Structural and Kinetic Studies of the Allosteric Transition in Sulfolobus solfataricus Uracil Phosphoribosyltransferase: Permanent Activation by Engineering of the C-Terminus

Journal of Molecular Biology

Volumn 393, Issue 2, 2009, Pages 464-477

  Christoffersen, Stig ^a   Kadziola, Anders ^a   Johansson, Eva ^a   Rasmussen, Michael ^a   Willemoës, Martin ^a   Jensen, Kaj Frank ^a  

^a UNIVERSITY OF COPENHAGEN   (Denmark)

Author keywords

Archaea; CTP; enzyme regulation; GTP; nucleotide biosynthesis; UMP

Indexed keywords

5 PHOSPHORIBOSYL ALPHA 1 DIPHOSPHATE; CYTIDINE TRIPHOSPHATE; GUANOSINE TRIPHOSPHATE; LYSINE; PROLINE; PYROPHOSPHATE; RIBOSE 5 PHOSPHATE; TETRAMER; TYROSINE; UNCLASSIFIED DRUG; URACIL PHOSPHORIBOSYLTRANSFERASE; URIDINE PHOSPHATE; ARCHAEAL PROTEIN; GLYCOSYLTRANSFERASE;

ALLOSTERISM; ARTICLE; CARBOXY TERMINAL SEQUENCE; CATALYSIS; COMPLEX FORMATION; CONTROLLED STUDY; ENZYME ACTIVATION; ENZYME ACTIVE SITE; ENZYME ANALYSIS; ENZYME ENGINEERING; ENZYME KINETICS; ENZYME STRUCTURE; HYDROGEN BOND; MOLECULAR INTERACTION; NONHUMAN; PRIORITY JOURNAL; PROTEIN HYDROLYSIS; PROTEIN PROTEIN INTERACTION; STEADY STATE; STRUCTURE ANALYSIS; SULFOLOBUS SOLFATARICUS; CHEMISTRY; ENZYME SPECIFICITY; ENZYMOLOGY; GENETICS; KINETICS; METABOLISM; PROTEIN BINDING; PROTEIN SECONDARY STRUCTURE; X RAY CRYSTALLOGRAPHY;

SULFOLOBUS SOLFATARICUS;

ALLOSTERIC REGULATION; ARCHAEAL PROTEINS; CATALYTIC DOMAIN; CRYSTALLOGRAPHY, X-RAY; CYTIDINE TRIPHOSPHATE; ENZYME ACTIVATION; GUANOSINE TRIPHOSPHATE; KINETICS; PENTOSYLTRANSFERASES; PROTEIN BINDING; PROTEIN STRUCTURE, SECONDARY; SUBSTRATE SPECIFICITY; SULFOLOBUS SOLFATARICUS; URIDINE MONOPHOSPHATE;

EID: 70349417705     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2009.08.019     Document Type: Article

References (31)

1. Jensen K.F., Dandanell G., Hove-Jensen B., and Willemoës M. Nucleotides, nucleosides and nucleobases. In: Böck A., Curtis III R., Kaper J.B., Karp P.D., Neidhardt F.C., Nyström T., Slauch J.M., and Squires C.L. (Eds). EcoSal-Escherichia coli and Salmonella: Cellular and Molecular Biology (2008), ASM Press, Washington, D.C. http://www.ecosal.org http://www.ecosal.org
2. Schramm V.L., and Grubmeyer C.T. Phosphoribosyltransferase mechanisms and roles in nucleic acid metabolism. In: Moldave K. (Ed). Progress in Nucleic Acids Research and Molecular Biology vol. 78 (2004), Academic Press, New York 261-304
3. Ozturk D., Dorfman R.H., Scapin G., Sacchettini J.C., and Grubmeyer C. Structure and function of Salmonella typhimurium orotate phosphoribosyltransferase: protein complementation reveals shared active sites. Biochemistry 34 (1995) 10764-10770
4. Henriksen A., Aghajari N., Jensen K.F., and Gajhede M. A flexible loop at the dimer interface is part of the active site of the adjacent monomer of Escherichia coli orotate phosphoribosyltransferase. Biochemistry 35 (1996) 3803-3809
5. Jensen K.F. Metabolism of 5-phosphoribosyl 1-pyrophosphate (PRPP) in Escherichia coli and Salmonella typhimurium. In: Munch-Petersen A. (Ed). Metabolism of Nucleotides, Nucleosides and Nucleobases in Microorganisms (1983), Academic Press, London 1-25
6. Jensen K.F., and Mygind B. Different oligimeric states are involved in the allosteric behavior of uracil phosphoribosyltransferase from Escherichia coli. Eur. J. Biochem. 240 (1996) 637-645
7. Schumacher M.A., Bashor C.J., Song M.H., Otsu K., Zhu S., Parry R.J., et al. The structural mechanism of GTP stabilized oligomerization and catalytic activation of the Toxoplasma gondii uracil phosphoribosyltransferase. Proc. Natl Acad. Sci. USA 99 (2002) 78-83
8. Schumacher M.A., Carter D., Scott D.M., Roos D.S., Ullman B., and Brennan R.G. Crystal structures of Toxoplasma gondii uracil phosphoribosyltransferase reveal the atomic basis of pyrimidine discrimination and prodrug binding. EMBO J 17 (1998) 3219-3232
9. Linde L., and Jensen K.F. Uracil phosphoribosyltransferase from the extreme thermophilic archaebacterium Sulfolobus shibatae is an allosteric enzyme, activated by GTP and inhibited by CTP. Biochim. Biophys. Acta 1296 (1996) 16-22
10. Jensen K.F., Arent S., Larsen S., and Schack L. Allosteric properties of the GTP activated and CTP inhibited uracil phosphoribosyltransferase from the thermo-acidophilic archaeon Sulfolobus solfataricus. FEBS J. 272 (2005) 1440-1453
11. Monod J., Wyman J., and Changeux J.-P. On the nature of allosteric transitions: a plausible model. J. Mol. Biol. 12 (1965) 88-118
12. Arent S., Harris P., Jensen K.F., and Larsen S. Allosteric regulation and communication between subunits in uracil phosphoribosyltransferase from Sulfolobus solfataricus. Biochemistry 44 (2005) 883-892
13. Kadziola A., Neuhard J., and Larsen S. Structure of product-bound Bacillus caldolyticus uracil phosphoribosyltransferase confirms ordered sequential substrate binding. Acta Crystallogr., Sect. D: Biol. Crystallogr. 58 (2002) 936-945
14. Hove-Jensen B., Harlow K.V., King C.J., and Switzer R.L. Phosphoribosylpyrophosphate synthetase of Escherichia coli. Properties of the purified enzyme and primary structure of the prs gene. J. Biol. Chem 261 (1986) 6765-6771
15. Hershey H.V., and Taylor M.W. Nucleotide sequence and deduced amino acid sequence of Escherichia coli adenine phosphoribosyltransferase and comparison with other analogous enzymes. Gene 43 (1986) 287-293
16. Seshadri T.P., Viswamitra M.A., and Kartha G. Structure of disodium uridine 5′-phosphate heptahydrate. Acta Crystallogr., Sect. B: Struct. Sci. 36 (1980) 925-927
17. McClard R.W., Holets E.A., MacKinnon A.L., and Witte J.F. Half-of-sites binding of orotidine 5′phosphate and α-d-5-phosphoribose 1-diphosphate to orotate phosphoribosyltransferase from Saccharomyces cerevisiae supports a novel variant of the Theorell-Chance mechanism with alternating site catalysis. Biochemistry 45 (2006) 5330-5342
18. O'Sullivan W.J., and Smithers G.W. Stability constants for biologically important metal-ligand complexes. Methods Enzymol. 63 (1979) 294-336
19. Willemoës M., and Hove-Jensen B. Binding of divalent magnesium by Escherichia coli phosphoribosyl diphosphate synthetase. Biochemistry 36 (1997) 5078-5083
20. Grabner G.K., and Switzer R.L. Kinetic studies of the uracil phosphoribosyltransferase reaction catalyzed by the Bacillus subtilis pyrimidine attenuation regulatory protein PyrR. J. Biol. Chem. 278 (2003) 6921-6927
21. Jancarik J., and Kim S.H. Sparse matrix sampling: a screening method for crystallization of proteins. J. Appl. Crystallogr. 24 (1991) 409-411
22. Cerenius Y., Ståhl K., Svensson L.A., Ursby T., Oskarsson Å., Albertson J., and Liljas A. The crystallography beamline I711 at MAX II. J. Synchrotron Rad. 7 (2000) 203-208
23. Otwinowski Z., and Minor W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276A (1997) 307-326
24. Navaza J. AMORE: an automated package for molecular replacement. Acta Crystallogr., Sect. A: Found. Crystallogr. 50 (1994) 157-163
25. Brünger A.T., Adams P.D., Clore G.M., DeLano W.L., Gros P., Grosse-Kunstleve R.W., et al. Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr., Sect. D: Biol. Crystallogr. 54 (1998) 905-921
26. Adams P.D., Grosse-Kunstleve R.W., Hung L.-W., Ioerger T.R., McCoy A.J., Moriarty N.W., et al. PHENIX: building new software for automated crystallographic structure determination. Acta Crystallogr., Sect. D: Biol. Crystallogr. 58 (2002) 1948-1954
27. Roussel A., and Cambillau C. Turbo-Frodo, Bibliographics and AFMB (1992), Architecture et fonction des Macromolécules Biologiques Marseille, France
28. Jones T.A., Zou J.-Y., Cowan S.W., and Kjeldgaard M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr., Sect. A: Found. Crystallogr. 47 (1991) 110-119
29. Laskowski R.A., MacArthur M.W., Moss D.S., and Thornton J.M. PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Crystallogr. 26 (1993) 283-291
30. Kraulis P.J. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr. 24 (1991) 946-950
31. Merritt E.A., and Bacon D.J. Raster3D photorealistic molecular graphics. Methods Enzymol. 277 (1997) 505-524