Crystal structures of a psychrophilic metalloprotease reveal new insights into catalysis by cold-adapted proteases

Proteins: Structure, Function and Genetics

Volumn 50, Issue 4, 2003, Pages 636-647

  Aghajari, Nushin ^a   Van Petegem, Filip ^b   Villeret, Vincent ^b   Chessa, Jean Pierre ^c   Gerday, Charles ^c   Haser, Richard ^a   Van Beeumen, Jozef ^b  

^a UNIVERSITÉ LYON 1   (France)

^b GHENT UNIVERSITY   (Belgium)

^c UNIVERSITY OF LIÈGE   (Belgium)

Author keywords

Adaptation; Crystallography; Extremophile; Psychrophile; Temperature

Indexed keywords

ALKALINE PROTEINASE; CALCIUM ION; METALLOPROTEINASE; TYROSINE;

ANTARCTICA; ARTICLE; CATALYSIS; COLD ACCLIMATIZATION; COMPARATIVE STUDY; CONFORMATIONAL TRANSITION; CRYSTAL STRUCTURE; ENZYME ACTIVE SITE; ENZYME BINDING; ENZYME SUBSTRATE; ENZYME SUBSTRATE COMPLEX; GENE DELETION; NONHUMAN; PRIORITY JOURNAL; PROTEIN CONFORMATION; PSEUDOMONAS; SPECIES; THERMOSTABILITY;

ADAPTATION, PHYSIOLOGICAL; AMINO ACID SEQUENCE; AMINO ACIDS; BINDING SITES; CALCIUM; CATALYSIS; CATALYTIC DOMAIN; COLD; CRYSTALLOGRAPHY, X-RAY; FLUORESCENCE; HYDROGEN BONDING; HYDROPHOBICITY; METALLOENDOPEPTIDASES; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN CONFORMATION; SEQUENCE ALIGNMENT; SERINE ENDOPEPTIDASES; STRUCTURE-ACTIVITY RELATIONSHIP;

PSEUDOMONAS;

EID: 0037342768     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.10264     Document Type: Article

References (47)

1. Russell NJ. Molecular adaptations in psychrophilic bacteria: potential for biotechnological applications. Adv Biochem Eng Biotech 1998;61:1-21.
2. Feller G, Gerday C. Psychrophilic enzymes: molecular basis of cold adaptation. Cell Mol Life Sci 1997;53:830-841.
3. Gerday C, Aittaleb M, Arpigny JL, Blaise E, Chessa J-P, Garsoux G, Petrescu I, Feller G. Psychrophilic enzymes: a thermodynamic challenge. Biochim Biophys Acta 1997;1342:119-131.
4. Feller G, Narinx E, Arpigny JL, Aittaleb M, Baise E, Genicots S., Gerday C. Enzymes from psychrophilic organisms. FEMS Microbiol Rev 1996;18:189-202.
5. Aghajari N, Feller G, Gerday C, Haser R. Structures of the psychrophilic Alteromonos haloplanctis α-amylase give insights into cold adaptation at a molecular level. Structure 1998;6:1503-1516.
6. Aghajari N, Feller G, Gerday C, Haser R. Crystal structures of the psychrophilic α-amylase from Alteromonas haloplanctis in its native form and complexed with an inhibitor. Protein Sci 1998;7:564-572.
7. Russell RJ, Gerike U, Danson MJ, Hough DW, Taylor GL. Structural adaptations of the cold-active citrate synthase from an Antarctic bacterium. Structure 1998;6:351-361.
8. Kim S-Y, Hwang KY, Kim S-H, Sung H-C, Han YS, Cho Y. Structural basis for cold adaptation. Sequence, biochemical properties, and crystal structure of malate dehydrogenase from a psychrophile Aquaspirillium arcticum. J Biol Chem 1999;274:11761-11767.
9. Alvarez M, Zeelen JP, Mainfroid V, Rentier-Delrue F, Martial JA, Wyns L, Wierenga RK, Maes D. Triose-phosphate isomerase (TIM) of the psychrophilic bacterium Vibrio marinus. Kinetic and structural properties. J Biol Chem 1998;273:2199-2206.
10. Feller G, Payan F, Theys F, Qian M, Haser R, Gerday C. Stability and structure analysis of α-amylase from the Antarctic psychrophile Alteromonas haloplanctis A23. Eur J Biochem 1994;222:441-447.
11. Arpigny JL, Lamotte J, Gerday C. Molecular adaptation to cold of an Antarctic bacterial lipase. J Mol Catal B 1997;3:29-35.
12. Narinx E, Baise E, Gerday C. Subtilisin from psychrophilic Antarctic bacteria: characterization and site-directed mutagenesis of residues possibly involved in the adaptation to cold. Protein Eng 1997;10:101-109.
13. Petrescu I, Lamotte-Brasseur J, Chessa J-P, Ntarima P, Claeyssens M, Devreese B, Marino G, Gerday C. Xylanase from the psychrophilic yeast Cryptococcus adeliae. Extremophiles 2000;4:137-144.
14. Bentahir M, Feller G, Aittaleb M, Lamotte-Brasseur J, Himri T, Chessa J-P, Gerday C. Structural, kinetic and calorimetric characterization of the cold-active phosphoglycerate kinase from the Antarctic Pseudomonas sp. TAC II 18. J Biol Chem 2000;275:11147-11153.
15. Chessa J-P, Petrescu I, Bentahir M, Van Beeumen J, Gerday C. Purification, physico-chemical characterization and sequence of a heat labile alkaline metalloprotease isolated from a psychrophilic Pseudomonas species. Biochim Biophys Acta 2000;36103:1-10.
16. Baumann U, Wu S, Flaherty KM, McKay DB. Three-dimensional structure of the alkaline protease of Pseudomonas aeruginosa: a two-domain protein with a calcium binding parallel beta roll motif. EMBO J 1993;12:3357-3364.
17. Miyatake H, Hata Y, Fujii T, Hamada K, Morihara K, Katsube Y. Crystal structure of the unliganded alkaline protease from Pseudomonas aeruginosa IFO3080 and its conformational changes on ligand binding. J Biochem 1995;118:474-479.
18. Baumann U. Crystal structure of the 50 kDa metallo protease from Serratia marcescens. J Mol Biol 1994;242:244-251.
19. Baumann U, Bauer M, Létoffé S, Delepelaire P, Wandersman C. Crystal structure of a complex between Serratia marcescens metallo-protease and an inhibitor from Erwinia chrysanthemi. J Mol Biol 1995;248:653-661.
20. Hamada K, Hata Y, Katsuya Y, Hiramatsu H, Fujiwara T, Katsube Y. Crystal structure of Serratia protease, a zinc-dependent proteinase from Serratia sp. E-15, containing a β-sheet coil motif at 2.0 Å resolution. J Biochem 1996;119:844-851.
21. Lakowicz JR, Weber G. Quenching of protein fluorescence by oxygen. Detection of structural fluctuations in proteins on the nanosecond time scale. Biochemistry 1973;12:4171-4179.
22. Lakowicz JR. Principles of fluorescence spectroscopy. New York: Plenum Press; 1983.
23. Villeret V, Chessa J-P, Gerday C, Van Beeumen J. Preliminary crystal structure determination of the alkaline protease from the Antarctic psychrophile Pseudomonas aeruginosa. Protein Sci 1997;6:2462-2464.
24. Aghajari N. PhD thesis. Université de la Méditerranée Aix-Marseille II & Université de Liège; 1998.
25. Navaza J. AMoRe: an Automated Package for Molecular Replacement. Acta Crystallogr 1994;A50:157-163.
26. The CCP4 Suite: Programs for protein crystallography. Acta Crystallogr 1994;D50:760-763.
27. Read RJ. Improved Fourier coefficients for maps using phase from partial structure with errors. Acta Crystallogr 1986;A42:140-149.
28. Roussel A, Cambillau C. In: Silicon Graphics geometry directory 86. Mountain View, CA: Silicon Graphics; 1991.
29. Brünger AT, Adams PD, Clore GM, DeLano WL, Gros P, Grosse-Kunstleve RW, Jiang JS, Kuszewski J, Nilges M, Pannu NS, Read RJ, Rice LM, Simonson T, Warren GL. Crystallography and NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr 1998;D54:905-921.
30. Laskowski RA, MacArthur MW, Moss DS, Thornton JM. PROCHECK: a program to check the stereochemistry of protein structures. J Appl Crystallogr 1993;26:283-291.
31. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994;22:4673-4680.
32. Kabsch W, Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983;22:2577-2637.
33. McDonald IK, Thornton JM. Satisfying hydrogen-bonding potential in proteins. J Mol Biol 1994;238:777-793.
34. Nicholls A, Sharp KA, Honig B. Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins 1991;11:281-296.
35. Bode W, Gomis-Rüth FX, Stöcker W. Astacins, serralysins, snake venom and matrix metalloproteinases exhibit identical zinc-binding environments (HEXXHXXGXXH and Met-turn) and topologies and should be grouped into a common family, the "metzincins." FEBS Lett 1993;331:134-140.
36. Lovell SC, Word JM, Richardson JS, Richardson DC. The penultimate rotamer library. Proteins 2000;40:389-408.
37. Gerike U, Danson MJ, Hough DW. Cold-active citrate synthase: mutagenesis of active-site residues. Protein Eng 2001;14:655-661.
38. Graziano G, Catanzano F, Riccio A, Barone GJ. A reassessment of the molecular origin of cold denaturation. Biochem 1997;122:395-401.
39. Smalås AO, Heimstad ES, Hordvik A, Willasen P, Male R. Cold adaptation of enzymes: structural comparison between salmon and bovine trypsins. Proteins 1994;20:149-166.
40. Wallon G, Lovett ST, Magyar C, Svingor A, Szilagvi A, Zadovsky P, Ringe D, Petsko GA. Sequence and homology model of 3-ispopropylmalate dehydrogenase from the psychrotrophic bacterium Vibrio sp 15 suggest reasons for thermal instability. Protein Eng 1997;10:665-672.
41. Ikai A. Thermostability and alphatic index of globular proteins. J Biochem 1980;88:1895-1898.
42. Kyte J, Doolittle RF. A simple method for displaying the hydropathic character of a protein. J Mol Biol 1982;157:105-132.
43. Davail S, Feller G, Narinx E, Gerday C. Cold adaptation of proteins. Purification, characterization, and sequence of the heatlabile subtilisin from the antarctic psychrophile Bacillus TA41. J Biol Chem 1994;269:17448-17453.
44. Gerday C, Aittaleb M, Bentahir M, Chessa J-P, Claverie P, Collins P, D'Amico S, Dumont J, Garsano G, Georlette D, Hoyoux A, Lonhienne T, Meuwis M-A, Feller G. Cold-adapted enzymes: from fundamentals to biotechnology. Trends Biotech 2000;18:103-107.
45. Kraulis PJ. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J Appl Crystallogr 1991;24:946-950.
46. Esnouf RM. An extensively modified version of MOLSCRIPT that includes greatly enhanced coloring capabilities. J Mol Graph 1997;15:132-134.
47. Gouet P, Courcelle E, Stuart DI, Metoz F. ESPript: multiple sequence alignments in PostScript. Bioinformatics 1999;15:305-308.