Mutation analysis of carbamoyl phosphate synthetase: Does the structurally conserved glutamine amidotransferase triad act as a functional dyad?

Protein Science

Volumn 17, Issue 7, 2008, Pages 1120-1128

  Hart, Emily J ^a   Powers Lee, Susan G ^a  

^a NORTHEASTERN UNIVERSITY   (United States)

Author keywords

Amidotransferase; Ammonia; Carbamoyl phosphate; Glutamine; Hydrolytic triad

Indexed keywords

AMMONIA; ASPARAGINE; ASPARTIC ACID; CARBAMOYL PHOSPHATE SYNTHASE; CYSTEINE; GLUTAMINE; GLUTAMINE AMIDOTRANSFERASE; HISTIDINE; TRANSFERASE;

AMINO ACID SUBSTITUTION; ARTICLE; BINDING SITE; CATALYSIS; CONFORMATIONAL TRANSITION; CONTROLLED STUDY; ENZYME ANALYSIS; ENZYME CONFORMATION; ENZYME KINETICS; ENZYME SPECIFICITY; ENZYME STRUCTURE; ENZYME SUBSTRATE COMPLEX; ESCHERICHIA COLI; GENETIC CONSERVATION; HYDROLYSIS; MUTATION; NONHUMAN; PRIORITY JOURNAL; SITE DIRECTED MUTAGENESIS;

CARBAMOYL-PHOSPHATE SYNTHASE (GLUTAMINE-HYDROLYZING); CARBON-NITROGEN LIGASES; CATALYSIS; KINETICS; MODELS, MOLECULAR; MUTAGENESIS, SITE-DIRECTED;

ESCHERICHIA COLI;

EID: 46449084319     PISSN: 09618368     EISSN: 1469896X     Source Type: Journal    
DOI: 10.1110/ps.073428008     Document Type: Article

References (39)

1. Abyzov, A., Errami, M., Leslin, C.M., and Ilyin, V.A. 2005. Friend, an integrated analytical front-end application for bioinformatics. Bioinformatics 21: 3677-3678.
2. Brannigan, J.A., Dodson, G., Duggleby, H.J., Moody, P.C., Smith, J.L., Tomchick, D.R., and Murzin, A.G. 1995. A protein catalytic framework with an N-terminal nucleophile is capable of self-activation. Nature 378: 416-419.
3. Chave, K.J., Auger, I.E., Galivan, J., and Ryan, T.J. 2000. Molecular modeling and site-directed mutagenesis define the catalytic motif in human γ-glutamyl hydrolase. J. Biol. Chem. 275: 40365-40370.
4. Chereau, D., Kodandapani, L., Tomaselli, K.J., Spada, A.P., and Wu, J.C. 2003. Structural and functional analysis of caspase active sites. Biochemistry 42: 4151-4160.
5. Corey, J.L., Guastella, J., Davidson, N., and Lester, H.A. 1994. GABA uptake and release by a mammalian cell line stably expressing a cloned rat brain GABA transporter. Mol. Membr. Biol. 11: 23-30.
6. Douangamath, A., Walker, M., Beismann-Driemeyer, S., Vega-Fernandez, M.C., Sterner, R., and Wilmanns, M. 2002. Structural evidence for ammonia tunneling across the (ba)8 barrel of the imidazole glycerol phosphate synthase bienzyme complex. Structure 10: 185-193.
7. 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.
8. Guillou, F., Rubino, S.D., Markovitz, R.S., Kinney, D.M., and Lusty, C.J. 1989. Escherichia coli carbamoyl-phosphate synthetase: Domains of glutaminase and synthetase subunit interaction. Proc. Natl. Acad. Sci. 86: 8304-8308.
9. Hagihara, S., Kumasawa, H., Goto, Y., Hayashi, G., Kobori, A., Saito, I., and Nakatani, K. 2004. Detection of guanine-adenine mismatches by surface plasmon resonance sensor carrying naphthyridine-azaquinolone hybrid on the surface. Nucleic Acids Res. 32: 278-286.
10. Holden, H.M., Thoden, J.B., and Raushel, F.M. 1999. Carbamoyl phosphate synthetase: An amazing biochemical odyssey from substrate to product. Cell. Mol. Life Sci. 56: 507-522.
11. 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.
12. Huang, X. and Raushel, F.M. 1999. Deconstruction of the catalytic array within the amidotransferase subunit of carbamoyl phosphate synthetase. Biochemistry 38: 15909-15914.
13. Huang, X. and Raushel, F.M. 2000. Role of the hinge loop linking the N- and C-terminal domains of the amidotransferase subunit of carbamoyl phosphate synthetase. Arch. Biochem. Biophys. 380: 174-180.
14. 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. 96: 9479-9484.
15. Korolev, S., Skarina, T., Evdokimova, E., Beasley, S., Edwards, A., Joachimiak, A., and Savchenko, A. 2002. Crystal structure of glutamine amidotransferase from Thermotoga maritima. Proteins 49: 420-422.
16. Kwok, S. and Higuchi, R. 1989. Avoiding false positives with PCR. Nature 339: 237-238.
17. Laemmli, U.K. 1970. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227: 680-685.
18. McGivan, J.D., Bradford, N.M., and Mendes-Mourao, J. 1976. The regulation of carbamoyl phosphate synthase activity in rat liver mitochondria. Biochem. J. 154: 415-421.
19. McKinzie, P.B. and Parsons, B.L. 2002. Detection of rare K-ras codon 12 mutations using allele-specific competitive blocker PCR. Mutat. Res. 517: 209-220.
20. Miles, B.W. and Raushel, F.M. 2000. Synchronization of the three reaction centers within carbamoyl phosphate synthetase. Biochemistry 39: 5051-5056.
21. Miles, B.W., Banzon, J.A., and Raushel, F.M. 1998. Regulatory control of the amidotransferase domain of carbamoyl phosphate synthetase. Biochemistry 37: 16773-16779.
22. Miran, S.G., Chang, S.H., and Raushel, F.M. 1991. Role of the four conserved histidine residues in the amidotransferase domain of carbamoyl phosphate synthetase. Biochemistry 30: 7901-7907.
23. Morollo, A.A. and Eck, M.J. 2001. Structure of the cooperative allosteric anthranilate synthase from Salmonella typhimurium. Nat. Struct. Biol. 8: 243-247.
24. Mouilleron, S. and Golinelli-Pimpaneau, B. 2007. Conformational changes in ammonia-channeling glutamine amidotransferases. Curr. Opin. Struct. Biol. 17: 653-664.
25. 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.
26. Nardini, M. and Dijkstra, B.W. 1999. a/b Hydrolase fold enzymes: The family keeps growing. Curr. Opin. Struct. Biol. 9: 732-737.
27. 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. 132: 759-765.
28. Pettersen, E.F., Goddard, T.D., Huang, C.C., Couch, G.S., Greenblatt, D.M., Meng, E.C., and Ferrin, T.E. 2004. UCSF chimera - a visualization system for exploratory research and analysis. J. Comput. Chem. 25: 1605-1612.
29. Roux, B. and Walsh, C.T. 1993. p-Aminobenzoate synthesis in Escherichia coli: Mutational analysis of three conserved amino acid residues of the amidotransferase PabA. Biochemistry 32: 3763-3768.
30. Rubino, S.D., Nyunoya, H., and Lusty, C.J. 1986. Catalytic domains of carbamyl phosphate synthetase. Glutamine-hydrolyzing site of Escherichia coli carbamyl phosphate synthetase. J. Biol. Chem. 261: 11320-11327.
31. 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.
32. Sambrook, J., Fritsch, E.F., and Maniatis, T. 2001. Molecular cloning: A laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York.
33. Spraggon, G., Kim, C., Nguyen-Huu, X., Yee, M.C., Yanofsky, C., and Mills, S.E. 2001. The structures of anthranilate synthase of Serratia marcescens crystallized in the presence of (i) its substrates, chorismate and glutamine, and a product, glutamate, and (ii) its end-product inhibitor, L-tryptophan. Proc. Natl. Acad. Sci. 98: 6021-6026.
34. Tesmer, J.J., 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.
35. 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.
36. Thoden, J.B., Miran, S.G., Phillips, J.C., Howard, A.J., Raushel, F.M., and Holden, H.M. 1998. Carbamoyl phosphate synthetase: Caught in the act of glutamine hydrolysis. Biochemistry 37: 8825-8831.
37. Thoden, J.B., Huang, X., Raushel, F.M., and Holden, H.M. 1999. The small subunit of carbamoyl phosphate synthetase: Snapshots along the reaction pathway. Biochemistry 38: 16158-16166.
38. Vernet, T., Tessier, D.C., Chatellier, J., Plouffe, C., Lee, T.S., Thomas, D.Y., Storer, A.C., and Menard, R. 1995. Structural and functional roles of asparagine 175 in the cysteine protease papain. J. Biol. Chem. 270: 16645-16652.
39. Zalkin, H. and Smith, J.L. 1998. Enzymes utilizing glutamine as an amide donor. Adv. Enzymol. Relat. Areas Mol. Biol. 72: 87-144.