Site-directed mutagenesis of catalytic residues in N 5- Carboxyaminoimidazole ribonucleotide synthetase

Biochemistry

Volumn 52, Issue 37, 2013, Pages 6559-6567

  Dewal, Mahender B ^a,b   Firestine, Steven M ^a  

^a WAYNE STATE UNIVERSITY   (United States)

^b MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CATALYTIC RESIDUE; KINETIC INVESTIGATIONS; MUTANT PROTEINS; RIBONUCLEOTIDES; SITE DIRECTED MUTAGENESIS; SUBSTRATE INHIBITION; SYNTHETASES; X-RAY CRYSTALLOGRAPHIC ANALYSIS;

CATALYSIS; PROTEINS; X RAY CRYSTALLOGRAPHY;

ENZYME ACTIVITY;

ADENOSINE TRIPHOSPHATE; BICARBONATE; MUTANT PROTEIN; N5 CARBOXYAMINOIMIDAZOLE RIBONUCLEOTIDE SYNTHETASE; SYNTHETASE; UNCLASSIFIED DRUG;

ARTICLE; BIOCATALYSIS; CONCENTRATION RESPONSE; CONTROLLED STUDY; ENZYME ACTIVE SITE; ENZYME BINDING; ENZYME INHIBITION; ENZYME INHIBITOR COMPLEX; ENZYME KINETICS; NONHUMAN; PRIORITY JOURNAL; SITE DIRECTED MUTAGENESIS; WILD TYPE;

ADENOSINE TRIPHOSPHATE; AMINO ACID SEQUENCE; AMINOIMIDAZOLE CARBOXAMIDE; BICARBONATES; BINDING SITES; CATALYSIS; CATALYTIC DOMAIN; ESCHERICHIA COLI; KINETICS; LIGASES; MODELS, MOLECULAR; MUTAGENESIS, SITE-DIRECTED; RIBONUCLEOTIDES;

EID: 84884216443     PISSN: 00062960     EISSN: 15204995     Source Type: Journal    
DOI: 10.1021/bi400444y     Document Type: Article

References (32)

1. Fawaz, M. V., Topper, M. E., and Firestine, S. M. (2011) The ATP-grasp enzymes Bioorg. Chem. 39, 185-191
2. Galperin, M. Y. and Koonin, E. V. (1997) A diverse superfamily of enzymes with ATP-dependent carboxylate-amine/thiol ligase activity Protein Sci. 6, 2639-2643 (Pubitemid 28006703)
3. Murzin, A. G. (1996) Structural classification of proteins: New superfamilies Curr. Opin. Struct. Biol. 6, 386-394 (Pubitemid 26197440)
4. Kappock, T. J., Ealick, S. E., and Stubbe, J. (2000) Modular evolution of the purine biosynthetic pathway Curr. Opin. Chem. Biol. 4, 567-572
5. Li, H., Fast, W., and Benkovic, S. J. (2009) Structural and functional modularity of proteins in the de novo purine biosynthetic pathway Protein Sci. 18, 881-892
6. Thoden, J. B., Holden, H. M., and Firestine, S. M. (2008) Structural analysis of the active site geometry of N5-carboxyaminoimidazole ribonucleotide synthetase from Escherichia coli Biochemistry 47, 13346-13353
7. Thoden, J. B., Holden, H. M., Paritala, H., and Firestine, S. M. (2010) Structural and Functional Studies of Aspergillus clavatus N-5- Carboxyaminoimidazole Ribonucleotide Synthetase Biochemistry 49, 752-760
8. Firestine, S. M. and Davisson, V. J. (1994) Carboxylases in de novo purine biosynthesis. Characterization of the Gallus gallus bifunctional enzyme Biochemistry 33, 11917-11926 (Pubitemid 24328002)
9. Bradford, M. M. (1976) A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding Anal. Biochem. 72, 248-254
10. Mueller, E. J., Meyer, E., Rudolph, J., Davisson, V. J., and Stubbe, J. (1994) N-5-Carboxyaminoimidazole Ribonucleotide: Evidence for a New Intermediate and two New Enzymatic Activities in the De Novo Purine Biosynthetic Pathway of Escherichia Coli Biochemistry 33, 2269-2278
11. Firestine, S. M., Misialek, S., Toffaletti, D. L., Klem, T. J., Perfect, J. R., and Davisson, V. J. (1998) Biochemical role of the Cryptococcus neoformans ADE2 protein in fungal de novo purine biosynthesis Arch. Biochem. Biophys. 351, 123-134 (Pubitemid 28373059)
12. Firestine, S. M., Paritala, H., Mcdonnell, J. E., Thoden, J. B., and Holden, H. M. (2009) Identification of inhibitors of N-5-carboxyaminoimidazole ribonucleotide synthetase by high-throughput screening Bioorg. Med. Chem. 17, 3317-3323
13. Attwood, P. V. and Wallace, J. C. (2002) Chemical and catalytic mechanisms of carboxyl transfer reactions in biotin-dependent enzymes Acc. Chem. Res. 35, 113-120
14. Knowles, J. R. (1989) The Mechanism of Biotin-Dependent Enzymes Annu. Rev. Biochem. 58, 195-221 (Pubitemid 19172969)
15. Raushel, F. M., Anderson, P. M., and Villafranca, J. J. (1978) Kinetic Mechanism of Escherichia-Coli Carbamoyl-Phosphate Synthetase Biochemistry 17, 5587-5591 (Pubitemid 9084422)
16. Raushel, F. M., Mullins, L. S., and Gibson, G. E. (1998) A stringent test for the nucleotide switch mechanism of carbamoyl phosphate synthetase Biochemistry 37, 10272-10278 (Pubitemid 28366384)
17. Climent, I. and Rubio, V. (1986) ATPase activity of biotin carboxylase provides evidence for initial activation of bicarbonate by ATP in the carboxylation of biotin Arch. Biochem. Biophys. 251, 465-470 (Pubitemid 17234244)
18. Gibson, G. E., Mullins, L. S., and Raushel, F. M. (1998) Carbamoyl phosphate synthetase from Escherichia coli does not catalyze the dehydration of bicarbonate to carbon dioxide Bioorg. Chem. 26, 255-268 (Pubitemid 29062109)
19. Blanchard, C. Z., Lee, Y. M., Frantom, P. A., and Waldrop, G. L. (1999) Mutations at four active site residues of biotin carboxylase abolish substrate-induced synergism by biotin Biochemistry 38, 3393-3400
20. Smith, A. C. and Cronan, J. E. (2012) Dimerization of the Bacterial Biotin Carboxylase Subunit Is Required for Acetyl Coenzyme A Carboxylase Activity In Vivo J. Bacteriol. 194, 72-78
21. Janiyani, K., Bordelon, T., Waldrop, G. L., and Cronan, J. E., Jr. (2001) Function of Escherichia coli biotin carboxylase requires catalytic activity of both subunits of the homodimer J. Biol. Chem. 276, 29864-29870
22. LiCata, V. J. and Allewell, N. M. (1997) Is substrate inhibition a consequence of allostery in aspartate transcarbamylase? Biophys. Chem. 64, 225-234 (Pubitemid 27148669)
23. Chou, C. Y. and Tong, L. (2011) Structural and Biochemical Studies on the Regulation of Biotin Carboxylase by Substrate Inhibition and Dimerization J. Biol. Chem. 286, 24417-24425
24. Chou, C. Y., Yu, L. P. C., and Tong, L. (2009) Crystal Structure of Biotin Carboxylase in Complex with Substrates and Implications for Its Catalytic Mechanism J. Biol. Chem. 284, 11690-11697
25. Stapleton, M. A., JavidMajd, F., Harmon, M. F., Hanks, B. A., Grahmann, J. L., Mullins, L. S., and Raushel, F. M. (1996) Role of conserved residues within the carboxy phosphate domain of carbamoyl phosphate synthetase Biochemistry 35, 14352-14361 (Pubitemid 26384432)
26. Pastra-Landis, S. C., Evans, D. R., and Lipscomb, W. N. (1978) The effect of pH on the cooperative behavior of aspartate transcarbamylase from Escherichia coli J. Biol. Chem. 253, 4624-4630 (Pubitemid 8372071)
27. 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 (Pubitemid 36800430)
28. Yifrach, O. and Horovitz, A. (1995) Nested Cooperativity in the Atpase Activity of the Oligomeric Chaperonin Groel Biochemistry 34, 5303-5308
29. Sloane, V. and Waldrop, G. L. (2004) Kinetic characterization of mutations found in propionic acidemia and methylcrotonylglycinuria-Evidence for cooperativity in biotin carboxylase J. Biol. Chem. 279, 15772-15778 (Pubitemid 38509262)
30. Janiyani, K., Bordelon, T., Waldrop, G. L., and Cronan, J. E. (2001) Function of Escherichia coli biotin carboxylase requires catalytic activity of both subunits of the homodimer J. Biol. Chem. 276, 29864-29870
31. Shen, Y., Chou, C. Y., Chang, G. G., and Tong, L. (2006) Is dimerization required for the catalytic activity of bacterial biotin carboxylase? Mol. Cell 22, 807-818
32. Firestine, S. M., Poon, S. W., Mueller, E. J., Stubbe, J., and Davisson, V. J. (1994) Reactions Catalyzed by 5-Aminoimidazole Ribonucleotide Carboxylases from Escherichia Coli and GallusGallus: a Case for Divergent Catalytic Mechanisms Biochemistry 33, 11927-11934