Molecular mechanism of distinct salt-dependent enzyme activity of two halophilic nucleoside diphosphate kinases

Biophysical Journal

Volumn 96, Issue 11, 2009, Pages 4692-4700

  Yamamura, Akihiro ^a   Ichimura, Takefumi ^a   Kamekura, Masahiro ^b   Mizuki, Toru ^c   Usami, Ron ^c   Makino, Tsukasa ^a   Ohtsuka, Jun ^a   Miyazono, Ken Ichi ^a   Okai, Masahiko ^a   Nagata, Koji ^a   Tanokura, Masaru ^a  

^a UNIVERSITY OF TOKYO   (Japan)

^b Noda Institute for Scientific Research   (Japan)

^c TOYO UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ARGININE; CYSTEINE; NUCLEOSIDE DIPHOSPHATE KINASE; SODIUM CHLORIDE; ARCHAEAL PROTEIN;

AMINO ACID SUBSTITUTION; ARTICLE; CONTROLLED STUDY; CRYSTAL STRUCTURE; ENZYME ACTIVITY; HALOARCULA; HALOARCULA QUADRATA; HAOARCULA SINAIIENSIS; NONHUMAN; PROTEIN QUATERNARY STRUCTURE; AMINO ACID SEQUENCE; CHEMICAL STRUCTURE; CHEMISTRY; CIRCULAR DICHROISM; CRYSTALLIZATION; ESCHERICHIA COLI; GENETICS; MOLECULAR GENETICS; PROTEIN SECONDARY STRUCTURE; PROTEIN STABILITY; PROTEIN TERTIARY STRUCTURE; STRUCTURAL HOMOLOGY; X RAY DIFFRACTION;

HALOARCULA QUADRATA; HALOBACTERIA;

AMINO ACID SEQUENCE; ARCHAEAL PROTEINS; CIRCULAR DICHROISM; CRYSTALLIZATION; ESCHERICHIA COLI; HALOARCULA; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NUCLEOSIDE-DIPHOSPHATE KINASE; PROTEIN STABILITY; PROTEIN STRUCTURE, QUATERNARY; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; SODIUM CHLORIDE; STRUCTURAL HOMOLOGY, PROTEIN; X-RAY DIFFRACTION;

EID: 68949143188     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2009.03.012     Document Type: Article

References (32)

1. Bernard, M. A., N. B. Ray, M. C. Olcott, S. P. Hendricks, and C. K. Mathews. 2000. Metabolic functions of microbial nucleoside diphosphate kinases. J. Bioenerg. Biomembr. 32:259-267.
2. Janin, J., C. Dumas, S. Moréra, Y. Xu, P. Meyer, et al. 2000. Three-dimensional structure of nucleoside diphosphate kinase. J. Bioenerg. Biomembr. 32:215-225.
3. Lascu, L., A. Giartosio, S. Ransac, and M. Erent. 2000. Quaternary structure of nucleoside diphosphate kinases. J. Bioenerg. Biomembr. 32:227-236.
4. Madern, D., C. Ebel, and G. Zaccai. 2000. Halophilic adaptation of enzymes. Extremophiles. 4:91-98.
5. Mevarech, M., F. Frolow, and L. M. Gloss. 2000. Halophilic enzymes: proteins with a grain of salt. Biophys. Chem. 86:155-164.
6. Polosina, Y. Y., K. F. Jarrell, O. V. Fedorov, and A. S. Kostyukova. 2000. Nucleoside diphosphate kinase from haloalkaliphilic archaeon Natronobacterium magadii: purification and characterization. Extremophiles. 2:333-338.
7. Besir, H., K. Zeth, A. Bracher, U. Heider, M. Ishibashi, et al. 2005. Structure of a halophilic nucleoside diphosphate kinase from Halobacterium salinarum. FEBS Lett. 579:6595-6600.
8. Ishibashi, M., T. Arakawa, J. S. Philo, K. Sakashita, Y. Yonezawa, et al. 2002. Secondary and quaternary structural transition of the halophilic archaeon nucleoside diphosphate kinase under high- and low-salt conditions. FEMS Microbiol. Lett. 216:235-241.
9. Ishibashi, M., S. Tatsuda, K. Izutsu, K. Kumeda, T. Arakawa, et al. 2007. A single Gly114Arg mutation stabilizes the hexameric subunit assembly and changes the substrate specificity of halo-archaeal nucleoside diphosphate kinase. FEBS Lett. 581:4073-4079.
10. Mizuki, T., M. Kamekura, M. Ishibashi, R. Usami, Y. Yoshida, et al. 2004. Nucleoside diphosphate kinase of halobacteria. Amino acid sequence and salt-response pattern. J. Jap. Soc. Extremophiles. 3: 18-27.
11. Otwinowski, Z., and W. Minor. 1997. Processing of x-ray diffraction collected in oscillation mode. Methods Enzymol. 276:307-326.
12. Collaborative Computational Project, Number 4. 1994. The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D Biol. Crystallogr. 50:760-763.
13. Vagin, A., and A. Teplyakov. 2000. An approach to multi-copy search in molecular replacement. Acta Crystallogr. D Biol. Crystallogr. 56:1622-1624.
14. McRee, D. E. 1999. XtalView/Xfit.-A versatile program for manipulating atomic coordinates and electron density. J. Struct. Biol. 125:156-165.
15. Brunger, A. T., P. D. Adams, G. M. Clore, W. L. DeLano, P. Gros, et al. 1998. Crystallography and NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr. D Biol. Crystallogr. 54:905-921.
16. Murshudov, G. N., A. A. Vagin, and E. J. Dodson. 1997. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D Biol. Crystallogr. 53:240-255.
17. Laskowski, R. A., M. W. MacArthur, D. S. Moss, and J. M. Thornton. 1993. PROCHECK: a program to check the stereochemistry quality of protein structures. J. Appl. Cryst. 26:283-291.
18. Holm, L., and J. Park. 2000. DaliLite workbench for protein structure comparison. Bioinformatics. 16:566-567.
19. Chen, Y. H., J. T. Yang, and H. Martinez. 1972. Determination of the secondary structures of proteins by circular dichroism and optical rotatory dispersion. Biochemistry. 11:4120-4131.
20. Matthews, B. W. 1968. Solvent content of protein crystals. J. Mol. Biol. 33:491-497.
21. Krissinel, E., and K. Henrick. 2005. Detection of protein assemblies in crystals. In CompLife 2005, LNBI 3695. M. R. Berthold, R. Glen, K. Diederichs, O. Kohlbacher, and I. Fischer, editors. Springer-Verlag, Berlin. 163-174.
22. Holm, L., and C. Sander. 1995. DALI: a network tool for protein structure comparison. Trends Biochem. Sci. 20:478-480.
23. Johansson, M., A. Mackenzie-Hose, I. Andersson, and C. Knorpp. 2004. Structure and mutational analysis of a plant mitochondrial nucleoside diphosphate kinase. Identification of residues involved in serine phosphorylation and oligomerization. Plant Physiol. 136:3034-3042.
24. Morera, S., M. Chiadmi, G. LeBras, I. Lascu, and J. Janin. 1995. Mechanism of phosphate transfer by nucleoside diphosphate kinase: x-ray structures of the phosphohistidine intermediate of the enzymes from Drosophila and Dictyostelium. Biochemistry. 34:11062-11070.
25. Min, K., H. K. Song, C. Chang, S. Y. Kim, K. J. Lee, et al. 2002. Crystal structure of human nucleoside diphosphate kinase A, a metastasis suppressor. Proteins. 46:340-342.
26. Emsley, P., and K. Cowtan. 2004. Coot: model-building tools for molecular graphics. Acta Crystallogr. D Biol. Crystallogr. 60:2126-2132.
27. Sakurai, K., M. Oobatake, and Y. Goto. 2001. Salt-dependent monomer-dimer equilibrium of bovine beta-lactoglobulin at pH 3. Protein Sci. 10:2325-2335.
28. Karlsson, A., S. Mesnildrey, Y. Xu, S. Moréra, J. Janin, et al. 1996. Nucleoside diphosphate kinase. Investigation of the intersubunit contacts by site-directed mutagenesis and crystallography. J. Biol. Chem. 271:19928-19934.
29. Williams, R. L., D. A. Oren, J. Munoz-Dorado, S. Inouye, M. Inouye, et al. 1993. Crystal structure of Myxococcus xanthus nucleoside diphosphate kinase and its interaction with a nucleotide substrate at 2.0 Å resolution. J. Mol. Biol. 234:1230-1247.
30. DeLano, W. L. 2002. The PyMOL Molecular Graphics System. DeLano Scientific, Palo Alto, CA.
31. Gouet, P., E. Courcelle, D. I. Stuart, and F. Metoz. 1999. ESPript: analysis of multiple sequence alignments in PostScript. Bioinformatics. 15:305-308.
32. Baker, N. A., D. Sept, S. Joseph, M. J. Holst, and J. A. McCammon. 2001. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA. 98:10037-10041.