Kinetic and inhibition studies of dihydroxybenzoate-AMP ligase from escherichia coli

Biochemistry

Volumn 49, Issue 17, 2010, Pages 3648-3657

  Sikora, Alison L ^a   Wilson, Daniel J ^b   Aldrich, Courtney C ^b   Blanchard, John S ^a  

^a ALBERT EINSTEIN COLLEGE OF MEDICINE   (United States)

^b UNIVERSITY OF MINNESOTA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADENYLATE; ADENYLATION; ANTIBACTERIAL DRUGS; BIOSYNTHETIC PATHWAY; DETAILED KINETICS; DIHYDROXYBENZOATE; DIHYDROXYBENZOIC ACIDS; ENTEROBACTIN; FINAL ASSEMBLY; FREE ENZYME; GENE CLUSTERS; INITIAL VELOCITIES; INTRACELLULAR IRON; IRON CHELATORS; ISOTHERMAL TITRATION CALORIMETRY; KINETIC MECHANISM; PATHOGENIC BACTERIUM; PICOMOLAR DISSOCIATION; SIDEROPHORES; SMALL MOLECULES; SYNTHETASES; TIGHT BINDING;

AROMATIC COMPOUNDS; BACTERIA; DISSOCIATION; ENZYMES; ESCHERICHIA COLI; EXPERIMENTS; REACTION INTERMEDIATES; STRATEGIC PLANNING;

ENZYME INHIBITION;

2,3 DIHYDROXYBENZOIC ACID; ADENOSINE PHOSPHATE; ENTEROCHELIN; LIGASE; PYROPHOSPHATE;

ADENYLATION; ARTICLE; COVALENT BOND; DISSOCIATION CONSTANT; ENZYME ACTIVITY; ENZYME DEGRADATION; ENZYME INHIBITION; ENZYME KINETICS; ENZYME RELEASE; ESCHERICHIA COLI; GENE CLUSTER; ISOTHERMAL TITRATION CALORIMETRY; MOLECULAR CLONING; NONHUMAN; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEIN PURIFICATION; STEADY STATE; THERMODYNAMICS;

BINDING SITES; CATALYSIS; CATALYTIC DOMAIN; DIMERIZATION; ENTEROBACTIN; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; KINETICS; LIGASES; MODELS, MOLECULAR; MULTIENZYME COMPLEXES; PANTOTHENIC ACID; PEPTIDE SYNTHASES; SUBSTRATE SPECIFICITY;

ESCHERICHIA COLI;

EID: 77951680623     PISSN: 00062960     EISSN: 15204995     Source Type: Journal    
DOI: 10.1021/bi100350c     Document Type: Article

References (35)

1. Miethke, M. and Marahiel, M. A. (2007) Siderophore-based iron acquisition and pathogen control Microbiol. Mol. Biol. Rev. 71, 413-451
2. Sandy, M. and Butler, A. (2009) Microbial iron acquisition: Marine and terrestrial siderophores Chem. Rev. 109, 4580-4595
3. Gehring, A. M., Bradley, K. A., and Walsh, C. T. (1997) Enterobactin biosynthesis in Escherichia coli: Isochorismate lyase (EntB) is a bifunctional enzyme that is phosphopantetheinylated by EntD and then acylated by EntE using ATP and 2,3-dihydroxybenzoate Biochemistry 36, 8495-8503
4. Raymond, K. N., Dertz, E. A., and Kim, S. S. (2003) Enterobactin: An archetype for microbial iron transport Proc. Natl. Acad. Sci. U.S.A. 100, 3584-3588
5. Gehring, A. M., Mori, I., and Walsh, C. T. (1998) Reconstitution and characterization of the Escherichia coli enterobactin synthetase from EntB, EntE, and EntF Biochemistry 37, 2648-2659
6. Sakaitani, M., Rusnak, F., Quinn, N. R., Tu, C., Frigo, T. B., Berchtold, G. A., and Walsh, C. T. (1990) Mechanistic studies on trans-2,3-dihydro-2,3- dihydroxybenzoate dehydrogenase (Ent A) in the biosynthesis of the iron chelator enterobactin Biochemistry 29, 6789-6798
7. Lambalot, R. H., Gehring, A. M., Flugel, R. S., Zuber, P., LaCelle, M., Marahiel, M. A., Reid, R., Khosla, C., and Walsh, C. T. (1996) A new enzyme superfamily: The phosphopantetheinyl transferases Chem. Biol. 3, 923-936
8. Ehmann, D. E., Shaw-Reid, C. A., Losey, H. C., and Walsh, C. T. (2000) The EntF and EntE adenylation domains of Escherichia coli enterobactin synthetase: Sequestration and selectivity in acyl-AMP transfers to thiolation domain cosubstrates Proc. Natl. Acad. Sci. U.S.A. 97, 2509-2514
9. Miethke, M., Bisseret, P., Beckering, C. L., Vignard, D., Eustache, J., and Marahiel, M. A. (2006) Inhibition of aryl acid adenylation domains involved in bacterial siderophore synthesis FEBS J. 273, 409-419
10. Gupte, A., Boshoff, H. I., Wilson, D. J., Neres, J., Labello, N. P., Somu, R. V., Xing, C., Barry, C. E., and Aldrich, C. C. (2008) Inhibition of siderophore biosynthesis by 2-triazole substituted analogues of 5′-O-[N-(salicyl)sulfamoyl]adenosine: Antibacterial nucleosides effective against Mycobacterium tuberculosis J. Med. Chem. 51, 7495-7507
11. Ferreras, J. A., Ryu, J. S., Di Lello, F., Tan, D. S., and Quadri, L. E. (2005) Small-molecule inhibition of siderophore biosynthesis in Mycobacterium tuberculosis and Yersinia pestis Nat. Chem. Biol. 1, 29-32
12. Neres, J., Wilson, D. J., Celia, L., Beck, B. J., and Aldrich, C. C. (2008) Aryl acid adenylating enzymes involved in siderophore biosynthesis: Fluorescence polarization assay, ligand specificity, and discovery of non-nucleoside inhibitors via high-throughput screening Biochemistry 47, 11735-11749
13. Drake, E. J., Nicolai, D. A., and Gulick, A. M. (2006) Structure of the EntB multidomain nonribosomal peptide synthetase and functional analysis of its interaction with the EntE adenylation domain Chem. Biol. 13, 409-419
14. Yin, J., Lin, A. J., Golan, D. E., and Walsh, C. T. (2006) Site-specific protein labeling by Sfp phosphopantetheinyl transferase Nat. Protoc. 1, 280-285
15. Zheng, R. and Blanchard, J. S. (2001) Steady-state and pre-steady-state kinetic analysis of Mycobacterium tuberculosis pantothenate synthetase Biochemistry 40, 12904-12912
16. Morrison, J. F. and Walsh, C. T. (1988) The behavior and significance of slow-binding enzyme inhibitors Adv. Enzymol. Relat. Areas Mol. Biol. 61, 201-301
17. Wiseman, T., Williston, S., Brandts, J. F., and Lin, L. N. (1989) Rapid measurement of binding constants and heats of binding using a new titration calorimeter Anal. Biochem. 179, 131-137
18. Velazquez-Campoy, A. and Freire, E. (2006) Isothermal titration calorimetry to determine association constants for high-affinity ligands Nat. Protoc. 1, 186-191
19. Khalil, S. and Pawelek, P. D. (2009) Ligand-induced conformational rearrangements promote interaction between the Escherichia coli enterobactin biosynthetic proteins EntE and EntB J. Mol. Biol. 393, 658-671
20. May, J. J., Kessler, N., Marahiel, M. A., and Stubbs, M. T. (2002) Crystal structure of DhbE, an archetype for aryl acid activating domains of modular nonribosomal peptide synthetases Proc. Natl. Acad. Sci. U.S.A. 99, 12120-12125
21. Rusnak, F., Faraci, W. S., and Walsh, C. T. (1989) Subcloning, expression, and purification of the enterobactin biosynthetic enzyme 2,3-dihydroxybenzoate-AMP ligase: Demonstration of enzyme-bound (2,3-dihydroxybenzoyl)adenylate product Biochemistry 28, 6827-6835
22. Keating, T. A., Suo, Z., Ehmann, D. E., and Walsh, C. T. (2000) Selectivity of the yersiniabactin synthetase adenylation domain in the two-step process of amino acid activation and transfer to a holo-carrier protein domain Biochemistry 39, 2297-2306
23. 3-diadenosine- 5′-tetraphosphate Biochemistry 48, 10827-10829
24. Kim, Y. S. and Kang, S. W. (1994) Steady-state kinetics of malonyl-CoA synthetase from Bradyrhizobium japonicum and evidence for malonyl-AMP formation in the reaction Biochem. J. 297 (Part 2) 327-333
25. Wu, R., Cao, J., Lu, X., Reger, A. S., Gulick, A. M., and Dunaway-Mariano, D. (2008) Mechanism of 4-chlorobenzoate:coenzyme A ligase catalysis Biochemistry 47, 8026-8039
26. Reger, A. S., Carney, J. M., and Gulick, A. M. (2007) Biochemical and crystallographic analysis of substrate binding and conformational changes in acetyl-CoA synthetase Biochemistry 46, 6536-6546
27. Somu, R. V., Boshoff, H., Qiao, C., Bennett, E. M., Barry, C. E., III, and Aldrich, C. C. (2006) Rationally designed nucleoside antibiotics that inhibit siderophore biosynthesis of Mycobacterium tuberculosis J. Med. Chem. 49, 31-34
28. de Carvalho, L. P., Argyrou, A., and Blanchard, J. S. (2005) Slow-onset feedback inhibition: Inhibition of Mycobacterium tuberculosis α-isopropylmalate synthase by l -leucine J. Am. Chem. Soc. 127, 10004-10005
29. Sculley, M. J., Morrison, J. F., and Cleland, W. W. (1996) Slow-binding inhibition: The general case Biochim. Biophys. Acta 1298, 78-86
30. Khalil, E. M., De Angelis, J., Ishii, M., and Cole, P. A. (1999) Mechanism-based inhibition of the melatonin rhythm enzyme: Pharmacologic exploitation of active site functional plasticity Proc. Natl. Acad. Sci. U.S.A. 96, 12418-12423
31. Faller, B., Farley, D., and Nick, H. (1993) Finasteride: A slow-binding 5α-reductase inhibitor Biochemistry 32, 5705-5710
32. Lightcap, E. S. and Silverman, R. B. (1996) Slow-binding inhibition of γ-aminobutyric acid aminotransferase by hydrazine analogues J. Med. Chem. 39, 686-694
33. Yu, M., Magalhaes, M. L., Cook, P. F., and Blanchard, J. S. (2006) Bisubstrate inhibition: Theory and application to N-acetyltransferases Biochemistry 45, 14788-14794
34. Neres, J., Labello, N. P., Somu, R. V., Boshoff, H. I., Wilson, D. J., Vannada, J., Chen, L., Barry, C. E., III, Bennett, E. M., and Aldrich, C. C. (2008) Inhibition of siderophore biosynthesis in Mycobacterium tuberculosis with nucleoside bisubstrate analogues: Structure-activity relationships of the nucleobase domain of 5′-O-[N-(salicyl)sulfamoyl]adenosine J. Med. Chem. 51, 5349-53470
35. Broom, A. D. (1989) Rational design of enzyme inhibitors: Multisubstrate analogue inhibitors J. Med. Chem. 32, 2-7