Cold adaptation of zinc metalloproteases in the thermolysin family from deep sea and arctic sea ice bacteria revealed by catalytic and structural properties and molecular dynamics: New insights into relationship between conformational flexibility and hydrogen bonding

Journal of Biological Chemistry

Volumn 284, Issue 14, 2009, Pages 9257-9269

  Xie, Bin Bin ^a   Bian, Fei ^a   Chen, Xiu Lan ^a   He, Hai Lun ^a   Guo, Jun ^a   Gao, Xiang ^a   Zeng, Yin Xin ^b   Chen, Bo ^b   Zhou, Bai Cheng ^a   Zhang, Yu Zhong ^a  

^a SHANDONG UNIVERSITY   (China)

^b Chongqing Institute of Geology and Mineral Resources   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ARCTIC SEA ICE; CATALYTIC EFFICIENCIES; CONFORMATIONAL FLEXIBILITY; DEEP SEA; DYNAMIC STRUCTURE; FLUORESCENCE QUENCHING; HYDROGEN BONDINGS; LOW TEMPERATURES; MELTING TEMPERATURES; MESOPHILIC; METALLOPROTEASES; MOLECULAR DYNAMICS SIMULATIONS; OPTIMAL TEMPERATURE; SALT BRIDGES; STRUCTURAL BASIS; STRUCTURAL DETERMINANTS; THERMOLYSIN; THREONINE RESIDUES;

AMINO ACIDS; HYDROGEN; HYDROGEN BONDS; IMAGE STORAGE TUBES; MELTING POINT; MOLECULAR DYNAMICS; OCEANOGRAPHY; OPTIMIZATION; PROTEINS; QUENCHING; SEA ICE; STRUCTURAL ANALYSIS; ZINC;

DYNAMICS;

ASPARAGINE; METALLOPROTEINASE; SERINE; THERMOLYSIN; THREONINE; UNCLASSIFIED DRUG; ZINC METALLOPROTEASE; ZINC;

ARCTIC; ARTICLE; BACTERIAL STRAIN; BACTERIUM CULTURE; CATALYSIS; COLD ACCLIMATIZATION; CONFORMATION; CONTROLLED STUDY; DEEP SEA; ESCHERICHIA COLI; FLUORESCENCE; GENE EXPRESSION; HYDROGEN BOND; MOLECULAR CLONING; MOLECULAR DYNAMICS; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PSEUDOALTEROMONAS; PSEUDOMONAS AERUGINOSA; SEQUENCE HOMOLOGY; TEMPERATURE; TERRESTRIAL SPECIES; ADAPTATION; AMINO ACID SEQUENCE; BIOCATALYSIS; BIOLOGY; CHEMICAL STRUCTURE; CHEMISTRY; CLASSIFICATION; COLD; COMPUTER SIMULATION; ENZYME STABILITY; ENZYMOLOGY; GENETICS; ICE COVER; METABOLISM; MICROBIOLOGY; MOLECULAR GENETICS; PSEUDOMONAS; SEA; SEQUENCE ALIGNMENT; STRUCTURAL HOMOLOGY;

BACTERIA (MICROORGANISMS);

ADAPTATION, BIOLOGICAL; AMINO ACID SEQUENCE; ARCTIC REGIONS; BIOCATALYSIS; COLD TEMPERATURE; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; CONSERVED SEQUENCE; ENZYME STABILITY; HYDROGEN BONDING; ICE COVER; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; OCEANS AND SEAS; PSEUDOMONAS; SEQUENCE ALIGNMENT; STRUCTURAL HOMOLOGY, PROTEIN; THERMOLYSIN; ZINC;

EID: 66149121843     PISSN: 00219258     EISSN: 1083351X     Source Type: Journal    
DOI: 10.1074/jbc.M808421200     Document Type: Article

References (44)

1. Feller, G., and Gerday, C. (2003) Nat. Rev. Microbiol. 1, 200-208
2. Lonhienne, T., Gerday, C., and Feller, G. (2000) Biochim. Biophys. Acta 1543, 1-10
3. Siddiqui, K. S., and Cavicchioli, R. (2006) Annu. Rev. Biochem. 75, 403-433
4. Georlette, D., Blaise, V., Collins, T., D'Amico, S., Gratia, E., Hoyoux, A., Marx, J. C., Sonan, G., Feller, G., and Gerday, C. (2004) FEMS Microbiol. Rev. 28, 25-42
5. Olufsen, M., Smalas, A. O., Moe, E., and Brandsdal, B. O. (2005) J. Biol. Chem. 280, 18042-18048
6. Russell, R. J., Gerike, U., Danson, M. J., Hough, D. W., and Taylor, G. L. (1998) Structure 6, 351-361
7. Brandsdal, B. O., Smalas, A. O., and Aqvist, J. (2001) FEBS Lett. 499, 171-175
8. Moe, E., Leiros, I., Riise, E. K., Olufsen, M., Lanes, O., Smalas, A., and Willassen, N. P. (2004) J. Mol. Biol. 343, 1221-1230
9. D'Amico, S., Claverie, P., Collins, T., Georlette, D., Gratia, E., Hoyoux, A., Meuwis, M. A., Feller, G., and Gerday, C. (2002) Philos. Trans. R. Soc. Lond. B Biol. Sci. 357, 917-925
10. Gianese, G., Bossa, F., and Pascarella, S. (2002) Proteins 47, 236-249
11. Leiros, H. K., Pey, A. L., Innselset, M., Moe, E., Leiros, I., Steen, I. H., and Martinez, A. (2007) J. Biol. Chem. 282, 21973-21986
12. Fedoy, A. E., Yang, N., Martinez, A., Leiros, H. K., and Steen, I. H. (2007) J. Mol. Biol. 372, 130-149
13. Svingor, A., Kardos, J., Hajdu, I., Nemeth, A., and Zavodszky, P. (2001) J. Biol. Chem. 276, 28121-28125
14. Wintrode, P. L., Miyazaki, K., and Arnold, F. H. (2000) J. Biol. Chem. 275, 31635-31640
15. Miyazaki, K., Wintrode, P. L., Grayling, R. A., Rubingh, D. N., and Arnold, F. H. (2000) J. Mol. Biol. 297, 1015-1026
16. Barrett, A. J., Rawlings, N. D., and Woessner, J. F. (2004) Handbook of Proteolytic Enzymes, 2nd Ed., pp. 374-412, Elsevier Academic Press, London
17. Adekoya, O. A., Helland, R., Willassen, N. P., and Sylte, I. (2006) Proteins 62, 435-449
18. Chen, X. L., Zhang, Y. Z., Gao, P. J., and Luan, X. W. (2003) Mar. Biol. 143, 989-993
19. Liu, Y.-G., and Whitter, R. F. (1995) Genomics 25, 674-681
20. Feder, J. (1968) Biochem. Biophys. Res. Commun. 32, 326-332
21. Marchler-Bauer, A., Anderson, J. B., Derbyshire, M. K., Weese-Scott, C., Gonzales, N. R., Gwadz, M., Hao, L., He, S., Hurwitz, D. I., Jackson, J. D., Ke, Z., Krylov, D., Lanczycki, C. J., Liebert, C. A., Liu, C., Lu, F., Lu, S., Marchler, G. H., Mullokandov, M., Song, J. S., Thanki, N., Yamashita, R. A., Yin, J. J., Zhang, D., and Bryant, S. H. (2007) Nucleic Acids Res. 35, D237-D240
22. Rawlings, N. D., Morton, F. R., Kok, C. Y., Kong, J., and Barrett, A. J. (2008) Nucleic Acids Res. 36, D320-D325
23. Emanuelsson, O., Brunak, S., von, H. G., and Nielsen, H. (2007) Nat. Protoc. 2, 953-971
24. Larkin, M. A., Blackshields, G., Brown, N. P., Chenna, R., McGettigan, P. A., McWilliam, H., Valentin, F., Wallace, I. M., Wilm, A., Lopez, R., Thompson, J. D., Gibson, T. J., and Higgins, D. G. (2007) Bioinformatics 23, 2947-2948
25. Hall, T. A. (1999) Nucleic Acids Symp. Ser. 41, 95-98
26. Thayer, M. M., Flaherty, K. M., and McKay, D. B. (1991) J. Biol. Chem. 266, 2864-2871
27. Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., Shindyalov, I. N., and Bourne, P. E. (2000) Nucleic Acids Res. 28, 235-242
28. Sali, A., and Blundell, T. L. (1993) J. Mol. Biol. 234, 779-815
29. Phillips, J. C., Braun, R., Wang, W., Gumbart, J., Tajkhorshid, E., Villa, E., Chipot, C., Skeel, R. D., Kale, L., and Schulten, K. (2005) J. Comput. Chem. 26, 1781-1802
30. MacKerell, A. D., Bashford, D., Bellott, M., Dunbrack, R. L., Evanseck, J. D., Field, M. J., Fischer, S., Gao, J., Guo, H., Ha, S., Joseph-McCarthy, D., Kuchnir, L., Kuczera, K., Lau, F. T. K., Mattos, C., Michnick, S., Ngo, T., Nguyen, D. T., Prodhom, B., Reiher, W. E., Roux, B., Schlenkrich, M., Smith, J. C., Stote, R., Straub, J., Watanabe, M., Wiorkiewicz-Kuczera, J., Yin, D., and Karplus, M. (1998) J. Phys. Chem. B 102, 3586-3616
31. Guex, N., and Peitsch, M. C. (1997) Electrophoresis 18, 2714-2723
32. Humphrey, W., Dalke, A., and Schulten, K. (1996) J. Mol. Graph. 14, 33-38
33. McDonald, I. K., and Thornton, J. M. (1994) J. Mol. Biol. 238, 777-793
34. Lee, S. O., Kato, J., Nakashima, K., Kuroda, A., Ikeda, T., Takiguchi, N., and Ohtake, H. (2002) Biosci. Biotechnol. Biochem. 66, 1366-136
35. Tronrud, D. E., Monzingo, A. F., and Matthews, B. W. (1986) Eur. J. Biochem. 157, 261-268
36. Banbula, A., Potempa, J., Travis, J., Fernandez-Catalan, C., Mann, K., Huber, R., Bode, W., and Medrano, F. (1998) Structure. 6, 1185-1193
37. D'Amico, S., Marx, J. C., Gerday, C., and Feller, G. (2003) J. Biol. Chem. 278, 7891-7896
38. Xu, Y., Feller, G., Gerday, C., and Glansdorff, N. (2003) J. Bacteriol. 185, 2161-2168
39. Collins, T., Meuwis, M. A., Gerday, C., and Feller, G. (2003) J. Mol. Biol. 328, 419-428
40. Georlette, D., Damien, B., Blaise, V., Depiereux, E., Uversky, V. N., Gerday, C., and Feller, G. (2003) J. Biol. Chem. 278, 37015-37023
41. Bae, E., and Phillips, G. N., Jr. (2004) J. Biol. Chem. 279, 28202-28208
42. Chessa, J. P., Petrescu, I., Bentahir, M., Van, B. J., and Gerday, C. (2000) Biochim. Biophys. Acta 1479, 265-274
43. Aghajari, N., Van, P. F., Villeret, V., Chessa, J. P., Gerday, C., Haser, R., and Van, B. J. (2003) Proteins 50, 636-647
44. Gouet, P., Courcelle, E., Stuart, D. I., and Metoz, F. (1999) Bioinformatics 15, 305-308