Crystal structure and structural stability of acylphosphatase from hyperthermophilic archaeon Pyrococcus horikoshii OT3

Proteins: Structure, Function and Genetics

Volumn 61, Issue 1, 2005, Pages 196-205

  Miyazono, Ken Ichi ^a   Sawano, Yoriko ^a   Tanokura, Masaru ^a  

^a UNIVERSITY OF TOKYO   (Japan)

Author keywords

Acylphosphatase; Archaea; Crystal structure determination; Denaturation; Structural stability

Indexed keywords

ACYLPHOSPHATASE; GUANIDINE; POTASSIUM ION; SODIUM ION;

ARCHAEBACTERIUM; ARTICLE; CRYSTAL STRUCTURE; DROSOPHILA MELANOGASTER; ENZYME ACTIVE SITE; HYDROGEN BOND; NONHUMAN; PRIORITY JOURNAL; PROTEIN DENATURATION; PROTEIN STABILITY; PROTEIN STRUCTURE; PYROCOCCUS HORIKOSHII; SITE DIRECTED MUTAGENESIS; STEREOCHEMISTRY; THERMOPHILIC BACTERIUM; THERMOSTABILITY;

ACID ANHYDRIDE HYDROLASES; AMINO ACID SEQUENCE; ANIMALS; BINDING SITES; CATTLE; CONSERVED SEQUENCE; CRYSTALLOGRAPHY, X-RAY; DROSOPHILA MELANOGASTER; ENZYME STABILITY; GUANIDINE; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; POTASSIUM; PROTEIN DENATURATION; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; PYROCOCCUS HORIKOSHII; SEQUENCE ALIGNMENT;

ARCHAEA; BOVINAE; EUKARYOTA; PYROCOCCUS HORIKOSHII;

EID: 24344505390     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.20535     Document Type: Article

References (41)

1. Jaenicke R, Bohm G. The stability of proteins in extreme environments. Curr Opin Struct Biol 1998;8:738-748.
2. Karshikoff A, Ladenstein R. Ion pairs and the thermotolerance of proteins from hyperthermophiles: a "traffic rule" for hot roads. Trends Biochem Sci 2001;26:550-556.
3. Yip KS, Britton KL, Stillman TJ, Lebbink J, de Vos WM, Robb FT, Vetriani C, Maeder D, Rice DW. Insights into the molecular basis of thermal stability from the analysis of ion-pair networks in the GluDH family. Eur J Biochem 1998;255:336-346.
4. Lebbink JH, Consalvi V, Chiaraluce R, Berndt KD, Ladenstein R. Structural and thermodynamic studies on a salt-bridge triad in the NADP-binding domain of glutamate dehydrogenase from Thermotoga maritima: cooperativity and electrostatic contribution to stability. Biochemistry 2002;41:15524-15535
5. Esposito L, Sica F, Raia CA, Giordano A, Rossi M, Mazzarella L, Zagari A. Crystal structure of the alcohol dehydrogenase from the hyperthermophilic archaeon Sulfolobus solfataricus at 1.85 Å resolution. J Mol Biol 2002;318:463-477.
6. Guy JE, Isupov MN, Littlechild JA. The structure of an alcohol dehydrogenase from the hyperthermophilic archaeon Aeropyrum pernix. J Mol Biol 2003;331:1041-1051.
7. Van Boxstael S, Cunin R, Khan S, Maes D. Aspartate transcarbamylase from the hyperthermophilic archaeon Pyrococcus abyssi: thermostability and 1.8 A" resolution crystal structure of the catalytic subunit complexed with the bisubstrate analogue N-phosphonacetyl-aspartate. J Mol Biol 2003;326:203-216.
8. Xiang T, Liu Q, Deacon AM, Koshy M, Kriksunov IA, Lei XG, Hao Q, Thiel DJ. Crystal structure of a heat-resilient phytase from Aspergillus fumigatus, carrying a phosphorylated histidine. J Mol Biol 2004;339:437-445.
9. Hennig M, Sterner R, Kirschner K, Jansonius JN. Crystal structure at 2.0 Å resolution of PRAI from the hyperthermophile Thermotoga maritima: possible determinants of protein stability. Biochemistry 1997;36:6009-6016.
10. Zhang X, Meining W, Fischer M, Bacher A, Ladenstein R. X-ray structure analysis and crystallographic refinement of lumazine synthase from the hyperthermophile Aquifex aeolicus at 1.6 Å resolution: determinants of thermostability revealed from structural comparisons. J Mol Biol 2001;306:1099-1114.
11. Knapp S, Kardinahl S, Hellgren N, Tibbelin G, Schafer G, Ladenstein R. Refined crystal structure of a superoxide dismutase from the hyperthermophilic archaeon Sulfolobus acidocaldarius at 2.2 Å resolution. J Mol Biol 1999;285:689-702.
12. Stefani M, Ramponi G. Acylphosphates phosphohydrolases. Life Chem Rep 1995;12:271-301.
13. Liguri G, Cecchi C, Pieri A, Raugei G, Vecchi M, Modesti A, Nassi P, Ramponi G. Expression of human acylphosphatase in Escherichia coli affects intracellular calcium levels. Biochem Mol Biol Int 1994;34:109-117.
14. Tadini-Buoninsegni F, Nassi P, Nediani C, Dolfi A, Guidelli R. Investigation of Na(+),K(+)-ATPase on a solid supported membrane: the role of acylphosphatase on the ion transport mechanism. Biochim Biophys Acta 2003;1611:70-80.
15. Mizuno Y, Ohba Y, Fujita H, Kanesaka Y, Tamura T, Shiokawa H. Distribution and classification of acylphosphatase isozymes. Arch Biochem Biophys 1990;278:437-443.
16. Pieri A, Magherini F, Liguri G, Raugei G, Taddei N, Bozzetti MP, Cecchi C, Ramponi G. Drosophila melanogaster acylphosphatase: a common ancestor for acylphosphatase isoenzymes of vertebrate species. FEBS Lett 1998;433:205-210.
17. Degl'Innocenti D, Ramazzotti M, Marzocchini R, Chiti F, Raugei G, Ramponi G. Characterization of a novel Drosophila melanogaster acylphosphatase. FEBS Lett 2003;535:171-174.
18. Pastore A, Saudek V, Ramponi G, Williams RJ. Three-dimensional structure of acylphosphatase. Refinement and structure analysis. J Mol Biol 1992;224:427-440.
19. Thunnissen MM, Taddei N, Liguri G, Ramponi G, Nordlund P. Crystal structure of common type acylphosphatase from bovine testis. Structure 1997;5:69-79.
20. Zuccotti S, Rosano C, Ramazzotti M, Degl'Innocenti D, Stefani M, Manao G, Bolognesi M. Three-dimensional structural characterization of a novel Drosophila melanogaster acylphosphatase. Acta Crystallogr D Biol Crystallogr 2004;60:1177-1179.
21. Taddei N, Chiti F, Paoli P, Fiaschi T, Bucciantini M, Stefani M, Dobson CM, Ramponi G. Thermodynamics and kinetics of folding of common-type acylphosphatase: comparison to the highly homologous muscle isoenzyme. Biochemistry 1999;38:2135-2142.
22. Taddei N, Buck M, Broadhurst RW, Stefani M, Ramponi G, Dobson CM. Equilibrium unfolding studies of horse muscle acylphosphatase. Eur J Biochem 1994;225:811-817.
23. Kawarabayasi Y, Sawada M, Horikawa H, Haikawa Y, Hino Y, Yamamoto S, Sekine M, Baba S, Kosugi H, Hosoyama A, et al. Complete sequence and gene organization of the genome of a hyper-thermophilic archaebacterium, Pyrococcus horikoshii OT3. DNA Res 1998;5:55-76.
24. Miyazono K, Kudo N, Tanokura M. Cloning, purification, crystallization and preliminary crystallographic analysis of acylphosphatase from Pyrococcus horikoshii OT3. Acta Crystallogr D Biol Crystallogr 2004;60:1135-1136.
25. Otwinowski Z, Minor W. Processing of X-ray diffraction data collected in oscillation mode. Meth Enzymol 1997;276:307-326.
26. Matthews BW. Solvent content of protein crystals. J Mol Biol 1968;33:491-497.
27. Collaborative Computational Project Number 4. The CCP4 suite: programs for protein crystallography. Acta Crystallogr D Biol Crystallogr 1994;50:760-763.
28. Brunger AT, Adams PD, Clore GM, DeLano WL, Gros P, Grosse-Kunstleve RW, Jiang JS, Kuszewski J, Nilges M, Pannu NS, et al. Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr D Biol Crystallogr 1998;54:905-921.
29. Lamzin VS, Wilson KS. Automated refinement for protein crystallography. Meth Enzymol 1997;277:269-305.
30. McRee DE. XtalView/Xfit-a versatile program for manipulating atomic coordinates and electron density. J Struct Biol 1999;125: 156-165.
31. Murshudov GN, Vagin AA, Dodson EJ. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr D Biol Crystallogr 1997;53:240-255.
32. Ramachandran GN, Sasisekharan V. Conformation of polypeptides and proteins. Adv Protein Chem 1968;23:283-438.
33. Laskowski RA, MacArthur MW, Moss DS, Thornton JM. PRO-CHECK: a program to check the stereochemistry quality of protein structures. J Appl Crystallog 1993;26:283-291.
34. Guex N, Peitsch MC. SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis 1997;18:2714-2723.
35. Gouet P, Courcelle E, Stuart DI, Metoz F. ESPript: analysis of multiple sequence alignments in PostScript. Bioinformatics 1999; 14:305-308.
36. Ho SN, Hunt HD, Horton RM, Pullen JK, Pease LR. Site-directed mutagenesis by overlap extension using the polymerase chain reaction. Gene 1989;77:51-59.
37. Su XD, Taddei N, Stefani M, Ramponi G, Nordlund P. The crystal structure of a low-molecular-weight phosphotyrosine protein phosphatase. Nature 1994;370:575-578.
38. Ramponi G, Stefani M. Structure and function of the low Mr phosphotyrosine protein phosphatases. Biochim Biophys Acta 1997;1341:137-156.
39. Via A, Ferre F, Brannetti B, Valencia A, Helmer-Citterich M. Three-dimensional view of the surface motif associated with the P-loop structure: cis and trans cases of convergent evolution. J Mol Biol 2000;303:455-456.
40. Rosano C, Zuccotti S, Bucciantini M, Stefani M, Ramponi G, Bolognesi M. Crystal structure and anion binding in the prokaryotic hydrogenase maturation factor HypF acylphosphatase-like domain. J Mol Biol 2002;321:785-796.
41. Taddei N, Magherini F, Chiti F, Bucciantini M, Raugei G, Stefani M, Ramponi G. C-terminal region contributes to muscle acylphosphatase three-dimensional structure stabilization. FEBS Lett 1996;384:172-176.