Proton affinity of the oxyanion hole in the active site of ketosteroid isomerase

Biochemistry

Volumn 49, Issue 12, 2010, Pages 2725-2731

  Childs, William ^a   Boxer, Steven G ^a  

^a STANFORD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACTIVE SITE; DEPROTONATED FORM; ISOMERASES; OXYANION HOLE; PROTON AFFINITY; PROTONATED; PROTONATION STATE; PSEUDOMONAS PUTIDA; REACTION INTERMEDIATE; SUBSTANTIAL VARIATIONS; SYSTEMATIC VARIATION; WILD TYPES;

BIOCHEMISTRY; HYDROGEN; POSITIVE IONS; PROTONATION; PROTONS; REACTION INTERMEDIATES;

HYDROGEN BONDS;

ANION; EQUILENIN; PROTON; STEROID DELTA ISOMERASE;

ABSORPTION SPECTROPHOTOMETRY; ARTICLE; BINDING AFFINITY; BINDING SITE; CATALYSIS; HYDROGEN BOND; NONHUMAN; PRIORITY JOURNAL; PROTON TRANSPORT; PSEUDOMONAS PUTIDA;

CATALYSIS; CATALYTIC DOMAIN; COMPUTATIONAL BIOLOGY; CRYSTALLOGRAPHY, X-RAY; HYDROGEN BONDING; KETOSTEROIDS; MODELS, MOLECULAR; MUTAGENESIS, SITE-DIRECTED; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PROTEIN CONFORMATION; PROTONS; PSEUDOMONAS PUTIDA; STATIC ELECTRICITY; STEROID ISOMERASES; STRUCTURE-ACTIVITY RELATIONSHIP; SUBSTRATE SPECIFICITY;

PSEUDOMONAS PUTIDA;

EID: 77949824987     PISSN: 00062960     EISSN: 15204995     Source Type: Journal    
DOI: 10.1021/bi100074s     Document Type: Article

References (36)

1. Gerlt, J. A., and Gassman, P. G. (1993) Understanding the rates of certain enzyme-catalyzed reactions: Proton abstraction from carbon acids, acyl transfer reactions, and displacement reactions of phospho-diesters. Biochemistry 32, 11934-11952.
2. Gerlt, J. A., and Gassman, P. G. (1993) An explanation for rapid enzyme-catalyzed proton abstraction from carbon acids: Importance of late transition states in concerted mechanisms. J. Am. Chem. Soc. 115, 11552-11568.
3. Cleland, W. W., and Kreevoy, M. M. (1994) Low-barrier hydrogen bonds and enzymic catalysis. Science 264, 1887-1890.
4. Frey, P. A., Whitt, S., and Tobin, J. (1994) A low-barrier hydrogen bond in the catalytic triad of serine proteases. Science 264,1927-1930.
5. Pollack, R. M. (2004) Enymatic mechanisms for catalysis of enolization: Ketosteroid isomerase. Bioorg. Chem. 32, 341-353.
6. 5-3-ketosteriod isomerase from Pseudomonasputida Biotype B. Biochemistry 39, 903-909.
7. 5-3-ketosteroid isomerase. Biochemistry 28,149-159.
8. 5-steroid isomerase. Arch. Biochem. Biophys. 370, 9-15.
9. Warshel, A., Papazyan, A., and Kollman, P. A. (1995) On low-barrier hydrogen bonds and enzyme catalysis. Science 269, 102-104.
10. Guthrie, J. P. (1996) Short strong hydrogen bonds: Can they explain enzymic catalysis? Chem. Biol. 3, 163-170.
11. Kraut, D. A., Sigala, P. A., Pybus, B., Liu, C. W., Ringe, D., Petsko, G. A., and Herschlag, D. (2006) Testing electrostatic complementarity in enzyme catalysis: Hydrogen bonding in the ketosteroid isomerase oxyanion hole. PLoS Biol. 4, e99.
12. 5-3-ketosteroid isomerase. Proc. Natl. Acad. Sci. U.S.A. 93, 8220-8224.
13. 5-3-ketosteroid isomerase from Pseudomonas testosteroni in complex with equilenin settles the correct hydrogen bonding scheme for transition state stabilization. J. Biol. Chem. 274, 32863-32868.
14. Cleland, W. W. (2000) Low-barrier hydrogen bonds and enzymatic catalysis. Arch. Biochem. Biophys. 382, 1-5.
15. Steiner, T. (2002) The hydrogen bond in the solid state. Angew. Chem., Int. Ed. 41, 48-76.
16. -1. J. Am. Chem. Soc. 99, 5207-5209.
17. -1. J. Am. Chem. Soc. 102, 3315-3322.
18. 5-3-ketosteroid isomerase with and without a reaction intermediate analogue. Biochemistry 36, 14030-14036.
19. Anderson, S., Crosson, S., and Moffat, K. (2004) Short hydrogen bonds in photoactive yellow protein. Acta Crystallogr. D60, 1008-1016.
20. Sigala, P. A., Tsuchida, M. A., and Herschlag, D. (2009) Hydrogen bond dynamics in the active site of photoactive yellow protein. Proc. Natl. Acad. Sci. U.S.A. 106, 9232-9237.
21. Yamaguchi, S., Kamikubo, H., Kurihara, K., Kuroki, R., Niimura, N., Shimizu, N., Yamazaki, Y., and Kataoka, M. (2009) Low-barrier hydrogen bond in photoactive yellow protein. Proc. Natl. Acad. Sci. U.S.A. 106, 440-444.
22. Garcia-Viloca, M., Gonzalez-Lafont, A , and Llunch, J. M. (1997) Theoretical study of the low-barrier hydrogen bond in the hydrogen maleate anion in the gas phase. Comparison with normal hydrogen bonds. J. Am. Chem. Soc. 119, 1081-1086.
23. Pan, Y., and McAllisster, M. A. (1998) Characterization of low-barrier hydrogen bond. 6. Cavity polarity effects on the formic acid-formate anion model system. An ab initio and DFT investigation. J. Am. Chem. Soc. 120, 166-169.
24. 5-3-ketosteroid isomerase. Biochemistry 32, 1816-1824.
25. Fafarman, A. T., Sigala, P. A., Herschlag, D., and Boxer, S. G. Manuscript in preparation.
26. Childs, W., and Boxer, S. G. Manuscript in preparation.
27. http : //www. scripps.edu/~cdputnam/protcalc.html.
28. Gill, S. C., and von Hippel, P. H. (1989) Calculation of protein extinction coefficients from amino acid sequence data. Anal. Biochem. 182, 319-326.
29. 5- steroid isomerase using the D38E and D38N mutations: The energetic basis for catalysis. Biochemistry 33, 12172-12183.
30. 5-steroid isomerase: Variation of ligand ionization state with the nature of the electrophilic component. Biochemistry 39, 110-116.
31. 5-3-ketos-teroid isomerase. Biochemistry 30, 4991-4997.
32. Kim,D.H.,Nam,G.H., Jang, D.S., Choi, G., Joo,S.,Kim, J. S.,Oh, B. H., and Choi, K. Y. (1999) Roles of active site aromatic residues in catalysis by ketosteroid isomerase from Pseudomonas putida Biotype B. Biochemistry 38, 13810-13819.
33. Zeng, B., and Pollack, R. M. (1991) Microscopic rate constants for the acetate ion catalyzed isomerization of 5-androstene-3,17-dione to 4-androstene-3,17-dione: A model for steroid isomerase. J. Am. Chem. Soc. 113, 3838-3842.
34. Shan, S. O., Loh, S., and Herschlag, D. (1996) The energetics of hydrogen bonds in model systems: Implications for enzymatic catalysis. Science 272, 97-101.
35. Kumar, G. A., and McAllister, M. A. (1998) Characterization of lowbarrier hydrogen bonds. 8. Substituent effects on the strength and geometry of the formic acid-formate anion model system. An ab initio and DFT investigation. J. Am. Chem. Soc. 120, 3159-3165.
36. Feierberg, I., and Åqvist, J. (2002) The catalytic power of ketosteroid isomerase investigated by computer simulation. Biochemistry 41, 15728-15735.