Skip to main content
Biochemical Journal logoLink to Biochemical Journal
. 2003 Feb 1;369(Pt 3):497–507. doi: 10.1042/BJ20021110

Aspartate-107 and leucine-109 facilitate efficient coupling of glutamine hydrolysis to CTP synthesis by Escherichia coli CTP synthase.

Akshai Iyengar 1, Stephen L Bearne 1
PMCID: PMC1223111  PMID: 12383057

Abstract

CTP synthase catalyses the ATP-dependent formation of CTP from UTP using either NH(3) or L-glutamine as the nitrogen source. GTP is required as an allosteric effector to promote glutamine hydrolysis. In an attempt to identify nucleotide-binding sites, scanning alanine mutagenesis was conducted on a highly conserved region of amino acid sequence (residues 102-118) within the synthase domain of Escherichia coli CTP synthase. Mutant K102A CTP synthase exhibited wild-type activity with respect to NH(3) and glutamine; however, the R105A, D107A, L109A and G110A enzymes exhibited wild-type NH(3)-dependent activity and affinity for glutamine, but impaired glutamine-dependent CTP formation. The E103A, R104A and H118A enzymes exhibited no glutamine-dependent activity and were only partially active with NH(3). Although these observations were compatible with impaired activation by GTP, the apparent affinity of the D107A, L109A and G110A enzymes for GTP was reduced only 2-4-fold, suggesting that these residues do not play a significant role in GTP binding. In the presence of GTP, the k (cat) values for glutamine hydrolysis by the D107A and L109A enzymes were identical with that of wild-type CTP synthase. Overall, the kinetic properties of L109A CTP synthase were consistent with an uncoupling of glutamine hydrolysis from CTP formation that occurs because an NH(3) tunnel has its normal structure altered or fails to form. L109F CTP synthase was prepared to block totally the putative NH(3) tunnel; however, this enzyme's rate of glutamine-dependent CTP formation and glutaminase activity were both impaired. In addition, we observed that mutation of amino acids located between residues 102 and 118 in the synthase domain can affect the enzyme's glutaminase activity, suggesting that these residues interact with residues in the glutamine amide transfer domain because they are in close proximity or via a conformationally dependent signalling mechanism.

Full Text

The Full Text of this article is available as a PDF (355.2 KB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Bearne S. L., Hekmat O., Macdonnell J. E. Inhibition of Escherichia coli CTP synthase by glutamate gamma-semialdehyde and the role of the allosteric effector GTP in glutamine hydrolysis. Biochem J. 2001 May 15;356(Pt 1):223–232. doi: 10.1042/0264-6021:3560223. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Bera A. K., Chen S., Smith J. L., Zalkin H. Interdomain signaling in glutamine phosphoribosylpyrophosphate amidotransferase. J Biol Chem. 1999 Dec 17;274(51):36498–36504. doi: 10.1074/jbc.274.51.36498. [DOI] [PubMed] [Google Scholar]
  3. Bera A. K., Chen S., Smith J. L., Zalkin H. Temperature-dependent function of the glutamine phosphoribosylpyrophosphate amidotransferase ammonia channel and coupling with glycinamide ribonucleotide synthetase in a hyperthermophile. J Bacteriol. 2000 Jul;182(13):3734–3739. doi: 10.1128/jb.182.13.3734-3739.2000. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Bera A. K., Smith J. L., Zalkin H. Dual role for the glutamine phosphoribosylpyrophosphate amidotransferase ammonia channel. Interdomain signaling and intermediate channeling. J Biol Chem. 2000 Mar 17;275(11):7975–7979. doi: 10.1074/jbc.275.11.7975. [DOI] [PubMed] [Google Scholar]
  5. Bourne H. R., Sanders D. A., McCormick F. The GTPase superfamily: conserved structure and molecular mechanism. Nature. 1991 Jan 10;349(6305):117–127. doi: 10.1038/349117a0. [DOI] [PubMed] [Google Scholar]
  6. Böhm G., Muhr R., Jaenicke R. Quantitative analysis of protein far UV circular dichroism spectra by neural networks. Protein Eng. 1992 Apr;5(3):191–195. doi: 10.1093/protein/5.3.191. [DOI] [PubMed] [Google Scholar]
  7. Chittur S. V., Klem T. J., Shafer C. M., Davisson V. J. Mechanism for acivicin inactivation of triad glutamine amidotransferases. Biochemistry. 2001 Jan 30;40(4):876–887. doi: 10.1021/bi0014047. [DOI] [PubMed] [Google Scholar]
  8. De Clercq E. Antiviral agents: characteristic activity spectrum depending on the molecular target with which they interact. Adv Virus Res. 1993;42:1–55. doi: 10.1016/s0065-3527(08)60082-2. [DOI] [PubMed] [Google Scholar]
  9. Dever T. E., Glynias M. J., Merrick W. C. GTP-binding domain: three consensus sequence elements with distinct spacing. Proc Natl Acad Sci U S A. 1987 Apr;84(7):1814–1818. doi: 10.1073/pnas.84.7.1814. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Gao W. Y., Johns D. G., Mitsuya H. Potentiation of the anti-HIV activity of zalcitabine and lamivudine by a CTP synthase inhibitor, 3-deazauridine. Nucleosides Nucleotides Nucleic Acids. 2000 Jan-Feb;19(1-2):371–377. doi: 10.1080/15257770008033015. [DOI] [PubMed] [Google Scholar]
  11. Harmark K., Anborgh P. H., Merola M., Clark B. F., Parmeggiani A. Substitution of aspartic acid-80, a residue involved in coordination of magnesium, weakens the GTP binding and strongly enhances the GTPase of the G domain of elongation factor Tu. Biochemistry. 1992 Aug 18;31(32):7367–7372. doi: 10.1021/bi00147a022. [DOI] [PubMed] [Google Scholar]
  12. Hatse S., De Clercq E., Balzarini J. Role of antimetabolites of purine and pyrimidine nucleotide metabolism in tumor cell differentiation. Biochem Pharmacol. 1999 Aug 15;58(4):539–555. doi: 10.1016/s0006-2952(99)00035-0. [DOI] [PubMed] [Google Scholar]
  13. Hendriks E. F., O'Sullivan W. J., Stewart T. S. Molecular cloning and characterization of the Plasmodium falciparum cytidine triphosphate synthetase gene. Biochim Biophys Acta. 1998 Aug 20;1399(2-3):213–218. doi: 10.1016/s0167-4781(98)00108-0. [DOI] [PubMed] [Google Scholar]
  14. Hofer A., Steverding D., Chabes A., Brun R., Thelander L. Trypanosoma brucei CTP synthetase: a target for the treatment of African sleeping sickness. Proc Natl Acad Sci U S A. 2001 May 15;98(11):6412–6416. doi: 10.1073/pnas.111139498. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Holden H. M., Thoden J. B., Raushel F. M. Carbamoyl phosphate synthetase: a tunnel runs through it. Curr Opin Struct Biol. 1998 Dec;8(6):679–685. doi: 10.1016/s0959-440x(98)80086-9. [DOI] [PubMed] [Google Scholar]
  16. Horisberger M. A. Interferon-induced human protein MxA is a GTPase which binds transiently to cellular proteins. J Virol. 1992 Aug;66(8):4705–4709. doi: 10.1128/jvi.66.8.4705-4709.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Huang X., Holden H. M., Raushel F. M. Channeling of substrates and intermediates in enzyme-catalyzed reactions. Annu Rev Biochem. 2001;70:149–180. doi: 10.1146/annurev.biochem.70.1.149. [DOI] [PubMed] [Google Scholar]
  18. Huang X., Raushel F. M. An engineered blockage within the ammonia tunnel of carbamoyl phosphate synthetase prevents the use of glutamine as a substrate but not ammonia. Biochemistry. 2000 Mar 28;39(12):3240–3247. doi: 10.1021/bi9926173. [DOI] [PubMed] [Google Scholar]
  19. Huang X., Raushel F. M. Restricted passage of reaction intermediates through the ammonia tunnel of carbamoyl phosphate synthetase. J Biol Chem. 2000 Aug 25;275(34):26233–26240. doi: 10.1074/jbc.275.34.26233. [DOI] [PubMed] [Google Scholar]
  20. Iyengar Akshai, Bearne Stephen L. An assay for cytidine 5(')-triphosphate synthetase glutaminase activity using high performance liquid chromatography. Anal Biochem. 2002 Sep 15;308(2):396–400. doi: 10.1016/s0003-2697(02)00240-3. [DOI] [PubMed] [Google Scholar]
  21. John J., Rensland H., Schlichting I., Vetter I., Borasio G. D., Goody R. S., Wittinghofer A. Kinetic and structural analysis of the Mg(2+)-binding site of the guanine nucleotide-binding protein p21H-ras. J Biol Chem. 1993 Jan 15;268(2):923–929. [PubMed] [Google Scholar]
  22. Kjaersgård I. V., Knudsen C. R., Wiborg O. Mutation of the conserved Gly83 and Gly94 in Escherichia coli elongation factor Tu. Indication of structural pivots. Eur J Biochem. 1995 Feb 15;228(1):184–190. doi: 10.1111/j.1432-1033.1995.tb20248.x. [DOI] [PubMed] [Google Scholar]
  23. Kjeldgaard M., Nyborg J., Clark B. F. The GTP binding motif: variations on a theme. FASEB J. 1996 Oct;10(12):1347–1368. [PubMed] [Google Scholar]
  24. Krahn J. M., Kim J. H., Burns M. R., Parry R. J., Zalkin H., Smith J. L. Coupled formation of an amidotransferase interdomain ammonia channel and a phosphoribosyltransferase active site. Biochemistry. 1997 Sep 16;36(37):11061–11068. doi: 10.1021/bi9714114. [DOI] [PubMed] [Google Scholar]
  25. Larsen T. M., Boehlein S. K., Schuster S. M., Richards N. G., Thoden J. B., Holden H. M., Rayment I. Three-dimensional structure of Escherichia coli asparagine synthetase B: a short journey from substrate to product. Biochemistry. 1999 Dec 7;38(49):16146–16157. doi: 10.1021/bi9915768. [DOI] [PubMed] [Google Scholar]
  26. Lee E., Taussig R., Gilman A. G. The G226A mutant of Gs alpha highlights the requirement for dissociation of G protein subunits. J Biol Chem. 1992 Jan 15;267(2):1212–1218. [PubMed] [Google Scholar]
  27. Levitzki A., Koshland D. E., Jr Cytidine triphosphate synthetase. Covalent intermediates and mechanisms of action. Biochemistry. 1971 Aug 31;10(18):3365–3371. doi: 10.1021/bi00794a008. [DOI] [PubMed] [Google Scholar]
  28. Levitzki A., Koshland D. E., Jr Ligand-induced dimer-to-tetramer transformation in cytosine triphosphate synthetase. Biochemistry. 1972 Jan 18;11(2):247–253. doi: 10.1021/bi00752a016. [DOI] [PubMed] [Google Scholar]
  29. Levitzki A., Koshland D. E., Jr Negative cooperativity in regulatory enzymes. Proc Natl Acad Sci U S A. 1969 Apr;62(4):1121–1128. doi: 10.1073/pnas.62.4.1121. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Levitzki A., Koshland D. E., Jr Role of an allosteric effector. Guanosine triphosphate activation in cytosine triphosphate synthetase. Biochemistry. 1972 Jan 18;11(2):241–246. doi: 10.1021/bi00752a015. [DOI] [PubMed] [Google Scholar]
  31. Lim R. L., O'Sullivan W. J., Stewart T. S. Isolation, characterization and expression of the gene encoding cytidine triphosphate synthetase from Giardia intestinalis. Mol Biochem Parasitol. 1996 Jun;78(1-2):249–257. doi: 10.1016/s0166-6851(96)02635-7. [DOI] [PubMed] [Google Scholar]
  32. Liu F., Dong Q., Fromm H. J. Site-directed mutagenesis of the phosphate-binding consensus sequence in Escherichia coli adenylosuccinate synthetase. J Biol Chem. 1992 Feb 5;267(4):2388–2392. [PubMed] [Google Scholar]
  33. Lochrie M. A., Simon M. I. G protein multiplicity in eukaryotic signal transduction systems. Biochemistry. 1988 Jul 12;27(14):4957–4965. doi: 10.1021/bi00414a001. [DOI] [PubMed] [Google Scholar]
  34. Long C. W., Pardee A. B. Cytidine triphosphate synthetase of Escherichia coli B. I. Purification and kinetics. J Biol Chem. 1967 Oct 25;242(20):4715–4721. [PubMed] [Google Scholar]
  35. Long C., Koshland D. E., Jr Cytidine triphosphate synthetase. Methods Enzymol. 1978;51:79–83. doi: 10.1016/s0076-6879(78)51014-8. [DOI] [PubMed] [Google Scholar]
  36. Morollo A. A., Eck M. J. Structure of the cooperative allosteric anthranilate synthase from Salmonella typhimurium. Nat Struct Biol. 2001 Mar;8(3):243–247. doi: 10.1038/84988. [DOI] [PubMed] [Google Scholar]
  37. Muchmore C. R., Krahn J. M., Kim J. H., Zalkin H., Smith J. L. Crystal structure of glutamine phosphoribosylpyrophosphate amidotransferase from Escherichia coli. Protein Sci. 1998 Jan;7(1):39–51. doi: 10.1002/pro.5560070104. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Nishiwaki T., Iwasaki H., Ishiura M., Kondo T. Nucleotide binding and autophosphorylation of the clock protein KaiC as a circadian timing process of cyanobacteria. Proc Natl Acad Sci U S A. 2000 Jan 4;97(1):495–499. doi: 10.1073/pnas.97.1.495. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Oliveira M. A., Carroll D., Davidson L., Momany C., Hackert M. L. The GTP effector site of ornithine decarboxylase from Lactobacillus 30a: kinetic and structural characterization. Biochemistry. 1997 Dec 23;36(51):16147–16154. doi: 10.1021/bi970605g. [DOI] [PubMed] [Google Scholar]
  40. Ostrander D. B., O'Brien D. J., Gorman J. A., Carman G. M. Effect of CTP synthetase regulation by CTP on phospholipid synthesis in Saccharomyces cerevisiae. J Biol Chem. 1998 Jul 24;273(30):18992–19001. doi: 10.1074/jbc.273.30.18992. [DOI] [PubMed] [Google Scholar]
  41. Raushel F. M., Mullins L. S., Gibson G. E. A stringent test for the nucleotide switch mechanism of carbamoyl phosphate synthetase. Biochemistry. 1998 Jul 14;37(28):10272–10278. doi: 10.1021/bi980753m. [DOI] [PubMed] [Google Scholar]
  42. Richardson J. S. The anatomy and taxonomy of protein structure. Adv Protein Chem. 1981;34:167–339. doi: 10.1016/s0065-3233(08)60520-3. [DOI] [PubMed] [Google Scholar]
  43. Robertson J. G., Villafranca J. J. Characterization of metal ion activation and inhibition of CTP synthetase. Biochemistry. 1993 Apr 13;32(14):3769–3777. doi: 10.1021/bi00065a032. [DOI] [PubMed] [Google Scholar]
  44. Saraste M., Sibbald P. R., Wittinghofer A. The P-loop--a common motif in ATP- and GTP-binding proteins. Trends Biochem Sci. 1990 Nov;15(11):430–434. doi: 10.1016/0968-0004(90)90281-f. [DOI] [PubMed] [Google Scholar]
  45. Smith J. L. Glutamine PRPP amidotransferase: snapshots of an enzyme in action. Curr Opin Struct Biol. 1998 Dec;8(6):686–694. doi: 10.1016/s0959-440x(98)80087-0. [DOI] [PubMed] [Google Scholar]
  46. Spraggon G., Kim C., Nguyen-Huu X., Yee M. C., Yanofsky C., Mills S. E. 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 U S A. 2001 May 22;98(11):6021–6026. doi: 10.1073/pnas.111150298. [DOI] [PMC free article] [PubMed] [Google Scholar]
  47. Sung Y. J., Carter M., Zhong J. M., Hwang Y. W. Mutagenesis of the H-ras p21 at glycine-60 residue disrupts GTP-induced conformational change. Biochemistry. 1995 Mar 14;34(10):3470–3477. doi: 10.1021/bi00010a040. [DOI] [PubMed] [Google Scholar]
  48. Teplyakov A., Obmolova G., Badet-Denisot M. A., Badet B., Polikarpov I. Involvement of the C terminus in intramolecular nitrogen channeling in glucosamine 6-phosphate synthase: evidence from a 1.6 A crystal structure of the isomerase domain. Structure. 1998 Aug 15;6(8):1047–1055. doi: 10.1016/s0969-2126(98)00105-1. [DOI] [PubMed] [Google Scholar]
  49. Teplyakov A., Obmolova G., Badet-Denisot M. A., Badet B. The mechanism of sugar phosphate isomerization by glucosamine 6-phosphate synthase. Protein Sci. 1999 Mar;8(3):596–602. doi: 10.1110/ps.8.3.596. [DOI] [PMC free article] [PubMed] [Google Scholar]
  50. Teplyakov A., Obmolova G., Badet B., Badet-Denisot M. A. Channeling of ammonia in glucosamine-6-phosphate synthase. J Mol Biol. 2001 Nov 9;313(5):1093–1102. doi: 10.1006/jmbi.2001.5094. [DOI] [PubMed] [Google Scholar]
  51. Tesmer J. J., Klem T. J., Deras M. L., Davisson V. J., Smith J. L. The crystal structure of GMP synthetase reveals a novel catalytic triad and is a structural paradigm for two enzyme families. Nat Struct Biol. 1996 Jan;3(1):74–86. doi: 10.1038/nsb0196-74. [DOI] [PubMed] [Google Scholar]
  52. Thoden J. B., Holden H. M., Wesenberg G., Raushel F. M., Rayment I. Structure of carbamoyl phosphate synthetase: a journey of 96 A from substrate to product. Biochemistry. 1997 May 27;36(21):6305–6316. doi: 10.1021/bi970503q. [DOI] [PubMed] [Google Scholar]
  53. Thoden James B., Huang Xinyi, Raushel Frank M., Holden Hazel M. Carbamoyl-phosphate synthetase. Creation of an escape route for ammonia. J Biol Chem. 2002 Jul 18;277(42):39722–39727. doi: 10.1074/jbc.M206915200. [DOI] [PubMed] [Google Scholar]
  54. Thompson J. D., Gibson T. J., Plewniak F., Jeanmougin F., Higgins D. G. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 1997 Dec 15;25(24):4876–4882. doi: 10.1093/nar/25.24.4876. [DOI] [PMC free article] [PubMed] [Google Scholar]
  55. Vitali J., Carroll D., Chaudhry R. G., Hackert M. L. Three-dimensional structure of the Gly121Tyr dimeric form of ornithine decarboxylase from Lactobacillus 30a. Acta Crystallogr D Biol Crystallogr. 1999 Dec;55(Pt 12):1978–1985. doi: 10.1107/s0907444999010756. [DOI] [PubMed] [Google Scholar]
  56. Wadskov-Hansen S. L., Willemoës M., Martinussen J., Hammer K., Neuhard J., Larsen S. Cloning and verification of the Lactococcus lactis pyrG gene and characterization of the gene product, CTP synthase. J Biol Chem. 2001 Aug 10;276(41):38002–38009. doi: 10.1074/jbc.M100531200. [DOI] [PubMed] [Google Scholar]
  57. Weng M. L., Zalkin H. Structural role for a conserved region in the CTP synthetase glutamine amide transfer domain. J Bacteriol. 1987 Jul;169(7):3023–3028. doi: 10.1128/jb.169.7.3023-3028.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  58. Weng M., Makaroff C. A., Zalkin H. Nucleotide sequence of Escherichia coli pyrG encoding CTP synthetase. J Biol Chem. 1986 Apr 25;261(12):5568–5574. [PubMed] [Google Scholar]
  59. Whelan J., Phear G., Yamauchi M., Meuth M. Clustered base substitutions in CTP synthetase conferring drug resistance in Chinese hamster ovary cells. Nat Genet. 1993 Apr;3(4):317–322. doi: 10.1038/ng0493-317. [DOI] [PubMed] [Google Scholar]
  60. Wylie J. L., Wang L. L., Tipples G., McClarty G. A single point mutation in CTP synthetase of Chlamydia trachomatis confers resistance to cyclopentenyl cytosine. J Biol Chem. 1996 Jun 28;271(26):15393–15400. doi: 10.1074/jbc.271.26.15393. [DOI] [PubMed] [Google Scholar]
  61. Zalkin H., Smith J. L. Enzymes utilizing glutamine as an amide donor. Adv Enzymol Relat Areas Mol Biol. 1998;72:87–144. doi: 10.1002/9780470123188.ch4. [DOI] [PubMed] [Google Scholar]
  62. Zalkin H. The amidotransferases. Adv Enzymol Relat Areas Mol Biol. 1993;66:203–309. doi: 10.1002/9780470123126.ch5. [DOI] [PubMed] [Google Scholar]

Articles from Biochemical Journal are provided here courtesy of The Biochemical Society

RESOURCES