A Novel Member of the Protein Disulfide Oxidoreductase Family from Aeropyrum pernix K1: Structure, Function and Electrostatics

Journal of Molecular Biology

Volumn 362, Issue 4, 2006, Pages 743-752

  D'Ambrosio, Katia ^a   Pedone, Emilia ^a   Langella, Emma ^a   De Simone, Giuseppina ^a   Rossi, Mosè ^b   Pedone, Carlo ^a,c   Bartolucci, Simonetta ^c  

^a CNR   (Italy)

^b INSTITUTE OF PROTEIN BIOCHEMISTRY   (Italy)

^c UNIVERSITY OF NAPLES FEDERICO II   (Italy)

Author keywords

continuum electrostatics; crystal structure; protein disulfide oxidoreductase; thioredoxin fold

Indexed keywords

CYSTEINE; PROTEIN DISULFIDE REDUCTASE (GLUTATHIONE); THIOREDOXIN;

AEROPYRUM; AEROPYRUM PERNIX; ARCHAEBACTERIUM; ARTICLE; BACTERIUM; CATALYSIS; CONTROLLED STUDY; CYTOSOL; DISULFIDE BOND; ELECTRICITY; ENZYME ACTIVE SITE; ENZYME ACTIVITY; ENZYME CONFORMATION; EUKARYOTE; ISOMERIZATION; MOLECULAR WEIGHT; NONHUMAN; OXIDATION; PKA; PRIORITY JOURNAL; PROTEIN FAMILY; PROTEIN FOLDING; PROTEIN FUNCTION; PROTEIN STRUCTURE; REDUCTION; THERMOPHILIC BACTERIUM; THREE DIMENSIONAL IMAGING;

AEROPYRUM PERNIX; ARCHAEA; EUKARYOTA;

EID: 33748331151     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2006.07.038     Document Type: Article

References (45)

1. Raczko A.M., Bujnicki J.M., Pawlowski M., Godlewska R., Lewandowska M., and Jagusztyn-Krynicka E.K. Characterization of new DsbB-like thiol-oxidoreductases of Campylobacter jejuni and Helicobacter pylori and classification of the DsbB family based on phylogenomic, structural and functional criteria. Microbiology 151 (2005) 219-223
2. Kadokura H., Katzen F., and Beckwith J. Protein disulfide bond formation in prokaryotes. Annu. Rev. Biochem. 72 (2003) 111-135
3. Ferrari D.M., and Söling H.D. The protein disulphide-isomerase family: unraveling a string of folds. Biochem. J. 339 (1999) 1-10
4. Tian G., Xiang S., Noiva R., Lennarz W.J., and Schindelin H. The crystal structure of yeast protein disulfide isomerase suggests cooperativity between its active sites. Cell 124 (2006) 61-73
5. Ren B., Tibbelin G., De Pascale D., Rossi M., Bartolucci S., and Ladenstein R. A protein disulfide oxidoreductase from the archaeon Pyrococcus furiosus contains two thioredoxin fold units. Nature Struct. Biol. 5 (1998) 602-611
6. Pedone E., Ren B., Ladenstein R., Rossi M., and Bartolucci S. Functional properties of the protein disulfide oxidoreductase from the archaeon Pyrococcus furiosus. Eur. J. Biochem. 271 (2004) 3437-3448
7. Pedone E., D'Ambrosio K., De Simone G., Rossi M., Pedone C., and Bartolucci S. Insights on a new PDI-like family: structural and functional analysis of a protein disulfide oxidoreductase from the bacterium Aquifex aeolicus. J. Mol. Biol. 356 (2006) 155-164
8. Mallick P., Boutz D.R., Eisenberg D., and Yeates T.O. Genomic evidence that the intracellular proteins of archaeal microbes contain disulfide bonds. Proc. Natl Acad. Sci. USA 99 (2002) 9679-9684
9. Beeby M., O'Connor B.D., Ryttersgaard C., Boutz D.R., Perry L.J., and Yeates T.O. The genomics of disulfide bonding and protein stabilization in thermophiles. PLoS Biol. 3 (2005) 1549-1558
10. Ren B., Tibbelin G., De Pascale D., Rossi M., Bartolucci S., and Ladenstein R. Crystallization and preliminary X-ray structure analysis of a hyperthermostable thioltransferase from the archaeon Pyrococcus furiosus. J. Struct. Biol. 119 (1997) 1-5
11. Freedman R.B. Novel disulfide oxidoreductase in search of a function. Nature Struct. Biol. 5 (1998) 531-532
12. Bartolucci S., De Pascale D., and Rossi M. Protein disulfide oxidoreductase from Pyrococcus furiosus: biochemical properties. Methods Enzymol. 334 (2001) 62-73
13. Ren B., and Ladenstein R. Protein disulfide oxidoreductase from Pyrococcus furiosus: structural properties. Methods Enzymol. 334 (2001) 74-88
14. D'Ambrosio K., De Simone G., Pedone E., Rossi M., Bartolucci S., and Pedone C. Crystallization and preliminary X-ray diffraction studies of a protein disulfide oxidoreductase from Aquifex aeolicus. Acta Crystallog. sect. D 60 (2004) 2076-2077
15. D'Ambrosio K., De Simone G., Pedone E., Rossi M., Bartolucci S., and Pedone C. Crystallization and preliminary X-ray diffraction studies of a protein disulfide oxidoreductase from Aeropyrum pernix K1. Acta Crystallog. sect. F 61 (2005) 335-336
16. Axelsson K., Eriksson S., and Mannervik B. Purification and characterization of cytoplasmic thioltransferase (glutathione:disulfide oxidoreductase) from rat liver. Biochemistry 17 (1978) 2978-2984
17. Ruddock L.W., Hirst T.R., and Freedman R.B. pH-dependence of the dithiol-oxidizing activity of DsbA (a periplasmic protein thiol:disulphide oxidoreductase) and protein disulphide-isomerase: studies with a novel simple peptide substrate. Biochem. J. 315 (1996) 1000-1005
18. Brünger A.T., Adams P.D., Clore G.M., DeLano W.L., Gros P., Grosse-Kunsteleve R.W., et al. Crystallography and NMR system (CNS): a new software system for macromolecular structure determination. Acta Crystallog. sect. D 54 (1998) 905-921
19. Laskowsky R.A., MacArthur M.W., Moss D.S., and Thornton J.M. PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Crystallog. 26 (1993) 283-291
20. Thornton J.M. Disulphide bridges in globular proteins. J. Mol. Biol. 151 (1981) 261-287
21. as of ionizable groups in proteins: atomic detail from a continuum electrostatic model. Biochemistry 29 (1990) 10219-10225
22. Beroza P., Fredkin D.R., Okamura M.Y., and Feher G. Protonation of interacting residues in a protein by a Monte Carlo method: application to lysozyme and the photosynthetic reaction center of Rhodobacter sphaeroides. Proc. Natl Acad. Sci. USA 88 (1991) 5804-5808
23. Yang A.S., Gunner M.R., Sampogna R., Sharp K., and Honig B. Proteins: Struct. Funct. Genet. 15 (1993) 252-265
24. Antosiewicz J., McCammon J.A., and Gilson M.K. Prediction of pH-dependent properties of proteins. J. Mol. Biol. 238 (1994) 415-436
25. a calculations and molecular dynamics simulations. Proteins: Struct. Funct. Bioinf. 64 (2006) 167-177
26. a values of ionizable groups in bacteriorhodopsin. J. Mol. Biol. 224 (1992) 473-486
27. as in the active site of Escherichia coli thioredoxin. Biochemistry 37 (1998) 10298-10306
28. a and redox properties in the thioredoxin superfamily. Protein Sci. 13 (2004) 2744-2752
29. Grauschopf U., Winther J.R., Korber P., Zander T., Dallinger P., and Bardwell J.C.A. Why is DsbA such an oxidizing disulfide catalyst?. Cell 83 (1995) 947-955
30. Kortemme T., Darby N.J., and Creighton T.E. Electrostatic interactions in the active site of the N-terminal thioredoxin-like domain of protein disulfide isomerase. Biochemistry 35 (1996) 14503-14511
31. Carvalho A.T., Fernandes P.A., and Ramos M.J. Determination of the Delta pKa between the active site cysteines of thioredoxin and DsbA. J. Comput. Chem. 27 (2006) 966-975
32. as and oxidising power for DsbA mutants. FEBS Letters 385 (1996) 105-108
33. Gane P.J., Freedman R.B., and Warwicker J. A molecular model for the redox potential difference between thioredoxin and DsbA, based on electrostatics calculations. J. Mol. Biol. 249 (1995) 376-387
34. Guddat L.W., Bardwell J.C., and Martin J.L. Crystal structures of reduced and oxidized DsbA: investigation of domain motion and thiolate stabilization. Structure 6 (1998) 757-767
35. Weichsel A., Gasdaska J.R., Powis G., and Montfort W.R. Crystal structures of reduced, oxidized, and mutated human thioredoxins: evidence for a regulatory homodimer. Structure 4 (1996) 735-751
36. Lappi A., Lensink M., Alanen H., Salo K., Lobell M., Juffer A., and Ruddock L. A conserved arginine plays a role in the catalytic cycle of the protein disulphide isomerases. J. Mol. Biol. 335 (2004) 283-295
37. Wilkinson B., and Gilbert H.F. Protein disulfide isomerase. Biochim. Biophys. Acta 1699 (2004) 35-44
38. Smith P.K., Krohn R.I., Hermanson G.T., Mallia A.K., Gartner F.H., Provenzano M.D., et al. Measurement of protein using bicinchoninic acid. Anal. Biochem. 150 (1995) 76-85
39. Rabilloud T., Vuillard L., Gilly C., and Lawrence J.J. Silver-staining of proteins in polyacrylamide gels: a general overview. Cell. Mol. Biol. 40 (1994) 57-75
40. Holmgren A. Thioredoxin catalyzes the reduction of insulin disulfides by dithiothreitol and dihydrolipoamide. J .Biol. Chem. 254 (1979) 9627-9632
41. Lambert N., and Freedman R.B. Kinetics and specificity of homogeneous protein disulphide-isomerase in protein disulphide isomerization and in thiol-protein-disulphide oxidoreduction. Biochem. J. 213 (1983) 235-243
42. Kunitz M. A spectrophotometric method for the measurement of ribonuclease activity. J. Biol. Chem. 164 (1946) 563-568
43. Jones T.A., Zou J.Y., Cowan S.W., and Kjeldgaard M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallog. sect. A 47 (1991) 110-119
44. Sitkoff D., Sharp K.A., and Honig B. Accurate calculation of hydration free energies using macroscopic solvent models. J. Phys. Chem. 98 (1994) 1978-1988
45. Hutchinson E.G., and Thornton J.M. PROMOTIF - a program to identify and analyze structural motifs in proteins. Protein Sci. 5 (1996) 212-220