Origin of Exopolyphosphatase Processivity: Fusion of an ASKHA Phosphotransferase and a Cyclic Nucleotide Phosphodiesterase Homolog

Structure

Volumn 14, Issue 8, 2006, Pages 1263-1272

  Alvarado, Johnjeff ^a   Ghosh, Anita ^a   Janovitz, Tyler ^a   Jauregui, Andrew ^a   Hasson, Miriam S ^a   Sanders, David Avram ^a  

^a PURDUE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACETATE AND SUGAR KINASE HEAT SHOCK PROTEIN 70 ACTIN PHOSPHOTRANSFERASE; CYCLIC NUCLEOTIDE PHOSPHODIESTERASE; DIMER; ECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE; ESCHERICHIA COLI PROTEIN; EXOPOLYPHOSPHATASE; GUANOSINE 3' DIPHOSPHATE 5' TRIPHOSPHATE; PHOSPHATASE; PHOSPHOTRANSFERASE; POLYPHOSPHATE; SULFATE; UNCLASSIFIED DRUG;

AMINO TERMINAL SEQUENCE; ARTICLE; CHEMICAL MODIFICATION; CONTROLLED STUDY; ENZYME ACTIVE SITE; ENZYME ASSAY; ENZYME BINDING; ENZYME DEGRADATION; ENZYME MECHANISM; ENZYME STRUCTURE; ESCHERICHIA COLI; EUKARYOTE; GENE FUSION; NONHUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN HYDROLYSIS; PROTEIN PROCESSING; STRUCTURAL HOMOLOGY; X RAY CRYSTALLOGRAPHY;

2',3'-CYCLIC-NUCLEOTIDE PHOSPHODIESTERASES; BINDING SITES; CRYSTALLIZATION; CRYSTALLOGRAPHY, X-RAY; ESCHERICHIA COLI; MODELS, MOLECULAR; PHOSPHOPROTEIN PHOSPHATASE; PHOSPHOTRANSFERASES; PROTEIN STRUCTURE, TERTIARY;

ESCHERICHIA COLI; EUKARYOTA;

EID: 33746826565     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.str.2006.06.009     Document Type: Article

References (40)

1. Akiyama M., Crooke E., and Kornberg A. An exopolyphosphatase of Escherichia coli. The enzyme and its ppx gene in a polyphosphate operon. J. Biol. Chem. 268 (1993) 633-639
2. Aravind L., and Koonin E.V. The HD domain defines a new superfamily of metal-dependent phosphohydrolases. Trends Biochem. Sci. 23 (1998) 469-472
3. Artymiuk P.J., Grindley H.M., Kumar K., Rice D.W., and Willett P. Three-dimensional structural resemblance between the ribonuclease H and connection domains of HIV reverse transcriptase and the ATPase fold revealed using graph theoretical techniques. FEBS Lett. 324 (1993) 15-21
4. Bolesch D.G., and Keasling J.D. Polyphosphate binding and chain length recognition of Escherichia coli exopolyphosphatase. J. Biol. Chem. 275 (2000) 33814-33819
5. Brunger A.T., Adams P.D., Clore G.M., DeLano W.L., Gros P., Grosse-Kunstleve R.W., Jiang J.S., Kuszewski J., Nilges M., Pannu N.S., et al. Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr. D Biol. Crystallogr. 54 (1998) 905-921
6. Buss K.A., Cooper D.R., Ingram-Smith C., Ferry J.G., Sanders D.A., and Hasson M.S. Urkinase: structure of acetate kinase, a member of the ASKHA superfamily of phosphotransferases. J. Bacteriol. 183 (2001) 680-686
7. Cardona S.T., Chavez F.P., and Jerez C.A. The exopolyphosphatase gene from Sulfolobus solfataricus: characterization of the first gene found to be involved in polyphosphate metabolism in archaea. Appl. Environ. Microbiol. 68 (2002) 4812-4819
8. Chatterji D., and Ojha A.K. Revisiting the stringent response, ppGpp and starvation signaling. Curr. Opin. Microbiol. 4 (2001) 160-165
9. Cowtan K. Joint CCP4 and ESF-EACBM Newsletter on Protein Crystallography 31 (1994) 34-38
10. Divne C., Stahlberg J., Teeri T.T., and Jones T.A. High-resolution crystal structures reveal how a cellulose chain is bound in the 50 Å long tunnel of cellobiohydrolase I from Trichoderma reesei. J. Mol. Biol. 275 (1998) 309-325
11. Hara A., and Sy J. Guanosine 5′-triphosphate, 3′-diphosphate 5′-phosphohydrolase. Purification and substrate specificity. J. Biol. Chem. 258 (1983) 1678-1683
12. Hogg T., Mechold U., Malke H., Cashel M., and Hilgenfeld R. Conformational antagonism between opposing active sites in a bifunctional RelA/SpoT homolog modulates (p)ppGpp metabolism during the stringent response. Cell 117 (2004) 57-68
13. Holmes K.C., Ander C., and Valencia A. A new ATP-binding fold in actin, hexokinase and Hsc70. Trends Cell Biol. 3 (1993) 53-59
14. Huai Q., Colicelli J., and Ke H. The crystal structure of AMP-bound PDE4 suggests a mechanism for phosphodiesterase catalysis. Biochemistry 42 (2003) 13220-13226
15. Hurley J.H. The sugar kinase/heat shock protein 70/actin superfamily- implications of conserved structure for mechanism. Annu. Rev. Biophys. Biomol. Struct. 25 (1996) 137-162
16. Hurley J.H., Faber H.R., Worthylake D., Meadow N.D., Roseman S., Pettigrew D.W., and Remington S.J. Structure of the regulatory complex of Escherichia coli IIIGlc with glycerol kinase. Science 259 (1993) 673-677
17. Jones T.A., Zou J.Y., Cowtan S.W., and Kjeldgaard M. Improved methods for binding protein models in electron density maps and the local of errors in these models. Acta Crystallogr A 47 (1991) 110-119
18. Keasling J.D., Bertsch L., and Kornberg A. Guanosine pentaphosphate phosphohydrolase of Escherichia coli is a long- chain exopolyphosphatase. Proc. Natl. Acad. Sci. USA 90 (1993) 7029-7033
19. Koonin E.V. Yeast protein controlling inter-organelle communication is related to bacterial phosphatases containing the Hsp 70-type ATP-binding domain. Trends Biochem. Sci. 19 (1994) 156-157
20. Kornberg A., Rao N.N., and Ault-Riche D. Inorganic polyphosphate: a molecule of many functions. Annu. Rev. Biochem. 68 (1999) 89-125
21. Kraulis P.J. MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr. 24 (1991) 946-950
22. Kristensen O., Laurberg M., Liljas A., Kastrup J.S., and Gajhede M. Structural characterization of the stringent response related exopolyphosphatase/guanosine pentaphosphate phosphohydrolase protein family. Biochemistry 43 (2004) 8894-8900
23. Kuroda A., Murphy H., Cashel M., and Kornberg A. Guanosine tetra- and pentaphosphate promote accumulation of inorganic polyphosphate in Escherichia coli. J. Biol. Chem. 272 (1997) 21240-21243
24. Kuroda A., Nomura K., Ohtomo R., Kato J., Ikeda T., Takiguchi N., Ohtake H., and Kornberg A. Role of inorganic polyphosphate in promoting ribosomal protein degradation by the Lon protease in E. coli. Science 293 (2001) 705-708
25. Liao D.I., Reiss L., Turner I., and Dotson G. Structure of glycerol dehydratase reactivase: a new type of molecular chaperone. Structure 11 (2003) 109-119
26. Liao X., and Butow R.A. RTG1 and RTG2: two yeast genes required for a novel path of communication from mitochondria to the nucleus. Cell 72 (1993) 61-71
27. Locher K.P., Hans M., Yeh A.P., Schmid B., Buckel W., and Rees D.C. Crystal structure of the Acidaminococcus fermentans 2-hydroxyglutaryl-CoA dehydratase component A. J. Mol. Biol. 307 (2001) 297-308
28. Otwinowski Z., and Minor W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276 (1996) 307-326
29. Pierce M.M., Maddelein M.L., Roberts B.T., and Wickner R.B. A novel Rtg2p activity regulates nitrogen catabolism in yeast. Proc. Natl. Acad. Sci. USA 98 (2001) 13213-13218
30. Rao N.N., and Kornberg A. Inorganic polyphosphate supports resistance and survival of stationary-phase Escherichia coli. J. Bacteriol. 178 (1996) 1394-1400
31. Rao N.N., Liu S., and Kornberg A. Inorganic polyphosphate in Escherichia coli: the phosphate regulon and the stringent response. J. Bacteriol. 180 (1998) 2186-2193
32. Reizer J., Reizer A., Saier Jr. M.H., Bork P., and Sander C. Exopolyphosphate phosphatase and guanosine pentaphosphate phosphatase belong to the sugar kinase/actin/hsp 70 superfamily. Trends Biochem. Sci. 18 (1993) 247-248
33. Terwilliger T.C. Automated structure solution, density modification and model building. Acta Crystallogr. D Biol. Crystallogr. 58 (2002) 1937-1940
34. van den Ent F., and Lowe J. Crystal structure of the cell division protein FtsA from Thermotoga maritima. EMBO J. 19 (2000) 5300-5307
35. van den Ent F., Amos L.A., and Lowe J. Prokaryotic origin of the actin cytoskeleton. Nature 413 (2001) 39-44
36. Webb M.R. A continuous spectrophotometric assay for inorganic phosphate and for measuring phosphate release kinetics in biological systems. Proc. Natl. Acad. Sci. USA 89 (1992) 4884-4887
37. Winn M.D., Isupov M.N., and Murshudov G.N. Use of TLS parameters to model anisotropic displacements in macromolecular refinement. Acta Crystallogr. D Biol. Crystallogr. 57 (2001) 122-133
38. Wolf Y.I., Aravind L., Grishin N.V., and Koonin E.V. Evolution of aminoacyl-tRNA synthetases-analysis of unique domain architectures and phylogenetic trees reveals a complex history of horizontal gene transfer events. Genome Res. 9 (1999) 689-710
39. Xu R.X., Hassell A.M., Vanderwall D., Lambert M.H., Holmes W.D., Luther M.A., Rocque W.J., Milburn M.V., Zhao Y., Ke H., and Nolte R.T. Atomic structure of PDE4: insights into phosphodiesterase mechanism and specificity. Science 288 (2000) 1822-1825
40. Yang F., Hicks-Berger C.A., Smith T.M., and Kirley T.L. Site-directed mutagenesis of human nucleoside triphosphate diphosphohydrolase 3: the importance of residues in the apyrase conserved regions. Biochemistry 40 (2001) 3943-3950