Structural features of halophilicity derived from the crystal structure of dihydrofolate reductase from the Dead Sea halophilic archaeon, Haloferax volcanii

Structure

Volumn 6, Issue 1, 1998, Pages 75-88

  Pieper, Ursula ^a   Kapadia, Geeta ^a   Mevarech, Moshe ^b   Herzberg, Osnat ^a  

^a UNIVERSITY OF MARYLAND BIOTECHNOLOGY INSTITUTE   (United States)

^b TEL AVIV UNIVERSITY   (Israel)

Author keywords

Dihydrofolate reductase; Haloferax volcanii; Halophilic archaea; X ray crystallography

Indexed keywords

ARCHAEA; BACTERIA (MICROORGANISMS); HALOFERAX VOLCANII;

EID: 0032518248     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0969-2126(98)00009-4     Document Type: Article

References (50)

1. Christian, J.H.B. & Waltho, J.A. (1962). Solute concentrations within celles of halophilic and non-halophilic bacteria. Biochem. Biophys. Acta 65, 506-508.
2. Lanyi, J.K. (1974). Salt-dependent properties of proteins from extremely halophilic bacteria. Bacteriol. Rev. 38, 272-290.
3. Jaenicke, R. (1981). Enzymes under extremes of physical conditions. Annu. Rev. Biophys. Bioeng. 10, 1-67.
4. Eisenberg, H. & Wachtel, E.J. (1987). Structural studies of halophilic proteins, ribosomes, and organelles of bacteria adapted to extreme salt concentrations. Annu. Rev. Biophys. Biophys. Chem. 16, 69-92.
5. Jaenicke, R. (1991). Protein stability and molecular adaptation to extreme conditions. Eur. J. Biochem. 202, 715-728.
6. Eisenberg, H., Mevarech, M. & Zacchai, G. (1992). Biochemical, structural, and molecular genetic aspects of halophilism. Adv. Protein Chem. 43, 1-62.
7. Dym, O., Mevarech, M. & Sussman, J.L. (1995). Structural features that stabilize halophilic malate dehydrogenase from an archaebacterium. Science 167, 1344-1346.
8. Frolow, F., Harel, M., Sussman, J.L., Mevarech, M. & Shoham, M. (1996). Insights into protein adaptation to a saturated salt environment from the crystal structure of a halophilic 2Fe-2S ferredoxin. Nat. Struct. Biol. 3, 452-458.
9. Böhm, G. & Jaenicke, R. (1994). A structure-based model for the halophilic adaptation of dihydrofolate reductase from Halobacterium volcanii. Protein Eng. 7, 213-220.
10. Böhm, G. & Jaenicke, R. (1994). Relevance of sequence statistics for the properties of extremophilic proteins. Int. J. Peptide Protein Res. 43, 97-106.
11. Bolin, J.T., Filman, D.J., Matthews, D.A., Hamlin, R.C. & Kraut, J. (1982). Crystal structures of Escherichia coli and Lactobacillus casei dihydrofolate reductase refined at 1.7 Å resolution. I. General features and binding of methotrexate. J. Biol. Chem. 257, 13650-13662.
12. Filman, D.J., Bolin, J.T., Matthews, D.A. & Kraut, J. (1982). Crystal structures of Escherichia coli and Lactobacillus casei dihydrofolate reductase refined at 1.7 Å resolution. II. Environment of bound NADPH and implications for catalysis. J. Biol. Chem. 257, 13663-13672.
13. Matthews, D.A., Alden, R.A., Freer, S.T., Zuong, N.-h. & Kraut, J. (1979). Dihydrofolate reductase from Lactobacillus casei, stereochemistry of NADPH binding. J. Biol. Chem. 254, 4144-4151.
14. Champness, J.N., Achari, A., Ballantine, S.P., Bryant, P.K., Delves, C.J. & Stammers, D.K. (1994). The structure of Pneumocystis carinii dihydrofolate reductase to 1.9 Å resolution. Structure 2, 915-924.
15. Matthews, D.A., et al., & Kraut, J. (1985). Refined crystal structures of Escherichia coli and chicken liver dihydrofolate reductase containing bound trimethoprim. J .Biol. Chem. 260, 381-391.
16. Stammers, D.K., et al., & North, A.C. (1987). The structure of mouse L1210 dihydrofolate reductase-drug complexes and the construction of a model of human enzyme. FEBS Lett. 218, 178-184.
17. Oefner, C., D'Arcy, A. & Winkler, F.K. (1988). Crystal structure of human dihydrofolate reductase complexed with folate. Eur. J. Biochem. 174, 377-385.
18. Pearson, W.R. & Lipman, D.J. (1988). Improved tools for biological sequence analysis. Proc. Natl. Acad. Sci. USA 85, 2444-2448.
19. Sturrock, S.S. & Collins, J.F. (1993). Mpsrch Version 1.3. Biocomputing Research Unit, University of Edinburgh, UK.
20. Abola, E.E., Bernstein, F.C., Bryant, S.H., Koetzle, T.F. & Weng, J. (1987). Protein Data Bank, in Crystallographic Databases - Information Content, Software Systems, Scientific Applications. (Allien, F.H., Bergerhoff, G. & Sievers, R., eds.), pp. 107-132, Data Commission of the International Union of Crystallography, Cambridge, UK.
21. Fidelis, K. (1996). Second Meeting on the critical assessment of techniques for protein structure prediction, Target No. T0001 CM1 20_1. http://PredictionCenter.llnl.gov.
22. Leahy, D.J., Axel, R. & Hendrickson, W.A. (1992). Crystal structure of a soluble form of the human T cell coreceptor CDS at 2.6 Å resolution. Cell 68, 1145-1162.
23. Navaza, J. (1994). AMoRe: an automated package for molecular replacement. Acta Cryst. A 50, 157-163.
24. Engh, R.A. & Huber, R. (1991). Accurate bond and angle parameters for X-ray protein structure refinement. Acta Cryst. A 47, 392-400.
25. Ramakrishnan, C. & Ramachandran, G.N. (1965). Stereochemical criteria for polypeptide and protein chain conformation. Biophys. J. 5, 909-933.
26. Sawaya, M.R. & Kraut, J. (1997). Loop and subdomain movements in the mechanism of Escherichia coli dihydrofolate reductase: crystallographic evidence. Biochem. 36, 586-603.
27. + ternary complex. Substrate binding and a model for the transition state. Biochem. 29, 3263-3277.
28. Blecher, O., Goldman, S. & Mevarech, M. (1993). High expression in Escherichia coli of the gene coding for dihydrofolate reductase of the extremely halophilic archaebacterium Haloferax volcanii. Reconstitution of the active enzyme and mutation studies. Eur. J. Biochem. 216, 199-203.
29. Kuntz, I.D. (1971). Hydration of macromolecules. IV. Polypeptide conformation in frozen solutions. J. Am. Chem. Soc. 93, 514-516.
30. Thanki, N., Thornton, J.M. & Goodfellow, J.M. (1988). Distributions of water around amino acid residues in proteins. J. Mol. Biol. 202, 637-657.
31. Cendrin, F., Chroboczek, J., Zaccai, G., Eisenberg, H. & Mevarech, M. (1993). Cloning, sequencing, and expression in Escherichia coli of the gene coding for malate dehydrogenase of the extremely halophilic archaebacterium Haloarcula marismortui. Biochemistry 32, 4308-4313.
32. Bajorath, J., Kitson, D., Kraut, J. & Hagler, A. (1991). The electrostatic potential of Escherichia coli dihydrofolate reductase. Proteins 11, 1-12.
33. Nicholls, A., Sharp, K.A. & Honig, B. (1991). Protein folding and association: insights from the interfacial and thermodynamical properties of hydrocarbons. Proteins 11, 281-296.
34. Werber, M.M. & Mevarech, M. (1978). Purification and characterization of a highly acidic 2Fe-2S ferredoxin from Halobacterium of the Dead Sea. Arch. Biochem. Biophys. 187, 447-456.
35. Zaccai, G., Cendrin, F., Haik, Y., Borochov, N. & Eisenberg, H. (1989). Stabilization of halophilic malate dehydrogenase. J. Mol. Biol. 208, 491-500.
36. Avbelj, F., Moult, J., Kitson, D.H., James, M.N. & Hagler, A.T. (1990). Molecular dynamics study of the structure and dynamics of a protein molecule in a crystalline ionic environment, Streptomyces griseus protease A. Biochem. 29, 8658-8676.
37. Herzberg, O. & James, M.N.G. (1988). Refined crystal structure of troponin C from turkey skeletal muscle at 2.0 Å resolution. J. Mol. Biol. 203, 761-779.
38. Rosenshine, I. & Mevarech, M. (1989). Isolation and partial characterization of plasmids found in three Halobacterium volcanii isolates. Can. J. Microbiol. 35, 92-95.
39. Zusman, T., Rosenshine, I., Böhm, G., Jaenicke, R., Leskiw, B. & Mevarech, M. (1989). Dihydrofolate reductase of the extremely halophilic archaebacterium Halobacterium volcanii. The enzyme and its coding gene. J. Biol. Chem. 264, 18878-18883.
40. Low, B.W. & Richards, F.M. (1952). The use of the gradient tube for the determination of crystal densities. J. Am. Chem. Soc. 74, 1660-1666.
41. Howard, A.J., Gilliland, G.L., Finzel, B.C., Poulos, T., Ohlendorf, D.O. & Salemme, F.R. (1987). The use of an imaging proportional counter in macromolecular crystallography. J. Appl. Cryst. 20, 383-387.
42. Brünger, A.T. (1992). X-PLOR Version 3.1: a System for X-ray Crystallography and NMR. Yale University Press, New Haven, CT.
43. Brünger, A.T. (1992). Free R-value: novel statistical quantity for assessing the accuracy of crystal structures. Nature 355, 472-475.
44. Roussel, A. & Cambillau, C. (1989). TURBO_FRODO. In Silicon Graphics Geometry Partners Directory, pp. 77-78, Silicon Graphics, Mountain View, CA.
45. Jones, T.A. (1992). a, yaap, asap, @#*? a set of averaging programs. In Molecular Replacement, Proceedings of the CCP4 Study Weekend. (Dodson, E.J., Glover, S. & Wolf, W., eds), pp. 92-105, SERC Daresbury Laboratory, Warrington, UK.
46. Kleywegt, G.J. & Jones, T.A. (1994). Halloween masks and bones. In From first Map to Final Model, Proceedings of the CCP4 Study Weekend. (Bailey, S., Hubbard, R. & Waller, D., eds), pp. 59-66, SERC Daresbury Laboratory, Warrington, UK.
47. Bacon, D.J. & Anderson, W.F. (1988). A fast algorithm for rendering space-filling molecule pictures. J. Mol. Graph. 6, 219-220
48. Merritt, E.A. & Murphy, M.E.P. (1994). Raster3D version 2.0. A program for photorealistic molecular graphics. Acta Cryst. D 50, 869-873.
49. Kabsch, W. & Sander, C. (1983). Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22, 2577-2637.
50. Kraulis, P.J. (1991). MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Cryst 24, 946-950.