Structure of diethyl phosphate bound to the binuclear metal center of phosphodiesterase

Biochemistry

Volumn 47, Issue 36, 2008, Pages 9497-9504

  Kim, Jungwook ^a   Tsai, Ping Chuan ^b   Chen, Shi Lu ^c   Himo, Fahmi ^c   Almo, Steven C ^a   Raushel, Frank M ^b  

^a ALBERT EINSTEIN COLLEGE OF MEDICINE   (United States)

^b TEXAS A AND M UNIVERSITY   (United States)

^c ROYAL INSTITUTE OF TECHNOLOGY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER NETWORKS; DENSITY FUNCTIONAL THEORY; DIELECTRIC DEVICES; ENZYME INHIBITION; ESTERIFICATION; ESTERS; HYDROLYSIS; MECHANISMS; METAL IONS; ORGANIC COMPOUNDS; OXYGEN; POSITIVE IONS; PROBABILITY DENSITY FUNCTION; RATE CONSTANTS; SEPARATION; SOLVENTS; THREE DIMENSIONAL;

BINUCLEAR METAL CENTER; ORGANOPHOSPHATE ESTERS; PRODUCT COMPLEX;

IONS;

AMINOACYLASE; DIHYDROOROTASE; HYDROLASE; METAL ION; PHOSPHOTRIESTERASE;

ARTICLE; CHEMICAL STRUCTURE; DENSITY FUNCTIONAL THEORY; ENZYME STRUCTURE; HYDROLYSIS; NONHUMAN; PRIORITY JOURNAL; SIMULATION;

BACTERIAL PROTEINS; BINDING SITES; HYDROLYSIS; METALS; MODELS, MOLECULAR; PHOSPHORIC ACID ESTERS; PHOSPHORIC TRIESTER HYDROLASES; PROTEIN STRUCTURE, TERTIARY; PSEUDOMONAS; STRUCTURAL HOMOLOGY, PROTEIN;

BACTERIA (MICROORGANISMS); BREVUNDIMONAS DIMINUTA;

EID: 51549089373     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi800971v     Document Type: Article

References (34)

1. Seibert, C. M., and Raushel, F. M. (2005) Structural and catalytic diversity within the amidohydrolase superfamily. Biochemistry 44, 6383-6391.
2. Benning, M. M., Shim, H., Raushel, F. M., and Holden, H. M. (2001) High resolution X-ray structures of different metal-substituted forms of phosphotriesterase from Pseudomonas diminuta. Biochemistry 40, 2712-2722.
3. Donarski, W. J., Dumas, D. P., Heitmeyer, D. P., Lewis, V. E., and Raushel, F. M. (1989) Structure-activity relationships in the hydrolysis of substrates by the phosphotriesterase from Pseudomonas diminuta. Biochemistry 28, 4650-4655.
4. Dumas, D. P., Durst, H. D., Landis, W. G., Raushel, F. M., and Wild, J. R. (1990) Purification and properties of the phosphotriesterase for Pseudomonas diminuta. Arch. Biochem. Biophys. 277, 155-159.
5. Caldwell, S. R., Newcomb, J. R., Schlecht, K. A., and Raushel, F. M. (1991) Limits of diffusion in the hydrolysis of substrates by the phosphotriesterase from Pseudomonas diminuta. Biochemistry 30, 7438-7444.
6. Raushel, F. M., and and Holden, H. M. (2000) Phosphotriesterase: An enzyme in search of its natural substrate. Adv. Enzymol. Relat. Areas Mol. Biol. 74, 51-93.
7. Omburo, G. A., Kuo, J. M., Mullins, L. S., and Raushel, F. M. (1992) Characterization of the zinc binding site of bacterial phosphotriesterase. J. Biol. Chem. 267, 13278-13283.
8. Aubert, S. D., Li, Y., and Raushel, F. M. (2004) Mechanism for the hydrolysis of organophosphates by the bacterial phosphotriesterase. Biochemistry 43, 5707-5715.
9. Chen, S.-L., Fang, W.-H., and Himo, F. (2007) Theoretical study of the phosphotriesterase reaction mechanism. J. Phys. Chem. B 111, 1253-1255.
10. Wong, K.-Y., and Gao, J. (2007) The reaction mechanism of paraoxon hydrolysis by phosphotriesterase from combined QM/MM simulations. Biochemistry 46, 13352-13369.
11. Jackson, C. J., Foo, J. L., Kim, H. K., Carr, P. D., Liu, J. W., Salem, G., and Ollis, D. L. (2008) In crystallo capture of a Michaelis complex and product-binding modes of a bacterial phosphotriesterase. J. Mol. Biol. 375, 1189-1196.
12. Samples, C. R., Raushel, F. M., and DeRose, V. J. (2007) Activation of the binuclear metal center through formation of phosphotriesterase-inhibitor complexes. Biochemistry 46, 3435-3442.
13. Jackson, C., Kim, H. K., Carr, P. D., Liu, J. W., and Ollis, D. L. (2005) The structure of an enzyme-product complex reveals the critical role of a terminal hydroxide nucleophile in the bacterial phosphotriesterase mechanism. Biochim. Biophys. Acta 1752, 56-64.
14. Kuiper, J. M., Hulst, R., and Engberts, J. B. F. N. (2003) A selective and mild synthetic route to dialkyl phosphates. Synthesis, 695-698.
15. Otwinowski, Z., and Minor, W. (1997) Macromolecular crystallography, part A. In Methods in Enzymology (Carter, C. W., Jr., andSweet, R. M., Eds.) pp 307-326, Academic Press, New York.
16. Vagin, A., and Teplyakov, A. (1997) MOLREP: An automated program for molecular replacement. J. Appl. Crystallogr. 30, 1022-1025.
17. Lamzin, V. S., Wilson, K. S., and Perrakis, A. (2001) Crystallography of biological macromolecules. In International Tables for Crystallography (Rossmann, M. G., and Arnold, E., Eds.) pp 720-722, Kluwer Academic Publishers, Dordrecht, The Netherlands.
18. Emsley, P., and Cowtan, K. (2004) Coot: Model-building tools for molecular graphics. Acta Crystallogr. D60 (Part 12, Special Issue 1), 2126-2132.
19. Murshudov, G. N., Vagin, A. A., and Dodson, E. J. (1997) Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D53, 240-255.
20. Becke, A. D. (1993) A new mixing of Hartree-Fock and local density-functional theories. J. Chem. Phys. 98, 1372-1377.
21. Becke, A. D. (1993) Density-functional thermochemistry III. The role of exact exchange. J. Chem. Phys. 98, 5648-5652.
22. Lee, C., Yang, W., and Parr, R. G. (1988) Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. Phys. Rev. B 37, 785-789.
23. Barone, V., and Cossi, M. (1998) Quantum calculation of molecular energies and energy gradients in solution by a conductor solvent model. J. Phys. Chem. A 102, 1995-2001.
24. Cammi, R., Mennucci, B., and Tomasi, J. (1999) Second-order Moller-Plesset analytical derivatives for the polarizable continuum model using the relaxed density approach. J. Phys. Chem. A 103, 9100-9108.
25. Klamt, A., and Schüürmann, G. (1993) COSMO: A new approach to dielectric screening in solvents with explicit expressions for the screening energy and its gradient. J. Chem. Soc., Perkin. Trans. 2, 799-800.
26. Tomasi, J., Mennucci, B., and Cammi, R. (2005) Quantum mechanical continuum solvation models. Chem. Rev. 105, 2999-3094.
27. Frisch, M. J., Trucks, G. W., Schlegel, H. B., et al. (2004) Gaussian 03, revision D.01, Gaussian, Inc., Wallingford, CT.
28. Chen-Goodspeed, M., Sogorb, M. A., Wu, F., Hong, S.-B., and Raushel, F. M. (2001) Structural determinants of the substrate and stereochemical specificity of phosphotriesterase. Biochemistry 40, 1325-1331.
29. Martí-Arbona, R., Fresquet, V., Thoden, J. B., Davis, M. L., Holden, H. M., and Raushel, F. M. (2005) Mechanism of the reaction catalyzed by isoaspartyl dipeptidase from Escherichia coli. Biochemistry 44, 7115-7124.
30. Thoden, J. B., Marti-Arbona, R., Raushel, F. M., and Holden, H. M. (2003) High-resolution X-ray structure of isoaspartyl dipeptidase from Escherichia coli. Biochemistry 42, 4874-4882.
31. Liaw, S.-H., Chen, S.-J., Ko, T.-P., Hsu, C.-S., Chen, C.-J., Wang, A. H.-J., and Tsai, Y.-C. (2003) Crystal structure of D-aminoacylase from Alcaligenes faecalis DA1. J. Biol. Chem. 278, 4957-4962.
32. Lai, W.-L., Chou, L.-Y., Ting, C.-Y., Kirby, R., Tsai, Y.-C., Wang, A. H.-J., and Liaw, S.-H. (2004) The functional role of the binuclear metal center in D-aminoacylase. J. Biol. Chem. 279, 13962-13967.
33. Thoden, J. B., Phillips, G. M., Neal, T. M., Raushel, F. M., and Holden, H. M. (2001) Molecular structure of dihydroorotase: A paradigm for catalysis through the use of a binuclear metal center. Biochemistry 40, 6989-6997.
34. Zheng, F., Znan, C.-G., and Ornstein, R. L. (2002) Theoretical determination of two structural forms of the active site in cadmium-containing phosphotriesterases. J. Phys. Chem. B 106, 717-722.