The active site cysteine of arginine kinase: Structural and functional analysis of partially active mutants

Biochemistry

Volumn 43, Issue 27, 2004, Pages 8680-8689

  Gattis, James L ^a   Ruben, Eliza ^a   Fenley, Marcia O ^a   Ellington, W Ross ^a   Chapman, Michael S ^a  

^a FLORIDA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING ENERGY; CATALYSIS; CHARGE TRANSFER; CONFORMATIONS; CRYSTALLOGRAPHY; ENZYME KINETICS;

BINDING CONSTANTS; BINDING SYNERGY; HOMOLOGY MODELS;

BIOCHEMISTRY;

ADENOSINE DIPHOSPHATE; ADENOSINE TRIPHOSPHATE; ALANINE; AMINO ACID; ARGININE; ARGININE KINASE; ASPARAGINE; ASPARTIC ACID; CHLORIDE; DNA; MUTANT PROTEIN; SERINE;

ARTICLE; CATALYSIS; CRAB; CRYSTALLIZATION; ENZYME ACTIVE SITE; ENZYME KINETICS; ENZYME STRUCTURE; ENZYME SUBSTRATE; MUTAGENESIS; NONHUMAN; PRIORITY JOURNAL; X RAY CRYSTALLOGRAPHY;

ARGININE KINASE; BINDING SITES; CHLORIDES; CRYSTALLOGRAPHY, X-RAY; CYSTEINE; KINETICS; MODELS, MOLECULAR; MUTATION; PROTEIN STRUCTURE, TERTIARY;

DECAPODA (CRUSTACEA); MEROSTOMATA;

EID: 3042856467     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi049793i     Document Type: Article

References (46)

1. Kenyon, G. L., and Reed, G. H. (1983) Creatine Kinase: Structure-activity Relationships, Adv. Enzymol. 54, 367-426.
2. Ellington, W. R. (2001) Evolution and Physiological Roles of Phosphagen Systems, Annu. Rev. Physiol. 63, 289-325.
3. Blethen, S. L. (1972) Kinetic Properties of the Arginine Kinase Isoenzymes of Limulus polyphemus, Arch. Biochem. Biophys. 149, 244-251.
4. Hansen, D. E., and Knowles, J. R. (1981) The Stereochemical Course of the Reaction Catalyzed by Creatine Kinase, J. Biol. Chem. 256, 5967-5969.
5. Morrison, J. F. (1973) in The Enzymes (Boyer, P. D., Ed.) pp 457-486, Academic Press, New York.
6. Virden, R., and Watts, D. C. (1966) The Role of Thiol Groups in the Structure and Mechanism of Action of Arginine Kinase, Biochem. J. 99, 162-172.
7. Zhou, G., Somasundaram, T., Blanc, E., Parthasarathy, G., Ellington, W. R., and Chapman, M. S. (1998) Transition state structure of arginine kinase: Implications for catalysis of bimolecular reactions, Proc. Natl. Acad. Sci. U.S.A. 95, 8449-8454.
8. -- Creatine Transition-State Analogue Complex, Biochemistry 41, 13861-13867.
9. Watts, D. C., and Rabin, B. R. (1962) A Study of the "Reactive" Sulphydryl Groups of Adenosine 5′-triphosphate-Creatine Phosphotransferase, Biochem. J. 85, 507-516.
10. Maggio, E. T., and Kenyon, G. L. (1977) Properties of a CH3-blocked creatine kinase with altered catalytic activity. Kinetic consequences of the presence of the blocking group, J. Biol. Chem. 252, 1202-1207.
11. Wu, H., Yao, Q.-Z., and Tsou, C.-L. (1989) Creatine kinase is modified by 2-chloromercuri-4-nitrophenol at the active site thiols with complete inactivation, Biochim. Biophys. Acta 997, 78-82.
12. Homemann, T., Rutishauser, D., and Wallimann, T. (2000) Why is creatine kinase a dimer? Evidence for cooperativity between the two subunits, Biochim. Biophys. Acta 1480, 365-373.
13. Furter, R., Furter-Graves, E. M., and Wallimann, T. (1993) Creatine Kinase: The Reactive Cysteine Is Required for Synergism But Is Nonessential for Catalysis, Biochemistry 32, 7022-7029.
14. Wang, P. F., McLeish, M. J., Kneen, M. M., Lee, G., and Kenyon, G. L. (2001) An unusually low pK(a) for Cys282 in the active site of human muscle creatine kinase, Biochemistry 40, 11698-11705.
15. Lin, L., Perrymann, M. B., Friedman, D., Roberts, R., and Ma, T. S. (1994) Determination of the Catalytic Site of Creatine Kinase by Site-directed Mutagenesis, Biochim. Biophys. Acta 1206, 97-104.
16. Yousef, M. S., Clark, S. A., Pruett, P. K., Somasundaram, T., Ellington, W. R., and Chapman, M. S. (2003) Induced fit in guanidino kinases-comparison of substrate-free and transition state analogue structures of arginine kinase, Protein Sci. 12, 103-111.
17. Fritz-Wolf, K., Schnyder, T., Wallimann, T., and Kabsch, W. (1996) Structure of Mitochondrial Creatine Kinase, Nature 381, 341-345.
18. Yousef, M. S., Fabiola, F., Gattis, J. L., Somasundaram, T., and Chapman, M. S. (2002) Refinement of the arginine kinase transition-state analogue complex at 1.2 A resolution: mechanistic insights, Acta Crystallogr., Sect. D: Biol. Crystallogr. 58, 2009-2017.
19. Zhou, G., Parthasarathy, G., Somasundaram, T., Ables, A., Roy, L., Strong, S. J., Ellington, W. R., and Chapman, M. S. (1997) Expression, Purification from Inclusion Bodies, and Crystal Characterization of Transition State Analog Complex of Arginine Kinase: a Model for Studying Phosphagen Kinases, Protein Sci. 6, 444-449.
20. Pruett, P. S., Azzi, A., Clark, S. A., Yousef, M., Gattis, J. L., Somasundaram, T., Ellington, W. R., and Chapman, M. S. (2003) The putative catalytic bases have, at most, an accessory role in the mechanism of arginine kinase, J. Biol. Chem. 29, 26952-26957.
21. Segel, I. H. (1975) in Enzyme Kinetics-Behaviour and Analysis of Rapid Equilibrium and Steady-State Enzyme Systems, Wiley, New York.
22. Otwinowski, Z., and Minor, W. (2001) in International Tables for Crystallography. Crystallography of Biological Molecules (Rossmann, M. G., and Arnold, E., Eds.) pp 226-235, International Union of Crystallography, Dortrecht.
23. Brünger, A. T., Adams, P. D., Clore, G. M., Gros, P., Gross-Kunstleve, R. W., Jiang, J.-S., Kurzewski, J., Nilges, M., Pannu, N. S., Read, R. J., Rice, L. M., Simonson, T., and Warren, G. L. (1998) Crystallography and NMR system: A new software system for macromolecular structure determination, Acta Crystallogr. D54, 905-921.
24. Kleywegt, G. J., and Jones, A. T. (1996) Efficient Rebuilding of Protein Structures, Acta Crystallogr. D52, 829-832.
25. Rocchia, W., Alexov, E., and Honig, B. (2001) Extending the Applicability of the Nonlinear Poisson-Boltzmann Equation: Multiple Dielectric Constants and Multivalent Ions, J. Phys. Chem. B 105, 6507-6514.
26. Bashford, D. (1997) in Lecture Notes in Computer Science: Scientific Computing in Object-Oriented Parallel Environments (Ishikawa, Y., Oldehoeft, R. R., Reynders, J. V. W., and Tholburn, M., Eds.) pp 233-240, Springer, Berlin.
27. Beroza, P., and Case, D. A. (1998) Calculations of proton-binding thermodynamics in proteins, Methods Enzymol. 295, 170-189.
28. Bayly, C. I., Cieplak, P., Cornell, W., and Kollman, P. A. (1993) A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP model, J. Phys. Chem. 97, 10269-10280.
29. Case, D. A., Pearlman, D. A., Caldwell, J. W., Cheatham, T. E., III, Ross, W. S., Simmerling, C. L., Darden, T. A., Merz, K. M., Stanton, R. V., Vincent, J. J., Crowley, M., Ferguson, D. M., Radmer, R. J., Seibel, G., Singh, U. C., Weiner, P. K., Caldwell, J., and Kollman, P. A. (1999) Amber 5.0, University of California, San Francisco.
30. Yousef, M. S., Fabiola, F., Gattis, J., Somasundaram, T., and Chapman, M. S. (2002) Refinement of Arginine Kinase Transition State Analogue Complex at 1.2 Å resolution; mechanistic insights, Acta Crystallogr., Sect. D: Biol. Crystallogr. 58, 2009-2017.
31. Guex, N., and Peitsch, M. C. (1997) SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling, Electrophoresis 18, 2714-2723.
32. Segel, I. H. (1975) Enzyme Kinetics-Behaviour and Analysis of Rapid Equilibrium and Steady-State Enzyme Systems, Wiley Classics Edition, 1993 ed., Wiley, New York.
33. Jeffrey, G. A., and Saenger, W. (1991) Hydrogen Bonding in Biological Structures, Springer-Verlag, Berlin.
34. Steiner, T., Schreurs, A. M. M., Kanters, J. A., and Kroons, J. (1998) Water molecules hydrogen bonding to aromatic acceptors of amino acids: the structure of Tyr-Tyr-Phe dihydrate and a crystallographic database study on peptides, Acta Crystallogr. 54, 25-31.
35. Ridder, I. S., Rozeboom, H. J., and Dijkstra, B. W. (1999) Haloalkane dehalogenase from Xanthobacter autotrophicus GJ10 refined at 1.15 Å resolution, Acta Crystallogr. D55, 1273-1290.
36. Backstrom, S., Wolf-Watz, M., Grundstrom, C., Hard, T., Grundstrom, T., and Sauer, U. H. (2002) The RUNX1 Runt domain at 1.25 Å resolution: a structural switch and specifically bound chloride ions modulate DNA binding, J. Mol. Biol. 322, 259-272.
37. Zhou, G., Wang, J., Blanc, E., and Chapman, M. S. (1998) Determination of the Relative Precision of Atoms in a Macromolecular Structure, Acta Crystallogr. D54, 391-399.
38. Kuby, S. A., Noda, L., and Lardy, H. A. (1954) Adenosinetriphosphate- Creatine Transphosphorylase III. Kinetic Studies, J. Biol. Chem. 210, 65-82.
39. Watts, D. C. (1973) in The Enzymes (Boyer, P. D., Ed.) pp 383-455, Academic Press, New York.
40. Polgar, L., and Halasz, P. (1973) On the reactivity of the thiol group of thiolsubtilisin, Eur. J. Biochem. 39, 421-429.
41. a of the essential Cys-12 residue of the ArsC arsenate reductase of plasmid R773, J. Biol. Chem. 271, 33256-33260.
42. Lo Bello, M., Parker, M. W., Desideri, A., Polticelli, F., Falconi, M., Del Boccio, G., Pennelli, A., Federici, G., and Ricci, G. (1993) Peculiar spectroscopic and kinetic properties of Cys-47 in human placental glutathione transferase. Evidence for an atypical thiolate ion pair near the active site, J. Biol. Chem. 268, 19033-19038.
43. as in proteins, Proteins 15, 252-265.
44. Cook, P. F., Kenyon, G. L., and Cleland, W. W. (1981) Use of pH Studies to Elucidate the Catalytic Mechanism of Rabbit Muscle Creatine Kinase, Biochemistry 20, 1204-1210.
45. Antosiewicz, J., McCammon, J. A., and Gilson, M. K. (1994) Prediction of pH-dependent properties of proteins, J. Mol. Biol. 238, 415-436.
46. Brünger, A. T. (1997) The Free R Value: A More Objective Statistic for Crystallography, Methods Enzymol. 277, 366-396.