Structural, thermodynamic, and mutational analyses of a psychrotrophic RNase HI

Biochemistry

Volumn 46, Issue 25, 2007, Pages 7460-7468

  Tadokoro, Takashi ^a   You, Dong Ju ^a   Abe, Yumi ^a   Chon, Hyongi ^a,c   Matsumura, Hiroyoshi ^a,b   Koga, Yuichi ^a   Takano, Kazufumi ^a,b   Kanaya, Shigenori ^a  

^a OSAKA UNIVERSITY   (Japan)

^b JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

^c NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ENZYMATIC PROPERTIES; INTRAMOLECULAR ION PAIRS; RIBONUCLEASE (RNASE);

CRYSTAL STRUCTURE; ESCHERICHIA COLI; MUTAGENESIS; THERMODYNAMIC STABILITY;

ENZYMES;

BACTERIAL ENZYME; RIBONUCLEASE H; RIBONUCLEASE HI; UNCLASSIFIED DRUG;

ARTICLE; BACTERIAL STRAIN; CRYSTAL STRUCTURE; ENZYME ANALYSIS; ENZYME CONFORMATION; ENZYME PURIFICATION; ENZYME STABILITY; ENZYME STRUCTURE; ESCHERICHIA COLI; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; SEQUENCE HOMOLOGY; SHEWANELLA ONEIDENSIS; SITE DIRECTED MUTAGENESIS; THERMODYNAMICS;

AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; BASE SEQUENCE; BINDING SITES; CIRCULAR DICHROISM; CONSERVED SEQUENCE; CRYSTALLIZATION; ENZYME STABILITY; ESCHERICHIA COLI; HYDROGEN-ION CONCENTRATION; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MUTAGENESIS, SITE-DIRECTED; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN DENATURATION; PROTEIN STRUCTURE, SECONDARY; RIBONUCLEASE H, CALF THYMUS; SEQUENCE HOMOLOGY, AMINO ACID; SHEWANELLA; SOLUBILITY; TEMPERATURE; THERMODYNAMICS; ULTRAFILTRATION; UREA; X-RAY DIFFRACTION;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; SHEWANELLA ONEIDENSIS MR-1;

EID: 34250810188     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi7001423     Document Type: Article

References (38)

1. Myers, C. R., and Nealson, K. H. (1988) Bacterial manganese reduction and growth with manganese oxide as the sole electron acceptor, Science 240, 1319-1321.
2. Heidelberg, J. F., Paulsen, I. T., Nelson, K. E., Gaidos, E. J., Nelson, W. C., Read, T. D., et al. (2002) Genome sequence of the dissimilatory metal ion-reducing bacterium Shewanella oneidensis, Nat. Biotechnol. 20, 1118-1123.
3. Abboud, R., Popa, R., Souza-Egipsy, V., Giometti, C. S., Tollaksen, S., Mosher, J. J., Findelay, R. H., and Nealson, K. H. (2005) Low-temperature growth of Shewanella oneidensis MR-1, Appl. Environ. Microbiol. 71, 811-816.
4. Morita, R. Y., and Moyer, C. L. (2000) Origin of psychrophiles, in Encyclopedia of biodiversity (Levin, S. A., Colwell, R., Dailey, G., Lubchenco, J., Mooney, H. A., Schulze, E. D., and Tilman, G. D., Eds.) pp 917-924, Vol. 4, Academic Press, San Diego.
5. Crouch, R. J., and Dirksen, M. L. (1982) Ribonuclease H, in Nuclease (Linn, S. M., and Robert, R. J., Eds.) pp 211-241, Cold Spring Harbor Laboratory Press, Plainview, NY.
6. Ohtani, N., Haruki, M., Morikawa, M., and Kanaya, S. (1999) Molecular diversities of RNases H, J. Biosci. Bioeng. 88, 12-19.
7. Kanaya, S. (1998) Enzymatic activity and protein stability of E. coli ribonuclease HI, in Ribonucleases H (Crouch, R. J., and Toulme, J. J., Eds.) pp 1-38, INSERM, Paris.
8. Mukaiyama, A., Takano, K., Haruki, M., Morikawa, M., and Kanaya, S. (2004) Kinetic robust monomeric protein from a hyperthermophile, Biochemistry 43, 13859-13866.
9. Hollien, J., and Marqusee, S. (1999) A thermodynamic comparison of mesophilic and thermophilic ribonucleases H, Biochemistry 38, 3831-3836.
10. Smalas, A. O., Leiros, H. K., Os, V., and Willassen, N. P. (2000) Cold adapted enzymes, Biotechnol. Annu. Rev. 6, 1-57.
11. Gianese, G., Bossa, F., and Pascarella, S. (2002) Comparative structural analysis of psychrophilic and meso- and thermophilic enzymes, Proteins 47, 236-249.
12. Feller, G., and Gerday, C. (2003) Psychrophilic enzymes: Hot topics in cold adaptation, Nat. Rev. Microbiol. 1, 200-208.
13. Siddiqui, K. S., and Cavicchioli, R. (2006) Cold-adapted enzymes, Annu. Rev. Biochem. 75, 403-433.
14. Ohtani, N., Haruki, M., Morikawa, M., and Kanaya, S. (2001) Heat labile ribonuclease HI from a psychrotrophic bacterium: Gene cloning, characterization and site-directed mutagenesis, Protein Eng. 14, 975-982.
15. Kanaya, S., Katsuda, C., Kimura, S., Nakai, T., Kitakuni, E., Nakamura, H., Katayanagi, K., Morikawa, K., and Ikehara, M. (1991) Stabilization of Escherichia coli ribonuclease H by introduction of an artificial disulfide bond, J. Biol. Chem. 266, 6038-6044.
16. Laemmli, U. K. (1970) Cleavage of structural proteins during assembly of the head of bacteriophage T4, Nature 227, 680-685.
17. Goodwin, T. W., and Morton, R. A. (1946) The spectrophotometric determination of tyrosine and tryptophan in proteins, Biochem. J. 40, 628-630.
18. Otwinowski, Z., and Minor, W. (1997) Processing of X-ray diffraction data collected in oscillation mode, Methods Enzymol. 276, 307-326.
19. Vagin, A., and Teplyakov, A. (1997) MOLREP: An automated program for molecular replacement, J. Appl. Crystallogr. 30, 1022-1025.
20. Emsley, P., and Cowtan, K. (2004) Coot: Model-building tools for molecular graphics, Acta Crystallogr. D60, 2126-2132.
21. Murshudov, G. N., Vagin, A. A., and Dodson, E. J. (1997) Refinement of macromolecular structures by the maximum-likelihood method, Acta Crystallogr. D53, 240-255.
22. Laskowski, R. A., MacArthur, M. W., Moss, D. S., and Thornton, J. M. (1993) PROCHECK: A program to check the stereochemical quality of protein structures, J. Appl. Crystallogr. 26, 283-291.
23. Sayle, R. A., and Milner-White, E. J. (1995) RASMOL: Biomolecular graphics for all, Trends Biochem. Sci. 20, 374.
24. Collaborative Computational Project, Number 4 (1994) The CCP4 suite: Programs for protein crystallography, Acta Crystallogr. D50, 760-763.
25. Nicholls, A., Sharp, K., and Honig, B. (1991) Protein folding and association: Insights from the interfacial and thermodynamic properties of hydrocarbons, Proteins: Struct., Funct., Genet. 11, 281-296.
26. Pace, C. N. (1990) Measuring and increasing protein stability, Trends Biotechnol. 8, 93-98.
27. Arnorsdottir, J., Kristjansson, M. M., and Ficner, R. (2005) Crystal structure of a subtilisin-like serine proteinase from a psychrotrophic Vibrio species reveals structural aspects of cold adaptation, FEBS J. 272, 832-845.
28. Bae, E., and Phillips, G. N., Jr. (2004) Structures and analysis of highly homologous psychrophilic, mesophilic, and thermophilic adenylate kinases, J. Biol. Chem. 279, 28202-28208.
29. D'Amico, S., Marx, J. C., Gerday, C., and Feller, G. (2003) Activity-stability relationships in extremephilic enzymes, J. Biol. Chem. 278, 7891-7896.
30. Kumer, S., Tsai, C. J., and Nussinov, R. (2001) Thermodynamic difference among thermophilic and mesophilic proteins, Biochemistry 40, 14152-14165.
31. Gomez, J., Hilser, V. J., Xie, D., and Freire, E. (1995) The heat capacity of proteins, Proteins: Struct., Funct., Genet. 22, 404-412.
32. Lee, C.-F., Allen, M. D., Bycroft, M., and Wong, K. B. (2005) Electrostatic interactions contribute to reduced heat capacity change of unfolding in a thermophilic ribosomal protein L30e, J. Mol. Biol. 348, 419-431.
33. Grattinger, M., Dankesreiter, A., Schurig, H., and Jaenicke, R. (1998) Recombinant phosphoglycerate kinase from the hyperthermophilic bacterium Thermotoga maritima: Catalytic, spectral and thermodynamic properties, J. Mol. Biol. 280, 525-533.
34. Uchiyama, S., Hasegawa, J., Tanimoto, Y., Moriguchi, H., Mizutani, M., Igarashi, Y., Sambongi, Y., and Kobayashi, Y. (2002) Thermodynamic characterization of variants of mesophilic cytochrome c and its thermophilic counterpart, Protein Eng. 15, 455-462.
35. Deutschman, W. A., and Dahlquist, F. W. (2001) Thermodynamic basis for the increased thermostability of CheY from the hyperthermophile Thermotoga maritima, Biochemistry 40, 13107-13113.
36. p of unfolding, Protein Eng. 14, 961-966.
37. Beadle, B. M., Baase, W. A., Wilson, D. B., Gilkes, N. R., and Shoichet, B. K. (1999) Comparing the thermodynamic stabilities of a related thermophilic and mesophilic enzyme, Biochemistry 38, 2570-2576.
38. Feller, G., d'Amico, D., and Gerday, C. (1999) Thermodynamic stability of a cold-active α-amylase from the Antarctic bacterium Alteromonas haloplanctis, Biochemistry 38, 4613-4619.