A complete structural description of the catalytic cycle of yeast pyrophosphatase

Biochemistry

Volumn 46, Issue 5, 2007, Pages 1228-1239

  Oksanen, Esko ^a   Ahonen, Anna Karoliina ^a,b   Tuominen, Heidi ^c   Tuominen, Vesa ^a   Lahti, Reijo ^c   Goldman, Adrian ^a   Heikinheimo, Pirkko ^a,b  

^a UNIVERSITY OF HELSINKI   (Finland)

^b UNIVERSITY OF TROMSØ   (Norway)

^c UNIVERSITY OF TURKU   (Finland)

Author keywords

[No Author keywords available]

Indexed keywords

CATALYSIS; GENETIC ENGINEERING; HYDROGEN BONDS; HYDROLYSIS; MAGNESIUM COMPOUNDS; MONOMERS; PHOSPHATES; POSITIVE IONS; YEAST;

ASYMMETRIC UNITS; CATALYTIC INTERMEDIATES; HYDROGEN BONDING NETWORKS; MUTATIONS;

ENZYME KINETICS;

MAGNESIUM ION; PHENYLALANINE; PHOSPHATASE; PHOSPHATE; PYROPHOSPHATE; TYROSINE;

ARTICLE; BINDING AFFINITY; CATALYSIS; CONTROLLED STUDY; DISSOCIATION; ENZYME ACTIVE SITE; ENZYME CONFORMATION; HYDROGEN BOND; HYDROLYSIS; HYDROPHOBICITY; MUTATION; NONHUMAN; PRIORITY JOURNAL; STRUCTURE ANALYSIS; THERMODYNAMICS; YEAST;

BINDING SITES; CATALYSIS; FUNGAL PROTEINS; HYDROGEN BONDING; HYDROPHOBICITY; INORGANIC PYROPHOSPHATASE; MAGNESIUM; MUTATION; PHOSPHATES;

EID: 33846821940     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi0619977     Document Type: Article

References (30)

1. Heikinheimo, P., Tuominen, V., Ahonen, A.-K., Teplyakov, A., Cooperman, B. S., Baykov, A., Lahti, R., and Goldman, A. (2001) Towards a Quantum-Mechanical Description of Metal Assisted Phosphoryl Transfer in Pyrophosphatase, Proc. Natl. Acad. Sci. U.S.A. 98, 3121-3126.
2. Cooperman, B. S., Baykov, A. A., and Lahti, R. (1992) Evolutionary conservation of the active site of soluble inorganic pyrophosphatase, Trends Biochem. Sci. 17, 262-266.
3. Halonen, P., Baykov, A. A., Goldman, A., Lahti, R., and Cooperman, B. S. (2002) Single-turnover kinetics of Saccharomyces cerevisiae inorganic pyrophosphatase, Biochemistry 41, 12025-12031.
4. Pohjanjoki, P., Fabrichniy, I. P., Kasho, V. N., Cooperman, B. S., Goldman, A., Baykov, A. A., and Lahti, R. (2001) Probing Essential Water in Yeast Pyrophosphatase by Directed Mutagenesis and Fluoride Inhibition Measurements, J. Biol. Chem. 276, 434-441.
5. Zyryanov, A. B., Pohjanjoki, P., Kasho, V. N., Shestakov, A. S., Goldman, A., Lahti, R., and Baykov, A. A. (2001) The electrophilic and leaving group phosphates in the catalytic mechanism of yeast pyrophosphatase, J. Biol. Chem. 276, 17629-17634.
6. Baykov, A. A., Cooperman, B. S., Goldman, A., and Lahti, R. (1999) Cytoplasmic inorganic pyrophosphatase, in Progress in Molecular and Subcellular Biology (Schröder, H. C., and Müller, W. E. G., Eds.) Vol. 23, pp 127-150, Springer-Verlag, Heidelberg, Germany.
7. Heikinheimo, P., Lehtonen, J., Baykov, A., Lahti, R., Cooperman, B. S., and Goldman, A. (1996) The structural basis for pyrophosphatase catalysis, Structure 4, 1491-1508.
8. i at atomic resolution and their mechanistic implications, J. Mol. Biol. 314, 633-645.
9. Baykov, A. A., and Shestakov, A. S. (1992) Two pathways of pyrophosphate hydrolysis and synthesis by yeast inorganic pyrophosphatase, Eur. J. Biochem. 206, 463-470.
10. Cooperman, B. S. (1982) The Mechanism of Action of Yeast Inorganic Pyrophosphatase, Methods Enzymol. 87, 526-548.
11. Belogurov, G. A., Fabrichniy, I. P., Pohjanjoki, P., Kasho, V. N., Lehtihuhta, E., Turkina, M. V., Cooperman, B. S., Goldman, A., Baykov, A. A., and Lahti, R. (2000) Catalytically Important Ionizations along the Reaction Pathway of Yeast Pyrophosphatase, Biochemistry 39, 13931-13938.
12. Baykov, A. A., Fabrichniy, I. P., Pohjanjoki, P., Zyryanov, A. B., and Lahti, R. (2000) Fluoride Effects Along the Reaction Pathway of Pyrophosphatase. Evidence for a second enzyme pyrophosphate intermediate, Biochemistry 39, 11939-11947.
13. Springs, B., Welsh, K. M., and Cooperman, B. S. (1981) Thermodynamics, Kinetics, and Mechanism in Yeast Inorganic Pyrophosphatase Catalysis in Inorganic Pyrophosphate: Inorganic Phosphate Equilibration, Biochemistry 20, 6384-6391.
14. Cooperman, B. S., Panackal, A., Springs, B., and Hamm, D. J. (1981) Divalent metal ion, inorganic phosphate, and inorganic phosphate analogue binding to yeast inorganic pyrophosphatase, Biochemistry 20, 6051-6060.
15. Zyryanov, A. B., Shestakov, A. S., Lahti, R., and Baykov, A. A. (2002) Mechanism by which metal cofactors control substrate specificity in pyrophosphatase, Biochem. J. 367, 901-906.
16. Heikinheimo, P., Pohjanjoki, P., Helminen, A., Tasanen, M., Cooperman, B. S., Goldman, A., Baykov, A., and Lahti, R. (1996) A site-directed mutagenesis study of Saccharomyces cerevisiae pyrophosphatase: Functional conservation of the active site of soluble inorganic pyrophosphatases, Eur. J. Biochem. 239, 138-143.
17. Pohjanjoki, P., Lahti, R., Goldman, A., and Cooperman, B. (1998) Evolutionary Conservation of Enzymatic Catalysis: Quantitative Comparison of the Effects of Mutation of Aligned Residues in Saccharomyces cerevisiae and Escherichia coli Inorganic Pyrophosphatase on Enzymatic Activity, Biochemistry 37, 1754-1761.
18. Tuominen, V., Heikinheimo, P., Kajander, T., Torkkel, T., Hyytiä, T. K. J., Lahti, R., Cooperman, B. S., and Goldman, A. (1998) The R78K and D117E Active-site Variants of Saccharomyces cerevisiae Soluble Inorganic Pyrophosphatase: Structural Studies and Mechanistic Implications, J. Mol. Biol. 284, 1565-1580.
19. Otwinowski, Z., and Minor, W. (1997) Processing of X-Ray Diffraction Data Collected in Oscillation Mode, Methods Enzymol. 276, 307-326.
20. Collaborative Computational Project Number 4 (1994) The CCP4 suite: Programs for Protein Crystallography, Acta Crystallogr. D50, 760-763.
21. Vagin, A., and Teplyakov, A. (1997) MOLREP: An automated program for molecular replacement, J. Appl. Crystallogr. 30, 1022-1025.
22. Perrakis, A., Morris, R., and Lamzin, V. S. (1999) Automated protein model building combined with iterative structure refinement, Nat. Struct. Biol. 6, 458-463.
23. Jones, T. A., Zou, J.-Y., Cowan, S. W., and Kjeldgaard, M. (1991) Improved Methods for Building Protein Models in Electron Density Maps and the Location of Errors in these Models, Acta Crystallogr. A47, 110-119.
24. 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.
25. Emsley, P., and Cowtan, K. (2004) Coot: Model-building tools for molecular graphics, Acta Crystallogr. D60, 2126-2132.
26. Kleywegt, G. J., and Jones, T. A. (1996) Efficient Rebuilding of Protein Structures, Acta Crystallogr. D52, 829-832.
27. Harutyunyan, E. H., Kuranova, I. P., Vainshtein, B. K., Höhne, W. E., Lamzin, V. S., Dauter, Z., Teplyakov, A. V., and Wilson, K. S. (1996) X-ray structure of yeast inorganic pyrophosphatase complexed with manganese and phosphate, Eur. J. Biochem. 239, 220-228.
28. Cannon, W. R., Singleton, S. F., and Benkovic, S. J. (1996) A perspective on biological catalysis, Nat. Struct. Biol. 3, 821-833.
29. Admiraal, S. J., and Herschlag, D. (1995) Mapping the transition state for ATP hydrolysis: Implications for enzymatic catalysis, Chem. Biol. 2, 729-739.
30. Fabrichniy, I. P., Kasho, V. N., Hyytia, T., Salminen, T., Halonen, P., Dudarenkov, V. Y., Heikinheimo, P., Chernyak, V. Y., Goldman, A., Lahti, R., Cooperman, B. S., and Baykov, A. A. (1997) Structural and functional consequences of substitutions at the tyrosine 55 lysine 104 hydrogen bond in Escherichia coli inorganic pyrophosphatase, Biochemistry 36, 7746-7753.