X-ray-diffraction. Angstrom resolution. Crystal-structure. Protein-structure. Model refinement. Enzymes. Aspergillus. Stability. Binding. Family.; Biochemistry & Biophysics in Current Contents(R)/Life Sciences. 1999 week 04 Reprint available from: Haser R. Inst Biol & Chim Prot, UPR 412, CNRS, 7 Passage du Vercors, F-69367 Lyon 07, France.
Abstract :
[en] Background: Enzymes from psychrophilic (cold-adapted) microorganisms operate at temperatures close to 0 degrees C, where the activity of their mesophilic and thermophilic counterparts is drastically reduced. It has generally been assumed that thermophily is associated with rigid proteins, whereas psychrophilic enzymes have a tendency to be more flexible. Results: Insights into the cold adaptation of proteins are gained on the basis of a psychrophilic protein's molecular structure. To this' end, we have determined the structure of the recombinant form of a psychrophilic a-amylase from Alteromonas haloplanctis at 2.4 Angstrom resolution. We have compared this with the structure of the wild-type enzyme, recently solved at 2.0 Angstrom resolution, and with available structures of their mesophilic counterparts. These comparative studies have enabled us to identify possible determinants of cold adaptation. Conclusions: We propose that an increased resilience of the molecular surface and a less rigid protein core, with less interdomain interactions, are determining factors of the conformational flexibility that allows efficient enzyme catalysis in cold environments. [References: 57] 57
Disciplines :
Biochemistry, biophysics & molecular biology
Author, co-author :
Aghajari, N.
Feller, Georges ; Université de Liège - ULiège > Département des sciences de la vie > Labo de biochimie
Gerday, Charles ; Université de Liège - ULiège > Services généraux (Faculté des sciences) > Relations académiques et scientifiques (Sciences)
Haser, R.
Language :
English
Title :
Structures of the psychrophilic Alteromonas haloplanctis a-amylase give insights into cold adaptation at a molecular level
Publication date :
1998
Journal title :
Structure
ISSN :
0969-2126
eISSN :
1878-4186
Publisher :
Cell Press, Cambridge, United States - Massachusetts
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Bibliography
Aguilar, A. (1996). Extremophile research in the European Union: from fundamental aspects to industrial expectations. FEMS Microbiol. Rev. 18, 89-92.
Feller, G, et al., & Gerday, Ch. (1996). Enzymes from psychrophilic organisms. FEMS Microbiol. Rev. 18, 189-202.
Feller, G. & Gerday, Ch. (1997). Psychrophilic enzymes: molecular basis of cold adaptation. Cell. Mol. Life Sci. 53, 830-841.
Gerday, Ch, et al., & Feller, G. (1997). Psychrophilic enzymes: a thermodynamic challenge. Biochim. Biophys. Acta 1342, 119-131.
Pennisi, E. (1997). In industry, extremophiles begin to make their mark. Science 276, 705-706.
Russell, N.J. (1998). Molecular adaptations in psychrophilic bacteria: potential for biotechnological applications. Adv. Bioch. Eng. Biotech. 61, 1-21.
Nichols, D.S., Nichols, P.D. & McMeekin, T.A. (1995). Ecology and physiology of psychrophilic bacteria from Antarctic saline lakes and sea-ice. Science Prog. 78, 311-347.
Feller, G., Lonhienne, T., Deroanne, C., Libioulle, C., Van Beeumen, J. & Gerday, Ch. (1992). Purification, characterization, and nucleotide sequence of the thermolabile α-amylase from the Antarctic psychrotroph Alteromonas hatoplanctis A23. J. Biol. Chem. 267, 5217-5221.
Feller, G., Payan F., Theys, F., Qian, M., Haser R. & Gerday, Ch. (1994). Stability and structure analysis of α-amylase from the Antarctic psychrophile Alteromonas haloplanctis A23. Eur. J. Biochem. 222, 441-447.
Arpigny, J.L., Lamotte, J. & Gerday, Ch. (1997). Molecular adaptation to cold of an Antarctic bacterial lipase. J. Mol. Catal. B, 3, 29-35.
Narinx, E., Baise, E. & Gerday, Ch. (1997). Subtilisin from psychrophilic Antarctic bacteria: characterization and site-directed mutagenesis of residues possibly involved in the adaptation to cold. Protein Eng. 10, 101-109.
Aghajari, N., Feller, G., Gerday, Ch. & Haser, R. (1998). Crystal structures of the psychrophilic α-amylase from Alteromonas haloplanctis in its native form and complexed with an inhibitor. Protein Sci. 7, 564-572.
Alvarez, M, et al., & Maes, D. (1998). Triose-phosphate isomerase (TIM) of the psychrophilic bacterium Vibrio marinus. J. Biol. Chem. 273, 2199-2206.
Russell, R.J.M., Gerike, U., Danson, M.J., Hough, D.W. & Taylor, G.L. (1998). Structural adaptations of the cold-active citrate synthase from an Antarctic bacterium. Structure 6, 351-361.
Qian, M., Haser, R. & Payan, F. (1993). Structure and molecular model refinement of pig pancreatic α-amylase at 2.1 Å resolution. J. Mol. Biol. 231, 785-799.
Larson, S.B., Greenwood, A., Cascio, D., Day, J. & McPherson, A. (1994). Refined molecular structure of pig pancreatic α-amylase at 2.1 Å resolution. J. Mol. Biol. 235, 1560-1584.
Brayer, G.D., Luo, Y. & Withers, S.G. (1995). The structure of human pancreatic α-amylase at 1.8 Å resolution and comparison with related enzymes. Protein Sci. 4, 1730-1742.
Ramasubbu, N., Paloth, V., Luo, Y., Brayer, G.D. & Levine, M.J. (1996). Structure of human salivary α-amylase at 1.6 Å resolution: implications for its role in the oral cavity. Acta Cryst. D 52, 435-446.
Matsuura, Y., Kunusoki, M., Harada, W. & Kakudo, M. (1984). Structure and possible catalytic residues of Taka-amylase A. J. Biochemistry 35, 697-702.
Swift, H.J, et al., & Wilkinson, A.J. (1991). Structure and molecular model refinement of Aspergillus oryzae (TAKA) α-amylase: an application of the simulated-annealing method. Acta Cryst. B 47, 535-544.
Boel, E, et al., & Woldike, H.F. (1990). Calcium binding in α-amylases: an X-ray diffraction study at 2.1 Å resolution of two enzymes from Aspergillus. Biochemistry 29, 6244-6249.
Brady, R.L., Brzozowski, A.M., Derewenda, Z.S., Dodson, E.J. & Dodson, G.G. (1991). Solution of the structure of Aspergillus niger acid α-amylase by combined molecular replacement and isomorphous replacement methods. Acta Cryst. B 47, 527-535.
Kadziola, A., Abe, J.-I., Svensson, B. & Haser, R. (1994). Crystal and molecular structure of barley α-amylase. J. Mol. Biol. 239, 104-121.
Machius, M., Wiegand, G. & Huber, R. (1995). Crystal structure of calcium-depleted Bacillus licheniformis α-amylase at 2.2 Å resolution. J. Mol. Biol. 246, 545-559.
Machius, M., Declerck, N., Huber, R. & Wiegand, G. (1998). Activation of Bacillus licheniformis α-amylase through a disorder → order transition of the substrate-binding site mediated by a calcium-sodium-calcium metal triad. Structure 6, 281-289.
MacGregor, E.A. (1988). α-Amylase structure and activity. J. Protein Chem. 7, 399-415.
Jespersen, H.M., MacGregor, E.A., Henrissat, B., Sierks, M.R. & Svensson, B. (1993). Starch-and glycogen-debranching enzymes. Prediction of structural features of the catalytic (βα)8-barrel domain and evolutionary relationship to other amylolytic enzymes. J. Protein Chem. 12, 791-805.
Janecek, S., Svensson, B. & Henrissat, B. (1997). Domain evolution in the α-amylase family. J. Mol. Evol. 45, 322-331.
Svensson, B. (1994). Protein engineering in the α-amylase family: catalytic mechanism, substrate specificity, and stability. Plant Mol. Biol. 25, 141-157.
Aghajari, N., Feller, G., Gerday, Ch. & Haser, R. (1996). Crystallization and preliminary X-ray diffraction studies of α-amylase from the Antarctic psychrophile Alteromonas haloplanctis A23. Protein Sci. 5, 2128-2129.
Feller, G., le Bussy, O. & Gerday, Ch. (1998). Expression of psychrophilic genes in mesophilic hosts: assessment of the folding state of a recombinant α-amylase. Appl. Environ. Microbiol. 64, 1163-1165.
Chan, M.K., Mukland, S., Kletzin, A., Adams, M.W.W. & Rees, D.C. (1995). Structure of a hyperthermophilic tungstopterin enzyme, aldehyde ferredoxin oxidoreductase. Science 267, 1463-1469.
Qian, M., Haser, R., Buisson, G., Duée, E. & Payan, F. (1994). The active center of a mammalian α-amylase. Structure of the complex of a pancreatic α-amylase with a carbohydrate inhibitor refined to 2.2 Å resolution. Biochemistry 33, 6284-6294.
Machius, M., Vértesy, L., Huber, R. & Wiegand, G. (1996). Carbohydrate and protein-based inhibitors of porcine pancreatic á-amylase: structure analysis and comparison of their binding characteristics. J. Mol. Biol. 260, 409-421.
Feller, G., le Bussy, O., Houssier, C. & Gerday, Ch. (1996). Structural and functional aspects of chloride binding to Alteromonas haloplanctis α-amylase. J. Biol. Chem. 271, 23836-23841.
Strobl, S., et al., & Glockshuber, R. (1998). Crystal structure of yellow meal worm α-amylase at 1.64 Å resolution. J. Mol. Biol. 278, 617-628.
Van den Akker, F., Feil, I.K., Roach, C., Platas, A.A., Merritt, E.A. & Hol, W.G.J. (1997). Crystal structure of heat-labile enterotoxin from Escherichia coli with increased thermostability introduced by an engineered disulfide bond in the A subunit. Protein Sci. 6, 2644-2649.
Janecek, S. (1997). α-Amylase family: molecular biology and evolution. Prog. Biophys. Mol. Biol. 67, 67-97.
Watanabe, K., Masuda, T., Ohasi, H., Mihara, H., & Suzuki, Y. (1994). Multiple proline substitutions cumulatively thermostabilize Bacillus cereus ATCC7064 oligo-1,6-glucosidase. Irrefragable proof supporting the proline rule. Eur. J. Biochem. 226, 277-283.
Watanabe, K., Hata, Y., Kizaki, H., Katsube, Y., & Suzuki, Y. (1997). The refined crystal structure of Bacillus cereus oligo-1,6-glucosidase at 2.0 Å resolution: structural characterization of proline substitution sites for protein thermostabilization. J. Mol. Biol. 269, 142-153.
Burley, S.K. & Petsko, G.A. (1985). Aromatic-Aromatic interaction: a mechanism of protein structure stabilization. Science 229, 23-28.
Shoemaker, K.R., Kim, P.S., York, E.J., Stewart, J.M. & Baldwin, R.L. (1987). Tests of the helix dipole model for the stabilisation of α-helices. Nature 326, 563-567.
Privalov, P.L. & Gill, S.J. (1988). Stability of protein structure and hydrophobic interaction. Adv. Protein Chem. 39, 191-234.
Otwinowski, Z. (1993). Oscillation data reduction program. In Proceedings of the CCP4 study weekend: Data Collection and Processing. (Sawyer, L., Isaacs, N. and Bailey, S, eds), pp. 56-62, SERC Daresbury Laboratory, England.
Minor, W. (1993). XDISPLAYF program. Purdue University, West Lafayette, IN.
Collaborative Computational Project Number 4. (1994). The CCP4 suite: Programs for protein crystallography. Acta Cryst. D 50, 760-763.
Navaza, J. (1994). AMoRe: an automated package for molecular replacement. Acta Cryst. A 50, 157-163.
Roussel, A. & Cambillau, C. (1991 ). In Silicon Graphics Geometry Directory 86. Silicon Graphics, Mountain View, CA.
Brünger, A.T., Krukowski, A. & Erickson, J. (1990). Slow-cooling protocols for crystallographic refinement by simulated annealing. Acta Cryst. A 46, 585-593.
Brünger, A.T. (1992). The free R-value: a novel statistical quantity for assessing the accuracy of crystal structures. Nature 355, 472-474.
Jiang, J.-S. & Brünger, A.T. (1994). Protein hydration observed by X-ray diffraction: solvation properties of penicillopepsin and neuraminidase crystal structures. J. Mol. Biol. 243, 100-115.
Kabsch, W. & Sander, C. (1983). Dictionary of protein secondary structure: pattern recognition of hydrogen bonded and geometrical features. Biopolymers 22, 2577-2637.
McDonald, I.K. & Thornton, J.M. (1994). Satisfying hydrogen-bonding potential in proteins. J. Mol. Biol. 238, 777-793.
Thompson, J.D., Higgins, D.G. & Gibson, T.J. (1994). CLUSTALW: improving the sensitivity of progressive multiple sequence alignment through weighting, position and specific gap penalties and weight matrix choice. Nucleic Acids Res. 22, 4673-4680.
Kraulis, P.J. (1991). MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Cryst. 24, 946-950.
Nicholls, A.J. (1993). GRASP: graphical representation and analysis of surface properties. Biophys. J. 64, A116.
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