Structural basis for thermostability and identification of potential active site residues for adenylate kinases from the archaeal genus Methanococcus

Proteins: Structure, Function and Genetics

Volumn 28, Issue 1, 1997, Pages 117-130

  Haney, P ^a   Konisky, J ^a   Koretke, K K ^a   Luthey Schulten, Z ^a   Wolynes, P G ^a  

^a UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

Author keywords

ATP binding; energy function alignment; hydrophobicity; salt bridges; structure prediction; threading

Indexed keywords

ADENYLATE KINASE; BRANCHED CHAIN AMINO ACID; PROLINE; URIDINE PHOSPHATE;

ARTICLE; ENZYME ACTIVE SITE; ENZYME ACTIVITY; ENZYME STABILITY; HYDROPHOBICITY; METHANOBACTERIUM; NONHUMAN; PRIORITY JOURNAL; PROTEIN STRUCTURE; PROTEIN TERTIARY STRUCTURE; SEQUENCE HOMOLOGY; SURFACE CHARGE; THERMOSTABILITY;

EID: 0030970741     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(199705)28:1<117::AID-PROT12>3.0.CO;2-M     Document Type: Article

References (55)

1. Adams, M. Enzymes from microorganisms in extreme environments. Chemical & Engineering News, 18:32-42, 1995.
2. Adams, M., Perler, F., Kelly, R. Extremozymes: Expanding the limits of biocatalysis. Biotechnology 13:662-668, 1995.
3. Britton, K., Baker, P., Borges, K., Engel, P., Pasquo, A., Rice, D., Robb, F., Scandurra, R., Stillman, T., Yip, K. Insights into thermal stability from a comparison of glutamate dehydrogenases from Pyrococcus furiosus and Thermococcus litoralis. FEBS 229:688-693, 1995.
4. Zuber, H. Temperature adaptation of lactate dehydrogenase: Structural, functional and genetic aspects. Biophys. Chem. 29:171-179, 1988.
5. Argos, P. Engineering protein thermal stability: Sequence statistics point to residue substitutions in alpha helices. J. Mol. Biol. 206:397-406, 1989.
6. Kelly, C., Nishiyama, M., Ohnishi, Y., Beppu, T., Birktoft, J. Determinants of protein thermostability observed in the 1.9a crystal structure of malate dehydrogenase from the thermophilic bacterium Thermus flavus. Biochemistry 32: 3913-3922, 1993.
7. Walker, J., Wonacott, A., Harris, J.I. Heat stability of a tetrameric enzyme, d-glyceraldehyde-3-phosphate dehydrogenase. Eur. J. Biochem. 108:581-586, 1980.
8. Perutz, M., Raidt, H. Stereochemical basis of heat stability in bacterial ferrodoxins and in haemoglobin 42. Nature 255:256-259, 1975.
9. Serrano, L., Sancho, J., Hirshberg, M., Fersht, A.R. α-Helix stability in proteins. J. Mol. Biol. 227:544-559, 1992.
10. Nicholson, H., Becktel, W.J., Matthews, B.W. Enhanced protein thermostability from designed mutations that interact with α-helix dipoles. Nature 336:651-655, 1988.
11. Matthews, B., Nicholson, H., Becktel, W. Enhanced protein thermostability from site-directed mutations that decrease the entropy of unfolding. Proc. Natl. Acad. Sci. USA 84: 6663-6667, 1987.
12. Jaenicke, R. Protein stability and molecular adaptation to extreme conditions. Eur. J. Biochem. 202:715-728, 1991.
13. Jaenicke, R., Zavodszky, P. Proteins under extreme physical conditions. FEBS 268:344-349, 1990.
14. Matthews, B. Structural and genetic analysis of protein stability. Annu. Rev. Biochem. 62:139-160, 1993.
15. Schlapfer, B., Zuber, H. Cloning and sequencing of the genes encoding glyceraldehyde-3-phosphate dehydrogenase, phosphoglycerate kinase and triosephosphate isomerase (gap operon) from mesophilic Bacillus megaterium: Comparison with corresponding sequences from thermophilic Bacillus stearothermophilus, Gene 122:53-62, 1992.
16. Bohm, G., Jaenicke, R. Relevance of sequence statistics for the properties of extremophilic proteins. Int. J. Peptide Prot. Res. 43:97-106, 1994.
17. Rusnak, P., Haney, P., Konisky, J. The adenylate kinases from a mesophilic and three thermophilic methanogenic members of the archaea. J. Bacteriol. 177:2977-2981, 1994.
18. Ferber, D.M., Haney, P.J., Berk, H., Lynn, D., Konisky, J. The adenylate kinase genes of Methanococcus jannaschii and Mehtanococcus igneus: Structural and phylogenetic analysis defines a new family of adenylate kinases. Genes (in press).
19. Schulz, G.E. Structural and functional relationships in the adenylate kinase family. Cold Spring Harbor Symp. Quant. Biol. LII:429-439, 1987.
20. Gerstein, M., Schulz, G.E., Chothia, C. Domain closure in adenylate kinase. Joints on either side of two helices close like neighboring fingers. J. Mol. Biol. 229:494-501, 1993.
21. Berry, M., Meador, B., Bilderback, T., Liang, P., Glaser, M., Phillips, G. The closed conformation of a highly flexible protein: The structure of E. coli adenylate kinase with bound amp and amppnp. Proteins 19:183-198, 1994.
22. Mullerdieckmann, H.J., Schulz, G.E. The structure of uridylate kinase with its substrates, showing the transition state geometry. J. Mol. Biol. 236:361-367, 1994.
23. Mullerdieckmann, H.J., Schulz, G.E. Substrate specificity and assembly of time catalytic center derived from two structures of ligated uridylate kinase. J. Mol. Biol. 246:522-530, 1995.
24. Scheffzek, K., Kliche, W., Wiesmuller, L., Reinstein, J. Crystal structure of the complex of ump/cmp kinase from Dictyostelium discoideum and the bisubstrate inhibitor pl-(5′-adenosyl) p5-(5′-uridyl) pentaphosphate (up5a) and mg2+ at 2.2 angstroms: Implications for water-mediated specificity. Biochemistry 35:9716-9727, 1996.
25. Kath, T., Schmid, R., Schafer, G. Identification, cloning, and expression of the gene for the adenylate kinase from the thermoacidophilic archaebacterium Sulfolobus acidocaldarius. Arch. Biochem. Biophys. 307:405-410, 1993.
26. Bonisch, H., Backmann, J., Kath, T., Naumann, D., Schafer, G. Adenylate kinase from Sulfolobus acidocaldarius: Expression in Escherchia coli and characterization by Fourier transform infrared spectroscopy. Arch. Biochem. Biophys. 333:75-84, 1996.
27. Koretke, K.K., Luthey-Schulten, Z., Wolynes, P.G. Self-consistently optimized statistical mechanical energy functions for sequence structure alignment. Prot. Sci. 6:1043-1059, 1990.
28. Goldstein, R., Luthey-Schulten, Z., Wolynes, P. Protein tertiary structure recognition using optimized hamiltonians with local interactions. Proc. Natl. Acad. Sci. USA, 89:9029-9033, 1992.
29. Goldstein, R., Luthey-Schulten, Z., Wolynes, P. A bayesian approach to sequence structure alignment algorithms for protein structure recognition. In "Proceedings of the 27th Hawaii International Conference on System Sciences." Los Alamitoos, CA: IEEE Computer Society Press, 1994:306-315.
30. Abola, E., Bernstein, F., Bryant, S., Koetzle, T., Weng, J. Protein data bank. In "Crystallographic Databases: Information Content, Software Systems, Scientific Applications." Allen, F.H., Bergerhoff, G., Sievers, R. (eds.). Bonn: Data Commissions of the International Union of Crystallography, 1987:107-132.
31. Bernstein, F., Koetzle, T., Williams, G., Meyer Jr., E., Brice, M., Rodgers, J., Kennard, O., Shimanouchi, T., Tasumi, M. The protein data bank: A computer-based archivai file for macromolecular structures. J. Mol. Biol. 112:535-542, 1977.
32. Genetics Computer Group, Madison, Wisconsin. "Program Manual for the Wisconsin Package," 8th edit. 1994.
33. Berry, M.B., Meador, B., Bilderback, T., Liang, P., Glaser, M., Phillips, G.N. The closed conformation of a highly flexible protein: The structure of E. coli adenylate kinase with bound amp and amppnp. Proteins 19:183-198, 1994.
34. Sali, A., Potterton, L., Yuan, F., van Vlijmen, H., Karplus, M. Evaluation of comparative protein modeling by modeller. Protein 23:318-326, 1995.
35. Berghuis, A.M., Guillemette, J.G., Smith, M., Brayer, G.D. Mutation of tyrosine-67 in cytochrome c significantly alters the local heme environment. J. Mol. Biol. 235:1328-1341, 1994.
36. Bunger, A.T.X-PLOR. New Haven, CT: The Howard Hughes Medical Institute and Department of Molecular Biophysics and Biochemistry, Yale University, 1988.
37. Brooks, B.R., Bruccoleri, R.E., Olafson, B.D., States, D.J., Swaminathan, S., Karplus, M. Charmm: A program for macromolecular energy, minimization and dynamics calculations. J. Comput. Chem. 4:187, 1983.
38. Tanford, C. Contribution of hydrophobic interactions to the stability of the globular conformation of proteins. J. Am. Chem. Soc. 84:4240-4247, 1964.
39. Bigelow, C. On the average hydrophobicity of proteins and the relation between it and protein structure. J. Theoret. Biol. 18:187-211, 1967.
40. Ikai, A. Thermostability and aliphatic index of globular proteins. J. Biochem. 88:1895-1898, 1980.
41. Karplus, P., Schulz, G, Prediction of chain flexibility in proteins: A tool for the selection of peptide antigens. Naturwissenschaften 72:212-213, 1985.
42. Sharp, K., Nicholls, A., Friedman, R., Honig, B. Extracting hydrophobic free energies from experimental data: Relationship to protein folding and theoretical models. Biochemistry 30:9686-9697, 1991.
43. Ahern, T., Klibanov, A. The mechanism of irreversible enzyme inactivation at 100°C. Science 228:1280-1284, 1985.
44. Mrabet, N.T., Den Broeck, A.V., Den Brande, I.V., Stanssens, P., Laroche, Y., Van Tilbeurgh, H., Rey, F., Quax, J.J., Laster, I., Maeyer, M.D., Wodak, S.J. Arginine residues as stabilizing elements in proteins. Biochemistry 31:2239-2253, 1992.
45. Reinstein, J., Sehlichting, I., Wittinghofer, A. Structurally and catalytically important residues in the phosphate binding loop of adenylate kinase of Escherichia coli. Biochemistry 29:7451-7459, 1990.
46. Tain, G., Yan, H., Jiang, R. Kishi, F., Nakazama, A., Tsai, M.-D. Mechanism of adenylate kinase: Are the essential lysines essential? Biochemistry 29:4296-4304, 1990.
47. Rose, T., Glaser, P., Surewicz, W., Mantsch, H., Reinstein, J., Blay, K.L., Gilles, A., Barzu, O. Structural and functional consequences of amino acid substitutions in the second conserved loop of Escherichia coli adenylate kinase. J. Biol. Chem. 266:23654-23659, 1991.
48. Dahnke, T., Shi, Z., Yan, H., Jiang, R., Tsai, M.-D. Mechanism of adenylate kinase structural and functional roles of the conserved arginine-97 and arginine-132. Biochemistry 31:6318-6328, 1992.
49. Monnot, M., Gillies, A., Girons, I., Michelson, S., Barzu, O., Fermandjian, S. Circular dichroism investigation of Escherichia coli adenylate kinase. J. Biol. Chem. 262:2502-2506, 1987.
50. Dreusicke, D., Schulz, G. The glycine-rich loop of adenylate kinase forms a giant anion hole. FEBS 208:301-304, 1986.
51. Muller, C.W., Schulz, G.E. Structure of the complex between adenylate kinase from Escherichia coli and the inhibitor ap5a refined at 1.9Å resolution. J. Mol. Biol. 224:159-177, 1992.
52. Dreusicke, D., Karplus, P.A., Schulz, G.E. Refined structure of porcine cytosolic adenylate kinase at 2.1 Å resolution. J. Mol. Biol. 199:359-371, 1988.
53. Anderson, D., Becktel, W., Dahlquist, F. pH-induced denaturation of proteins: A single salt bridge contributes 3-5 kcal/mol to the free energy of folding of t4 lysozyme. Biochemistry 29:2403-2408, 1990.
54. Dao-pin, S., Sauer, U., Nicholson, H., Matthews, B. Contributions of engineered surface salt bridges to the stability of t4 lysozyme determined by directed mutagenesis. Biochemistry 30:7142-7153, 1991.
55. Humphrey, W.F., Dalke, A., Schulten, K. VMD: Visual molecular dynamics. J. Mol. Graphics 14:33-38, 1996.