Alternate modes of binding in two crystal structures of alkaline phosphatase-inhibitor complexes

Protein Science

Volumn 9, Issue 5, 2000, Pages 907-915

  Holtz, Kathleen M ^a   Stec, Boguslaw ^b   Myers, Jason K ^c   Antonelli, Stephen M ^c   Widlanski, Theodore S ^c   Kantrowitz, Evan R ^a  

^a BOSTON COLLEGE   (United States)

^b RICE UNIVERSITY   (United States)

^c INDIANA UNIVERSITY   (United States)

Author keywords

Inhibitors; Phosphatase; Phosphonates; Phosphonic acid; X ray crystallography

Indexed keywords

ALKALINE PHOSPHATASE; BACTERIAL ENZYME;

ARTICLE; CRYSTAL STRUCTURE; ENZYME BINDING; ENZYME INHIBITION; ENZYME INHIBITOR COMPLEX; ESCHERICHIA COLI; NONHUMAN; PRIORITY JOURNAL; STRUCTURE ANALYSIS; X RAY CRYSTALLOGRAPHY;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; PAA;

EID: 0034119452     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1110/ps.9.5.907     Document Type: Article

References (43)

1. Bartlett PA, Hanson JE, Giannousis PP. 1990. Potent inhibition of pepsin and penicillopepsin by phosphorus-containing peptide analogues. J Org Chem 55:6268-6274.
2. Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M. 1983. CHARMM: A program for macromolecular energy, minimization, and dynamics calculations. J Comp Chem 4:187-217.
3. Brünger AT. 1992. X-PLOR, version 3.1. New Haven, CT: Yale University Press.
4. Carlow DC, Smith AA, Yang CC, Short SA, Wolfenden R. 1995. Major contribution of a carboxymethyl group to transition-state stabilization by cytidine deaminase: Mutation and rescue. Biochemistry 34:4220-4224.
5. Chaidaroglou A, Brezinski DJ, Middleton SA, Kantrowitz ER. 1988. Function of arginine-166 in the active site of Escherichia coli alkaline phosphatase. Biochemistry 27:8338-8343.
6. Chakrabarti P. 1989. Geometry of interaction of metal ions with sulfur-containing ligands in protein structures. Biochemistry 28:6081-6085.
7. Cleland WW, Kreevoy MM. 1994. Low-barrier hydrogen bonds and enzymatic catalysis. Science 264:1887-1890.
8. Coleman JE. 1992. Structure and mechanism of alkaline phosphatase. Annu Rev Biophys Biomol Struct 27:441-483.
9. Desiraju GR. 1991. The C-H⋯O hydrogen bond in crystals: What is it? Acc Chem Res 24:290-296.
10. Desiraju GR, Steiner T. 1999. The weak hydrogen bond: In structural chemistry and biology New York: Oxford University Press Inc.
11. Engel R. 1977. Phosphonates as analogues of natural phosphates. Chem Rev 77:349-367.
12. Flint DH. 1994. Initial kinetic and mechanistic characterization of Escherichia coli fumarase A. Arch Biochem Biophys 311:509-516.
13. Flint DH, Emptage MH, Guest JR. 1992. Fumarase A from Escherichia coli: Purification and characterization as an iron-sulfur cluster containing enzymes. Biochemistry 31:10331-10337.
14. Frey PA, Whitt SA, Tobin JB. 1994. A low-barrier hydrogen bond in the catalytic triad of serine proteases. Science 264:1927-1930.
15. Garen A, Leventhal C. 1960. A fine-structure genetic and chemical study of the enzyme alkaline phosphatase of E. coli. I. Purification and characterization of alkaline phosphatase. Biochim Biophys Acta 38:470-483.
16. Gerlt JA, Gassman PG. 1993. Understanding the rates of certain enzyme-catalyzed reactions: Proton abstraction from carbon acids, acyl-transfer reactions, and displacement reactions of phosphodieslers. Biochemistry 32: 11943-11956.
17. Holden HM, Tronrud DE, Monzingo AF, Weaver LH, Matthews BW. 1987. Slow-and fast-binding inhibitors of thermolysin display different modes of binding: Crystallographic analysis of extended phosphonamidate transition-state analogues. Biochemistry 26:8542-8553.
18. Holtz KM, Stec B, Kantrowitz ER. 1999. A model of the transition state in the alkaline phosphatase reaction. J Biol Chem 274:8351-8354.
19. Hough E, Hansen LK, Birknes B, Jynge K, Hansen S, Hordvik A, Little C, Dodson EJ, Derewenda Z. 1989. High resolution (1.5 Å) crystal structure of phospholipase C from Bacillus cereus. Nature 338:357-360.
20. Kennedy MC, Stout CD. 1992. Aconitase: An iron-sulfur enzyme. In: Cammack R et al., ed. Advances in inorganic chemistry. London: Academic Press Inc. pp 323-339.
21. Kim EE, Wyckoff HW. 1991. Reaction mechanism of alkaline phosphatase based on crystal structures. Two-metal ion catalysis. J Mol Biol 218:449-464.
22. Kim H, Lipscomb WN. 1990. Crystal structure of the complex of carboxypeptidase a with a strongly bound phosphonate in a new crystalline form: Comparison with structures of other complexes. Biochemistry 29:5546-5555.
23. Lejczak B, Kafarski P, Zygmunt J. 1989. Inhibition of aminopeptidases by aminophosphonates. Biochemistry 28:3549-3555.
24. Lopez V, Stevens T, Lindquist RN. 1976. Vanadium ion inhibition of alkaline phosphatase-catalyzed phosphate ester hydrolysis. Arch Biochem Biophys 175:31-38.
25. Morgan BP, Scholtz JM, Ballinger MD, Zipkin ID, Bartlett PA. 1991. Differential binding energy: A detailed evaluation of the influence of hydrogen-bonding and Hydrophobic groups on the inhibition of thermolysin by phosphorus-containing inhibitors. J Am Chem Soc 113:297-307.
26. Murphy JE, Stec B, Ma L, Kantrowitz ER. 1997. Trapping and visualization of a covalent enzyme-phosphate intermediate. Nat Struct Biol 4:618-622.
27. Myers JK, Antonelli SM, Widlanski TS. 1997. Motifs for metallophosphatase inhibition. J Am Chem Soc 119:3163-3164.
28. Ohlsson JT, Wilson IB, 1974. The inhibition of alkaline phosphatase by periodate and permanganate. Biochim Biophys Acta 350:48-53.
29. Plocke DJ, Vallee BL. 1962. Interaction of alkaline phosphatase of E. coli with metal ions and chelating agents. Biochemistry 1:1039-1043.
30. Reid TW, Wilson IB. 1971. E. coli. alkaline phosphatase. In: Boyer PD, ed. The enzymes. New York: Academic Press, pp 373-415.
31. Shan S, Loh S, Herschlag D. 1996. The energetics of hydrogen bonds in model systems: Implications for enzymatic catalysis. Science 272:97-101.
32. Sharp K, Honig B. 1990. Electrostatic interactions in macromolecules: Theory and applications. Annu Rev Biophys Chem 19:301-332.
33. Sheldrick GM, Schneider TR. 1997. SHELXL: High-resolution refinement. Methods Enzymol 277:319-343.
34. Soman K, Yang AS, Honig B, Fletterick R. 1989. Electrical potentials in trypsin isozymes. Biochemistry 28:9918-9926.
35. Sowadski JM, Handschumacher MD, Murthy HM, Foster BA, Wyckoff HW. 1985. Refined structure of alkaline phosphatase from Escherichia coli at 2.8 Å resolution. J Mol Biol 186:417-433.
36. Sowadski JM, Handschumacher MD, Murthy HM, Kundrot CE, Wyckoff HW. 1983. Crystallographic observations of the metal ion triple in the active site region of alkaline phosphatase. J Mol Biol 170:575-581.
37. Steiner T, Saenger W. 1993. Role of C-H⋯O hydrogen bonds in the coordination of water molecules. Analysis of neutron diffraction data. J Am Chem Soc 115:4540-4547.
38. Taylor R, Kennard O. 1982. Crystallographic evidence for the existence of C-H⋯O. C-H⋯N. and C-H⋯Cl hydrogen bonds. J Am Chem Soc 104:5063-5070.
39. Usher KC, Remington SJ, Martin DP, Drueckhammer DG. 1994. A very short hydrogen bond provides only moderate stabilization of an enzyme-inhibitor complex of citrate synthase. Biochemistry 33:7753-7759.
40. Volbeda A, Lahm A, Sakiyama F, Suck D. 1991. Crystal structure of Penicillium citrinum P1 nuclease at 2.8 Å resolution. EMBO J 10:1607-1618.
41. Wiberg KB, Waldron RF, Schulte G, Saunders M. 1991. Lactones. 1. X-ray crystallongraphic studies of nonanotactone and tridecanolactone: Nature of CH⋯O nonbonded interactions. J Am Chem Soc 113:971-977.
42. Zhang E, Brewer JM, Minor W, Carreira LA, Lebioda L. 1997. Mechanism of enolase: The crystal structure of asymmetric dimer enolase - 2-phospho-D-glycerate/enolase - phosphoenolpyruvate at 2.0 Å resolution. Biochemistry 36:12526-12534.
43. Zhang ZY, Dixon JE. 1994. Protein tyrosine phosphatases: Mechanism of catalysis and substrate specificity. Adv Enzymol Relat Areas Mol Biol 68:1-36.