-3616.
33. Darden, T., York, D., and Pedersen, L. (1993) J. Chem. Phys. 98, 10089-10092.
34. Lang, D., Thoma, R., Henn-Sax, M., Sterner, R., and Wilmanns, M. (2000) Structural evidence for evolution of the β/α barrel scaffold by gene duplication and fusion, Science 289, 1546-1550.
35. Huang, X., and Raushel, F. M. (1999) Deconstruction of the catalytic array within the amidotransferase subunit of carbamoyl phosphate synthetase, Biochemistry 38, 15909-15914.
36. Klem, T. J., Chen, Y., and Davisson, V. J. (2001) Subunit interactions and glutamine utilization by Escherichia coli imidazole glycerol phosphate synthase, J. Bacteriol. 183, 989-996.
37. Amaro, R., Myers, R. S., Davisson, V. J., and Luthey-Schulten, Z. (2005) Evidence of the allosteric effect in IGP synthase, manuscript in preparation.
38. Amaro, R. E., Myers, R. S., Davisson, V. J., and Luthey-Schulten, Z. A. (2005) Structural elements in IGP synthase exclude water to optimize ammonia transfer, Biophys. J. 89, 475-487.
39. Korolev, S., Skarina, T., Evdokimova, E., Edwards, A., Joachimiak, A., and Savchenko, A. (2002) Crystal structure of glutamine amidotransferase from Thermotoga maritima, Proteins: Struct., Funct., Genet. 49, 420-422.
40. Saeed-Kothe, A., and Powers-Lee, S. G. (2002) Specificity determining residues in ammonia- and glutamine-dependent carbamoyl phosphate synthetases, J. Biol. Chem. 277, 7231-7238.
41. Saeed-Kothe, A., and Powers-Lee, S. G. (2003) Gain of glutaminase function in mutants of the ammonia-specific frog carbamoyl phosphate synthetase, J. Biol. Chem. 278, 26722-26726.
42. Mathews, D. A., Alden, R. A., Birktoft, J. J., Freer, S. T., and Kraut, J. (1975) X-ray crystallographic study of boronic acid adducts with subtilisin BPN' (Novo): a model for the catalytic transition state, J. Biol. Chem. 250, 7120-7126.
43. Thoden, J. B., Miran, S. G., Philips, J. C., Howard, A. J., Raushel, F. M., Holden, H. M. (1998) Carbamoyl phosphate synthetase: caught in the act of glutamine hydrolysis, Biochemistry 37, 8825-8831.
44. Barrette-Ng, I. H., Ng, K. K.-S., Mark, B. L., van Aken, D., Cherney, M. M., Garen, C., Kolodenko, Y., Gorbalenya, A. E., Snijder, E. J., and James, M. N. G. (2002) Structure of Arterivirus nsp4: the smallest chymotripsin-like proteinase with an α/β C-terminal extension and alternate conformations of the oxyanion hole, J. Biol. Chem. 277, 39960-39966.
45. Morollo, A. A., and Bauerle, R. (1993) Characterization of composite aminodeoxyisochorismate synthase and aminodeoxy-isochorismate lyase activities of anthranilate synthase, Proc. Natl. Acad. Sci. U.S.A. 90, 9983-9987.
46. Hoskins, A. A., Anand, R., Ealick, S. E., and Stubbe, J. (2004) The formylglycinamide ribonucleotide amidotransferase complex from Bacillus subtilis: metabolite-mediated complex formation, Biochemistry 43, 10314-10327.