The structure of SAICAR synthase: An enzyme in the de novo pathway of purine nucleotide biosynthesis

Structure

Volumn 6, Issue 3, 1998, Pages 363-376

  Levdikov, Vladimir M ^a   Barynin, Vladimir V ^a   Grebenko, Albina I ^a   Melik Adamyan, William R ^a   Lamzin, Victor S ^b   Wilson, Keith S ^b,c  

^a SHUBNIKOV INSTITUTE OF CRYSTALLOGRAPHY   (Russian Federation)

^b EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

^c UNIVERSITY OF YORK   (United Kingdom)

Author keywords

ATP binding protein; Crystal structure; Phosphoribosylaminoimidazolesuccinocarboxamide (SAICAR) synthase; Purine biosynthesis

Indexed keywords

SACCHAROMYCES CEREVISIAE;

EID: 0032521456     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0969-2126(98)00038-0     Document Type: Article

References (58)

1. Miller, R.W. & Buchanan, J.M. (1962). Biosynthesis of the purines: XXVII. N-(5-amino-1-ribosyl-4-imidazolylcarbonyl)-L-aspartic acid 5′-phosphate kinosynthetase J. Biol. Chem. 237, 458-490.
2. Zalkin, H. & Dixon, J.E. (1992). De Novo purine nucleotide biosynthesis. Prog. Nucl. Acid Res. Mol. Biol. 42, 259-287.
3. Poland, B.W., et al., & Honzatko, R.B. (1993) Crystal structure of adenylosuccinate synthetase from Escherichia coli. J. Biol. Chem. 268, 25334-25342.
4. Lukens, L.N. & Buchanan, J.M. (1959). Biosynthesis of the purines: XXIII. The enzymatic synthesis of N-(5-amino-1-ribosyl-4-imidazolylcarbonyl)-L-aspartic acid 5′-phosphate. J. Biol. Chem. 234, 1791-1798.
5. Myasnikov, A.N., Plavnik, Y.A., Sasnauskas, K.V., Gedminene, G.K., Janulaitis, A.A. & Smirnov, M.N. (1986). Nucleotide sequence of ADE1 gene of yeast Saccharomyces cerevisiae. Bioorg. Khimia (USSR) 12, 555-558.
6. Ostanin, K.V., Alenin, V.V., Domkin, V.D. & Smirnov, M.N. (1989). Isolation and properties of phosphoribosyl-succinocarboxamide-aminoimidazole synthetase from the yeast Saccharomyces cerevisiae. Biokhimiya (USSR) 54, 1265-1273.
7. Alenin, V.V., Ostanin, K.V., Kostikova, T.R., Domkin, V.D., Zubova, V.A. & Smirnov, M.N. (1992). Substrate specificity of Phosphoribosyl-aminoimidazole-succinocarboxamide-synthetase (SAICAR-synthetase) of the yeast Saccharomyces cerevisiae. Biokhimiya (USSR) 57, 845-855.
8. Nishiya, Y. (1994). Primary structure of the ADE1 gene from Candida utilis. Biosci. Biotechnol. Biochem. 58, 208-210.
9. Sasnauskas, K., Jomantiene, R., Geneviciute, E., Januska, A. & Lebedys, J. (1991). Molecular cloning of the Candida maltosa ADE1 gene. Gene 107, 161-164.
10. Kawai, S., Hikiji, T., Murao, S., Takagi, M. & Yano, K. (1991). Isolation and sequencing of a gene, C-ADE1, and its use for a host-vector system in Candida maltosa with two genetic markers. Agric. Biol. Chem. 55, 59-65.
11. Chapman, K.A., Delauney, A.J., Kim, J.H. & Verma, D.P. (1994). Structural organization of de novo purine biosynthesis enzymes in plants: 5-aminoimidazole ribonucleotide carboxylase and 5-aminoimidazole-4-N-succinocarboxamide ribonucleotide synthetase cDNAs from Vigna aconitifolia. Plant Mol. Biol. 24, 389-395.
12. Hui, F.M. & Morrison, D.A. (1993). Identification of a purC gene from Streptococcuspneumoniae. J. Bacteriol. 175, 6364-6367.
13. Ebbole, D.J. & Zalkin, H. (1987). Cloning and characterization of a 12-gene cluster from Bacillus subtilis encoding nine enzymes for de novo purine nucleotide synthesis. J. Biol. Chem. 262, 8274-8287.
14. Tiedemann, A.A., Demarini, D.J., Parker, J. & Smith J.M. (1990). DNA Sequence of the purC gene encoding 5′-phosphoribosyl-5-aminoimidazole-4-N-succinocarboxamide synthetase and organization of the dapA-purC region of Escherichia coli K-12. J. Bacteriol. 172, 6035-6041.
15. Bouvier, J., Pugsley, A.P. & Stragier, P. (1991). A gene for a new lipoprotein in the dapA-purC interval of the Escherichia coli chromosome. J. Bacteriol. 173, 5523-5531.
16. Meyer, E., Leonard, N.J., Bhat, B., Stubbe, J. & Smith J.M. (1992). Purification and characterization of the purE, purK. and purC gene products: identification of a previously unrecognized energy requirement in the purine biosynthetic pathway. Biochemistry 31, 5022-5032.
17. Chen, Z., Dixon, J.E. & Zalkin H. (1990). Cloning of a chicken liver cDNA encoding 5-aminoimidazole ribonucleotide carboxylase and 5-aminoimidazole-4-N-succinocarboxamide ribonucleotide synthetase by functional complementation of Escherichia coli pur mutants. Proc. Natl. Acad. Sci. USA. 87, 3097-3101.
18. Minet, M. & Lacroute, F. (1990). Cloning and sequencing of human cDNA coding for a multifunctional polypeptide of the purine pathway by complementation of the ADE2-101 mutant in Saccharomyces cerevisiae. Curr. Genet. 18, 287-291.
19. Rossmann, M.G., Moras, D. & Olsen, K.W. (1974). Chemical and biological evolution of a nucleotide-binding protein. J. Mol. Biol. 250, 194-199.
20. Rossmann, M.G., Liljas, A., Brändén, C.-I. & Banaszak, L.J. (1975). Evolutionary and structural relationships among dehydrogenases. In The Enzymes. 3rd edition, (Boyer, P.D., ed.) 11A, pp. 61-102 Academic Press, New York.
21. Saraste, M., Sibbald, P.R. & Wittinghofer, A. (1990). The P-loop - a common motif in ATP- and GTP-binding proteins. Trends. Biochem. Sci. 15, 430-434.
22. Flaherty, K.M., McKay, D.B., Kabsch, W. & Holmes, K.S. (1991). Similarity of the three-dimensional structure of actin and the ATPase fragment of a 70K heat-shock cognate protein. Proc. Natl. Acad. Sci. USA 88, 5041-5045.
23. Schulz, G.E. (1992). Binding of nucleotides to proteins. Curr. Opin. Struct. Biol. 2, 61-67.
24. Murzin, A.G., Brenner, S.E., Hubbard, T. & Chothia, C. (1995). SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247, 536-540.
25. Flaherty, K.M., DeLuca-Flaherty, C. & McKay, D.B. (1990). Three-dimensional structure of the ATPase fragment of a 70K heat-shock cognate protein. Nature 346, 623-628.
26. Kabsch, W., Mannherz, H.G., Suck, D., Pai, E.F. & Holmes, K.C. (1990). Atomic structure of the actin: DNase I complex. Nature 347, 37-44.
27. Knighton, D.R., et al., & Sowadski, J.M. (1991). Crystal structure of the catalytic subunit of cyclic adenosine monophosphate-dependent protein kinase. Science 253, 407-414.
28. Yamaguchi, H., et al., & Katsube, Y. (1993). Three-dimensional structure of the glutathione synthetase from Escherichia coli B at 2.0 Å resolution. J. Mol. Biol. 229, 1083-1100.
29. Fan, C., Moews, P.C., Walsh, CT. & Knox, J.R. (1994). Vancomycin resistance: structure of D-alanine:D-alanine ligase at 2.5 Å resolution. Science 266, 439-443.
30. Waldrop, G.L., Rayment, I. & Holden, H.M. (1994). Three-dimensional structure of the biotin carboxylase subunit of acetyl-CoA carboxylase. Biochemistry 33, 10249-10256.
31. Read, R.J. (1986). Improved Fourier coefficients for maps using phases from partial structures with errors. Acta Cryst. A 42, 140-149.
32. Ramakrishnan, C. & Ramachandran, G.N. (1965). Stereochemical criteria for polypeptide and protein chain conformations. Biophys. J. 5, 909-903.
33. Laskowski, R.A., MacArthur, M.W., Moss, D.S. & Thornton, J.M. (1993). PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Cryst. 26, 283-291.
34. Lamzin, V.S., Dauter, Z., Popov, A.O., Harutyunyan, E.H., & Wilson, K.S. (1994). High resolution structures of holo and apo formate dehydrogenase. J. Mol. Biol. 236, 759-785.
35. Wilmot, C.M. & Thornton, J.M. (1990). β-Turns and their distortions: proposed new nomenclature. Protein Eng. 3, 479-493.
36. Wada, A. (1976) The α-helix as an electric macro-dipole. Adv. Biophys. 9, 1-63.
37. Hol, W.G.J., Van Duijnen, P.T. & Berendsen, H.J.C. (1978). The α-helix dipole and properties of proteins. Nature 273, 443-446.
38. Davies, C.J. & Hutchison, C.A., III. (1991). A directed DNA sequencing strategy based upon Tn3 transposon mutagenesis: application to the ADE1 locus on Saccharomyces cerevisiae chromosome I. Nucleic Acids Res. 19, 5731-5738.
39. Bairoch, A. (1990). SwissProt Protein Sequence Databank User Manual, Release 14.0, EMBL Data Library, Heidelberg, FRG.
40. Higgins, D.G., Bleasby, A.J. & Fuchs, R. (1992). CLUSTAL V: improved software for multiple sequence alignment. Comput. Appl. Biosci. 8, 189-191.
41. Bork, P., Sander, C. & Valencia, A. (1992). An ATPase domain common to prokaryotic cell cycle proteins, sugar kinases, actin, and hsp70 heat shock proteins. Proc. Natl. Acad. Sci. USA 89, 7290-7294.
42. Artymiuk, P.J., Poirrette, A.R., Raice, D.W. & Willett, P. (1995). Biotin carboxylase comes into the fold. Nat. Struct. Biol. 3, 128-132.
43. Kobayashi, N. & Go, N. (1997). ATP binding proteins with different folds share a common ATP-binding structural motif. Nat. Struct. Biol. 4, 6-7.
44. Matsuda, K., Mizugichi, K., Nishioka, T., Kato, H., Go, N. & Oda, J. (1996). Crystal structure of glutathione synthetase at optimal pH: domain architecture and structural similarity with other proteins. Protein Eng. 9, 1083-1092.
45. Walsh, C.T., Fisher, S.L., Park, I.S., Prahalad, M. & Wu, Z. (1996). Bacterial resistance to vancomycin: five genes and one missing hydrogen bond tell the story. Chem. Bio3, 21-28.
46. Fan, C., Moews, P.C., Shi, Y., Walsh, C.T. & Knox, J.R. (1995). A common fold for peptide synthetases cleaving ATP to ADP: glutathione synthetase and D-alanine:D-alanine ligase of Escherichia coll. Proc. Natl. Acad Sci. USA 92, 1172-1176.
47. Myasnikov, A.N., Sasnauskas, K.V., Janulaitis, A.A. & Smirnov, M.N. (1991). The Saccharomyces cerevisiae ADE1 gene: structure, overexpression and possible regulation by general amino acid control. Gene 107, 143-147.
48. Grebenko, A.I., Levdikov, V.M., Barynin, V.V., Melik-Adamyan, W.R. & Myasnikov, A.N. (1992). Crystallization and preliminary X-ray investigation of phosphoribosylaminoimidazolesuccinocarboxamide synthase from the yeast Saccharomyces cerevisiae. J. Mol. Biol. 228, 298-299.
49. Davies, D.R. & Segal, D.M. (1971). Protein crystallization: micro techniques involving vapour diffusion. In Methods in Enzymology. (Jakoby, W.B., ed.), 22, pp. 266-269, Academic Press, New York and London.
50. Otwinowski, Z. & Minor, W. (1993). DENZO: a film processing program for macromolecular crystallography. Yale University, New Haven, CT, USA.
51. Otwinowski, Z. (1991). Isomorphous replacement and anomalous scattering. In Proceedings of the CCP4 Study Weekend (Wolf, W., Evans, P.R. & Leslie, G.W., eds.), pp. 80-86. SERC Daresbury Laboratory, Warrington, UK.
52. CCP4: Collaborative Computational Project, Number 4 (1994). The CCP4 suite: programs for protein crystallography. Acta Cryst. D 50, 760-763.
53. Zhang, K.Y.J. & Main, P. (1990). Histogram matching as a new density modification technique for phase refinement and extension of protein molecules. Acta Cryst. A 46, 41-46.
54. Lamzin, V.S. & Wilson, K.S. (1993). Automated refinement of protein models. Acta Cryst. D 49, 129-147.
55. Jones, T.A. (1978) A graphics model building and refinement system for macromolecules. J. Appl. Cryst. 11, 268-272.
56. Konnert, J.H. & Hendrickson, W.A. (1980). A restrained-parameter thermal-factor refinement procedure. Acta Cryst. A 36, 344-350.
57. Murshudov, G.N., Vagin, A.A. & Dodson, E.J. (1997). Refinement of macromolecular structures by the maximum-likelihood method. Acta Cryst. D 53, 240-255.
58. Bernstein, F.C., et al., & Tasumi, M. (1977). The Protein Data Bank: a computer-based archival file for macromolecular structures. J. Mol. Biol. 112, 535-542.