Theoretical analysis of the reaction mechanism of biotin carboxylase

Journal of Chemical Theory and Computation

Volumn 4, Issue 2, 2008, Pages 366-374

  Ito, Yuko ^a   Kondo, Hiroki ^a   Shiota, Yoshihito ^b   Yoshizawa, Kazunari ^b  

^a KYUSHU INSTITUTE OF TECHNOLOGY   (Japan)

^b KYUSHU UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 58149129370     PISSN: 15499618     EISSN: None     Source Type: Journal    
DOI: 10.1021/ct700260f     Document Type: Article

References (68)

1. Wood, H. G.; Barden, R. E. Biotin enzymes. Annu. Rev. Biochem. 1977, 46, 385.
2. Knowood, H. G.; Barden, R. E.; Bioles, J. R. The mechanism of biotin-dependent enzymes. Annu. Rev. Biochem. 1989, 58, 195.
3. Kaziro, Y.; Hass, L. F.; Boyer, P. D.; Ochoa, S. Mechanism of the, propionyl carboxylase reaction. J. Biol. Chem. 1962, 237, 1460.
4. 2 and the mechanism of enzymatic carboxylation reactions. Proc. Natl. Acad. Sci. U.S.A. 1970, 65, 805.
5. Hansen, D. E.; Knowles, J. R. The stereochemical course at phosphorus of the reaction catalyzed by phosphoenolpyruvate carboxylase. J. Biol. Chem. 1982, 257, 14795.
6. Ogita, T.; Knowles, J. R. On the intermediacy of carboxyphosphate in biotin-dependent carboxylations. Biochemistry 1988, 27, 8028.
7. Hansen, D. E.; Knowles, J. R. N-carboxybiotin formation by pyruvate carboxylase: The stereochemical. correspondence at phosphorus. J. Am. Chem. Soc. 1985, 107, 8304.
8. Polakis, S. E.; Guchhait, R. B.; Zwergel, E. E.; Lane, M. D. Acetyl coenzyme A carboxylase system of Escherichia coli. J. Biol. Chem. 1974, 249, 6657.
9. 2 fixation. J. Biol. Chem. 1975, 250, 14.
10. Attwood, P. V.; Graneri, B. D. L. A. Pyruvate carboxylase catalysis of phosphate transfer between carbamoyl phosphate and ADP. Biochem. J. 1991, 273, 443.
11. Phillips, N. F. B.; Snoswell, M. A.; Chapman-Smith, A.; Keech, D. B.; Wallace, J. C. Isolation of carboxyphosphate intermediate and the locus of acetyl-CoA action in the pyruvate carboxylase reaction. Biochemistry 1992, 31, 9445.
12. Attwood, P. V. Locus of action of acetyl CoA in the biotincarboxylation reaction of pyuvate carboxylase. Biochemistry 1993, 32, 12736.
13. Jitrapakdee, S.; Wallace, J. C. Structure function and regulation of pyruvate carboxylase. Biochem. J. 1999, 340, 1.
14. Attwood, P. V.; Wallace, J. C. Chemical and catalytic mechanisms of carboxyl transfer reactions in biotin-dependent enzymes. Acc. Chem. Res. 2002, 35, 113.
15. Kondo, H.; Shiratsuchi, K.; Yoshimoto, T.; Masuda, T.; Kitazono, A.; Tsuru, D.; Anai, M.; Sekiguchi, M.; Tanabe, T. Acetyl-CoA carboxylase from Escherichia coli: gene organization and nucleotide sequence of the biotin carboxylase subunit. Proc. Natl. Acad. Sci. U.S.A. 1991, 88, 9730.
16. Waldrop, G. L.; Rayment, I.; Holden, H. M. Three-dimensional structure of the biotin carboxylase subunit of acetyl-CoA carboxylase. Biochemistry 1994, 33, 10249.
17. 2 as Carbonic-Phosphoric Anhydride: Isolation of the Corresponding Trimethyl Derivative from the Active Site of Glutamine-Dependent Carbamyl Phosphate Synthetase. Proc. Natl. Acad. Sci. U.S.A. 1976, 73, 3020.
18. Powers, S. G.; Meister, A. Carbonic-phosphoric anhydride (carboxy phosphate). Significance in catalysis and regulation of glutamine-dependent carbamyl phosphate synthetase. J. Biol. Chem. 1978, 253, 1258.
19. Wimmer, M. J.; Rose, I. A.; Powers, S. G.; Meister, A. Evidence that carboxyphosphate is a kinetically competent intermediate in the carbamyl phosphate synthetase reaction. J. Biol. Chem. 1979, 254, 1854.
20. Stapleton, M. A.; Javid-Majd, F.; Harmon, M. F.; Hanks, B. A.; Grahmann, J. L.; Mullins, L. S.; Raushel, F. M. Role conserved residues within the carboxy phosphate. domain of carbamoyl phosphate synthetase. Biochemistry 1996, 35, 14352.
21. Javid-Majd, F.; Stapleton, M. A.; Harmon, M. F.; Hanks, B. A.; Mullins, L. S.; Raushel, F. M. Comparison of the functional differences for the homologous residues within the carboxy phosphate and carbamate domains of carbamoyl phosphate synthetase. Biochemistry 1996, 35, 14362.
22. Lee, C.; Yang, W.; Parr, R. G. Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. Phys. Rev. B 1988, 37, 785.
23. Becke, A. D. Density-functional thermochemistry. III. The role of exact exchange. J. Chem. Phys. 1993, 98, 5648.
24. Muetterties, E. L.; Bleeke, J. R.; Wucherer, E. J.; Albright, T. A. Structural stereochemical, and electronic features of arene-metal complexes. Chem. Rev. 1982, 82, 499.
25. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Montgomery, J. A., Jr.; Vreven, T.; Kudin, K. N.; Burant, J. C.; Millam, J. M.; Iyengar, S. S.; Tomasi, J.; Barone, V.; Mennucci, B.; Cossi, M.; Scalmani, G.; Rega, N.; Petersson, G. A.; Nakatsuji, H.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Klene, M.; Li, X.; Knox, J. E.; Hratchian, H. P.; Cross, J. B.; Adamo, C.; Jaramillo, J.; Gomperts, r.; Stratmann, R. E.; Yazyev, O.; Austin, A. J.; Cammi, R.; Pomelli, C.; Ochterski, J. W.; Ayala, P. Y.; Morokuma, K.; Voth, G. A.; Salvador, P.; Dannenberg, J. J.; Zakrzewski, V. G.; Dapprich, S.; Daniels, A. D.; Strain, M. C.; Farkas, O.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman, J. B.; Ortiz, J. V.; Cui, Q.; Baboul, A. G.; Clifford, S.; Cioslowski, J.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Martin, R. L.; Fox, D. J.; Keith, T.; Al-Laham, M. A.; Peng, C. Y.; Nanayakkara, A.; Challacombe, M.; Gill, P. M. W.; Johnson, B.; Chen, W.; Wong, M. W.; Gonzalez, C.; Pople, J. A. Gaussian 03; Gaussian, Inc.: Wallingford, CT, 2004.
26. Miller, W. H.; Handy, N. C.; Adams, J. E. Reaction Path Hamiltonian for Polyatomic Molecules. J. Chem. Phys. 1980, 72, 99.
27. Page, M.; Mclver, J. W., Jr. On evaluating the reaction path Hamiltonian. J. Chem. Phys. 1988, 88, 922.
28. Fukui, K. The path of chemical reactions. The IRC approach. Acc. Chem. Res. 1981, 14, 363.
29. Gonzalez, C.; Schlegel, H. B. An improved algorithm for reaction path following. J. Chem. Phys. 1989, 90, 2154.
30. Gonzalez, C.; Schlegel, H. B. Reaction path following in mass-weighted internal coordinates. J. Chem. Phys. 1990, 94, 5523.
31. Thoden, J. B.; Blanchard, C. Z.; Holden, H. M.; Waldrop, G. L. Movement of the biotin carboxylase B-domain as a result of ATP binding. J. Biol. Chem. 2000, 275, 16183.
32. Cook, D. The interaction of Friedel-Crafts catalysts with organic molecules: II. Boron trifluoride with benzoic anhydride. Can. J. Chem. 1962, 40, 445.
33. Silverstein, R. M.; Webster, F. X. In Spectrometric Identification of Organic Compounds, 6th ed.; John Wiley and Sons Ltd.: New York, 1998.
34. 8 on silver electrode revealed by Fourier transform Raman scattering studies. J. Mol. Struct. 1996, 377, 1.
35. Mamedov, S.; Stachel, D.; Soltwisch, M.; Quitmann, D. Local environment and dynamics of PO4 tetrahedra in NaAl-PO3 glasses and melts. J. Chem. Phys. 2005, 123, 124515.
36. Coates, J. Interpretation of infrared spectra: A practical approach. In Encyclopedia of Analytical Chemistry; Meyers, R. A., Ed.; John Wiley and Sons Ltd.: Chichester, U.K., 2000; pp 10815-10837.
37. Torres, R. A.; Himo, F.; Bruice, T. C.; Noodleman, L.; Lovell, T. Theoretical Examination of Mg(2+)-Mediated Hydrolysis of a Phosphodiester Linkage as Proposed for the Hammerhead Ribozyme. J. Am. Chem. Soc. 2003, 125, 9861.
38. De Meis, L. The concept of energy-rich phosphate compounds: water, transport ATPases and entropic energy. Arch. Biochem. Biophys. 1993, 306, 287.
39. De Meis, L. Role of water in the energy of hydrolysis of phosphate compounds: energy transduction in biological membranes. Biochim. Biophys. Acta 1989, 973, 333.
40. Attwood, P. V.; Tipton, P. A.; Cleland, W. W. Carbon-13 and deuterium isotope effects on oxalacetate decarboxylation by pyruvate carboxylase. Biochemistry 1986, 25, 8197.
41. Attwood, P. V. The structure and the mechanism of action of pyruvate carboxylase. Int. J. Biochem. Cell Biol. 1995, 27, 231.
42. Shriver, D. F.; Atkins, P. W.; Langford, C. H. In Inorganic Chemistry, 2nd ed.; Oxford University Press: Oxford, 1994.
43. Clayden, J.; Greeves, N.; Warren, S.; Wothers, P. In Organic Chemistry; Oxford University Press: New York, 2001.
44. Williams, A.; Naylor R. A. Hydrolysis of phosphinic esters: general-base catalysis by imidazole. J. Chem. Soc. B 1971, 1967.
45. Khanna, R. K.; Moore, M. H. Carbamic acid: molecular structure and IR spectra. Spectrochim. Acta, Part A 1999, 55A, 961.
46. Hegarty, A. F.; Bruice, T. C.; Benkovic, S. J. Biotin and the Nucleophilicity of 2-Methoxy-2-Imidazoline Toward the sp2 Carbonyl Carbon. J. Chem. Soc., Chem. Commun. 1969, 20, 1173.
47. Stallings, W.; Detitta, G. T. Cristallographic investigations of biotin and carboxybiotin derivatives. Ann. NY Acad. Sci. 1985, 447, 152.
48. Maggiora, G. M. Theoretical aspects of the structural chemistry of biotin I. The electronic structure of biotin and protonated biotins. J. Theor. Biol. 1973, 41, 523.
49. Capon, B.; Rycroft, D. S.; Watson, T. W.; Zueco, C. Simple enols. 1. The generation of vinyl alcohol in solution and its detection and characterization by NMR spectroscopy. J. Am. Chem. Soc. 1981, 103, 1761.
50. Capon, B.; Zueco, C. Simple enols 2. Kinetics and mechanism of the ketonization of vinyl alcohol. J. Am. Chem. Soc. 1982, 104, 7567.
51. Kraut, J. Serine proteases: structure and mechanism of catalysis. Annu. Rev. Biochem. 1977, 46, 331.
52. Lolis, E.; Petsko, G. A. Transition state analogues in protein. crystallography: probes of the structural source of enzyme catalysis. Annu. Rev. Biochem. 1990, 59, 597.
53. Fastrez, J.; Fersht, A. R. Demonstration of the acyl-enzyme mechanism for the hydrolysis of peptides and anilides by chymotrypsin. Biochemistry 1973, 12, 2025.
54. Sigler, P. B.; Blow, D. M.; Matthews, B. W.; Henderson, R. Structure of crystalline alpha-chymotrypsin. II. A preliminary report including a hypothesis for the activation mechanism. J. Mol. Biol. 1968, 35, 143.
55. Carter, P.; Wells, J. A. Dissecting the catalytic triad of a serine protease. Nature 1988, 322, 564.
56. Carter, P.; Wells, J. A. Functional interaction among catalytic residues in subtilisin BPN . Protein 1990, 7, 335.
57. Koepke, J.; Ermler, U.; Warkentin, E.; Wenzl, G.; Flecker, P. Crystal structure of cancer chemopreventive Bowman-Birk inhibitor in ternary complex with bovine trypsin at 2.3 Å resolution. Structural basis of Janus-faced serine protease inhibitor specificity. J. Mol. Biol. 2000, 298, 477.
58. Gaboriaud, C.; Rossi, V.; Bally, I.; Arlaud, G. J.; Fontecilla-Camps, J. C. Crystal structure of the catalytic domain of human complement C1s: a serine protease with a handle. EMBO J. 2000, 19, 1755.
59. 1-Carboxybiotin. J. Am. Chem. Soc. 2002, 124, 11334.
60. Levert, K. L.; Lloyd, R. B.; Waldrop, G. L. Do cysteine 230 and lysine 238 of biotin carboxylase play a role in the activation of biotin? Biochemistry 2000, 39, 4122.
61. Kazuta, Y.; Tokunaga, E.; Aramaki, E.; Kondo, H. Identification of lysine-238 of Escherichia coli biotin carboxylase as an ATP-binding residue. FEBS Lett. 1998, 427, 377.
62. Jitrapakdee, S.; Booker, G. W.; Cassady, A. I.; Wallace, J. C. Cloning sequencing and expression of rat liver pyruvate carboxylase. Biochem. J. 1996, 316, 631.
63. Blanchard, C. Z.; Lee, Y. M.; Frantom, P. A.; Waldrop, G. L. Mutations at four active site residues of biotin carboxylase abolish substrate-induced synergism by biotin. Biochemistry 1999, 38, 3393.
64. Sloane, V.; Blanchard, C. Z.; Guillot, F.; Waldrop, G. L. Site-directed Mutagenesis of ATP Binding Residues of Biotin Carboxylase: Insight into the Mechanism of Catalysis. J. Biol. Chem. 2001, 276, 24991.
65. Yong-Biao, J.; Islam, M. N.; Sueda, S.; Kondo, H. Identification of the catalytic residues involved in the carboxyl transfer of pyruvate carboxylase. Biochemistry 2004, 43, 5912.
66. Hall, P. R.; Zheng, R.; Antony, L.; Pustai-Carey, M.; Carey, P. R.; Yee. V. C. Transcarboxylase 5S structures: assembly and catalytic mechanism of a multienzyme complex subunit. EMBO J. 2004, 23, 3621.
67. Blanchard, C. Z.; Waldrop, G. L. Overexpression and kinetic characterization of the carboxyltransferase component of acetyl-CoA carboxylase. J. Biol. Chem. 1998, 273, 19140.
68. Tipton, P. A.; Cleland, W. W. Mechanism of decarboxylation of carboxybiotin. J. Am. Chem. Soc. 1988, 110, 5866.