A novel member of the protein disulfide oxidoreductase family from Aeropyrum pernix K1: Structure, function and electrostatics(475 views) D'Ambrosio K, Pedone E, Langella E, De Simone G, Rossi M, Pedone C, Bartolucci S
Keywords: Continuum Electrostatics, Crystal Structure, Pka Computation, Protein Disulfide Oxidoreductase, Thioredoxin Fold, Cysteine, Protein Disulfide Reductase (glutathione), Aeropyrum, Aeropyrum Pernix, Archaebacterium, Article, Catalysis, Controlled Study, Cytosol, Disulfide Bond, Electricity, Enzyme Active Site, Enzyme Activity, Enzyme Conformation, Eukaryote, Isomerization, Molecular Weight, Nonhuman, Oxidation, Priority Journal, Protein Family, Protein Folding, Protein Function, Protein Structure, Reduction, Thermophilic Bacterium, Three Dimensional Imaging, Animals, Binding Sites, Cattle, Crystallography, X-Ray, Hydrogen-Ion Concentration, Insulin, Oxidation-Reduction, Protein Disulfide-Isomerase, Secondary, Static Electricity, Structure-Activity Relationship,
Affiliations: *** IBB - CNR ***
Istituto di Biostrutture e Bioimmagini, C.N.R., Napoli, Italy
Istituto di Biochimica delle Proteine, C.N.R., Napoli, Italy
Dipartimento delle Scienze Biologiche, Università degli Studi di Napoli Federico II, Napoli, Italy
Dipartimento di Biologia Strutturale e Funzionale, Università degli Studi di Napoli Federico II, Napoli, Italy
References: Raczko, A.M., Bujnicki, J.M., Pawlowski, M., Godlewska, R., Lewandowska, M., 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 (2005) Microbiology, 151, pp. 219-22
Kadokura, H., Katzen, F., Beckwith, J., Protein disulfide bond formation in prokaryotes (2003) Annu. Rev. Biochem., 72, pp. 111-135
Ferrari, D.M., Söling, H.D., The protein disulphide-isomerase family: unraveling a string of folds (1999) Biochem. J., 339, pp. 1-10
Tian, G., Xiang, S., Noiva, R., Lennarz, W.J., Schindelin, H., The crystal structure of yeast protein disulfide isomerase suggests cooperativity between its active sites (2006) Cell, 124, pp. 61-73
Ren, B., Tibbelin, G., De Pascale, D., Rossi, M., Bartolucci, S., Ladenstein, R., A protein disulfide oxidoreductase from the archaeon Pyrococcus furiosus contains two thioredoxin fold units (1998) Nature Struct. Biol., 5, pp. 602-611
Pedone, E., Ren, B., Ladenstein, R., Rossi, M., Bartolucci, S., Functional properties of the protein disulfide oxidoreductase from the archaeon Pyrococcus furiosus (2004) Eur. J. Biochem., 271, pp. 3437-3448
Pedone, E., D'Ambrosio, K., De Simone, G., Rossi, M., Pedone, C., Bartolucci, S., Insights on a new PDI-like family: structural and functional analysis of a protein disulfide oxidoreductase from the bacterium Aquifex aeolicus (2006) J. Mol. Biol., 356, pp. 155-164
Mallick, P., Boutz, D.R., Eisenberg, D., Yeates, T.O., Genomic evidence that the intracellular proteins of archaeal microbes contain disulfide bonds (2002) Proc. Natl Acad. Sci. USA, 99, pp. 9679-9684
Beeby, M., O'Connor, B.D., Ryttersgaard, C., Boutz, D.R., Perry, L.J., Yeates, T.O., The genomics of disulfide bonding and protein stabilization in thermophiles (2005) PLoS Biol., 3, pp. 1549-1558
Freedman, R.B., Novel disulfide oxidoreductase in search of a function (1998) Nature Struct. Biol., 5, pp. 531-532
Bartolucci, S., De Pascale, D., Rossi, M., Protein disulfide oxidoreductase from Pyrococcus furiosus: biochemical properties (2001) Methods Enzymol., 334, pp. 62-73
Axelsson, K., Eriksson, S., Mannervik, B., Purification and characterization of cytoplasmic thioltransferase (glutathione:disulfide oxidoreductase) from rat liver (1978) Biochemistry, 17, pp. 2978-2984
Ruddock, L.W., Hirst, T.R., 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 (1996) Biochem. J., 315, pp. 1000-1005
Brünger, A.T., Adams, P.D., Clore, G.M., DeLano, W.L., Gros, P., Grosse-Kunsteleve, R.W., Crystallography and NMR system (CNS): a new software system for macromolecular structure determination (1998) Acta Crystallog. sect. D, 54, pp. 905-921
Laskowsky, R.A., MacArthur, M.W., Moss, D.S., Thornton, J.M., PROCHECK: a program to check the stereochemical quality of protein structures (1993) J. Appl. Crystallog., 26, pp. 283-291
Thornton, J.M., Disulphide bridges in globular proteins (1981) J. Mol. Biol., 151, pp. 261-287
Bashford, D., Karplus, M., pKas of ionizable groups in proteins: atomic detail from a continuum electrostatic model (1990) Biochemistry, 29, pp. 10219-10225
Beroza, P., Fredkin, D.R., Okamura, M.Y., 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 (1991) Proc. Natl Acad. Sci. USA, 88, pp. 5804-5808
Yang, A.S., Gunner, M.R., Sampogna, R., Sharp, K., Honig, B., (1993) Proteins: Struct. Funct. Genet., 15, pp. 252-265
Antosiewicz, J., McCammon, J.A., Gilson, M.K., Prediction of pH-dependent properties of proteins (1994) J. Mol. Biol., 238, pp. 415-436
Langella, E., Improta, R., Crescenzi, O., Barone, V., Assessing the acid-base and conformational properties of histidine residues in human prion protein (125-228) by means of pKa calculations and molecular dynamics simulations (2006) Proteins: Struct. Funct. Bioinf., 64, pp. 167-177
Bashford, D., Gerwert, K., Electrostatic calculations of the pKa values of ionizable groups in bacteriorhodopsin (1992) J. Mol. Biol., 224, pp. 473-486
Dillet, V., Dyson, H.J., Bashford, D., Calculations of electrostatic interactions and pKas in the active site of Escherichia coli thioredoxin (1998) Biochemistry, 37, pp. 10298-10306
Moutevelis, E., Warwickwe, J., Prediction of pKa and redox properties in the thioredoxin superfamily (2004) Protein Sci., 13, pp. 2744-2752
Grauschopf, U., Winther, J.R., Korber, P., Zander, T., Dallinger, P., Bardwell, J.C.A., Why is DsbA such an oxidizing disulfide catalyst? (1995) Cell, 83, pp. 947-955
Kortemme, T., Darby, N.J., Creighton, T.E., Electrostatic interactions in the active site of the N-terminal thioredoxin-like domain of protein disulfide isomerase (1996) Biochemistry, 35, pp. 14503-14511
Carvalho, A.T., Fernandes, P.A., Ramos, M.J., Determination of the Delta pKa between the active site cysteines of thioredoxin and DsbA (2006) J. Comput. Chem., 27, pp. 966-975
Warwicker, J., Gane, P.J., Calculation of Cys 30 delta pKas and oxidising power for DsbA mutants (1996) FEBS Letters, 385, pp. 105-108
Gane, P.J., Freedman, R.B., Warwicker, J., A molecular model for the redox potential difference between thioredoxin and DsbA, based on electrostatics calculations (1995) J. Mol. Biol., 249, pp. 376-387
Guddat, L.W., Bardwell, J.C., Martin, J.L., Crystal structures of reduced and oxidized DsbA: investigation of domain motion and thiolate stabilization (1998) Structure, 6, pp. 757-767
Weichsel, A., Gasdaska, J.R., Powis, G., Montfort, W.R., Crystal structures of reduced, oxidized, and mutated human thioredoxins: evidence for a regulatory homodimer (1996) Structure, 4, pp. 735-751
Lappi, A., Lensink, M., Alanen, H., Salo, K., Lobell, M., Juffer, A., Ruddock, L., A conserved arginine plays a role in the catalytic cycle of the protein disulphide isomerases (2004) J. Mol. Biol., 335, pp. 283-295
Wilkinson, B., Gilbert, H.F., Protein disulfide isomerase (2004) Biochim. Biophys. Acta, 1699, pp. 35-44
Smith, P.K., Krohn, R.I., Hermanson, G.T., Mallia, A.K., Gartner, F.H., Provenzano, M.D., Measurement of protein using bicinchoninic acid (1995) Anal. Biochem., 150, pp. 76-85
Rabilloud, T., Vuillard, L., Gilly, C., Lawrence, J.J., Silver-staining of proteins in polyacrylamide gels: a general overview (1994) Cell. Mol. Biol., 40, pp. 57-75
Holmgren, A., Thioredoxin catalyzes the reduction of insulin disulfides by dithiothreitol and dihydrolipoamide (1979) J .Biol. Chem., 254, pp. 9627-9632
Lambert, N., Freedman, R.B., Kinetics and specificity of homogeneous protein disulphide-isomerase in protein disulphide isomerization and in thiol-protein-disulphide oxidoreduction (1983) Biochem. J., 213, pp. 235-243
Kunitz, M., A spectrophotometric method for the measurement of ribonuclease activity (1946) J. Biol. Chem., 164, pp. 563-568
Jones, T.A., Zou, J.Y., Cowan, S.W., Kjeldgaard, M., Improved methods for building protein models in electron density maps and the location of errors in these models (1991) Acta Crystallog. sect. A, 47, pp. 110-119
Sitkoff, D., Sharp, K.A., Honig, B., Accurate calculation of hydration free energies using macroscopic solvent models (1994) J. Phys. Chem., 98, pp. 1978-1988
Hutchinson, E.G., Thornton, J.M., PROMOTIF - a program to identify and analyze structural motifs in proteins (1996) Protein Sci., 5, pp. 212-220
Raczko, A. M., Bujnicki, J. M., Pawlowski, M., Godlewska, R., Lewandowska, M., 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 (2005) Microbiology, 151, pp. 219-22
Ferrari, D. M., S ling, H. D., The protein disulphide-isomerase family: unraveling a string of folds (1999) Biochem. J., 339, pp. 1-10
Freedman, R. B., Novel disulfide oxidoreductase in search of a function (1998) Nature Struct. Biol., 5, pp. 531-532
Ruddock, L. W., Hirst, T. R., 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 (1996) Biochem. J., 315, pp. 1000-1005
Br nger, A. T., Adams, P. D., Clore, G. M., DeLano, W. L., Gros, P., Grosse-Kunsteleve, R. W., Crystallography and NMR system (CNS): a new software system for macromolecular structure determination (1998) Acta Crystallog. sect. D, 54, pp. 905-921
Laskowsky, R. A., MacArthur, M. W., Moss, D. S., Thornton, J. M., PROCHECK: a program to check the stereochemical quality of protein structures (1993) J. Appl. Crystallog., 26, pp. 283-291
Thornton, J. M., Disulphide bridges in globular proteins (1981) J. Mol. Biol., 151, pp. 261-287
Yang, A. S., Gunner, M. R., Sampogna, R., Sharp, K., Honig, B., (1993) Proteins: Struct. Funct. Genet., 15, pp. 252-265
Carvalho, A. T., Fernandes, P. A., Ramos, M. J., Determination of the Delta pKa between the active site cysteines of thioredoxin and DsbA (2006) J. Comput. Chem., 27, pp. 966-975
Gane, P. J., Freedman, R. B., Warwicker, J., A molecular model for the redox potential difference between thioredoxin and DsbA, based on electrostatics calculations (1995) J. Mol. Biol., 249, pp. 376-387
Guddat, L. W., Bardwell, J. C., Martin, J. L., Crystal structures of reduced and oxidized DsbA: investigation of domain motion and thiolate stabilization (1998) Structure, 6, pp. 757-767
Smith, P. K., Krohn, R. I., Hermanson, G. T., Mallia, A. K., Gartner, F. H., Provenzano, M. D., Measurement of protein using bicinchoninic acid (1995) Anal. Biochem., 150, pp. 76-85
Jones, T. A., Zou, J. Y., Cowan, S. W., Kjeldgaard, M., Improved methods for building protein models in electron density maps and the location of errors in these models (1991) Acta Crystallog. sect. A, 47, pp. 110-119
Hutchinson, E. G., Thornton, J. M., PROMOTIF - a program to identify and analyze structural motifs in proteins (1996) Protein Sci., 5, pp. 212-220
A novel member of the protein disulfide oxidoreductase family from Aeropyrum pernix K1: Structure, function and electrostatics