Deamidation in proteins: The crystal structure of bovine pancreatic ribonuclease with an isoaspartyl residue at position 67(488 views) Capasso S, Di Donato A, Esposito L, Sica F, Sorrentino G, Vitagliano L, Zagari A, Mazzarella L
Affiliations: Ctro. di Stud. di Biocristallografia, CNR, Univ. di Napoli Federico II, Via Mezzocannone 4, I-80134 Napoli, Italy
Dipto. di Chim. Organica e Biologica, Univ. di Napoli Federico II, Via Mezzocannone 16, I-80134 Napoli, Italy
References: Artigues, A., Farrant, H., Schirch, V., Cytosolic serine hydroxymethyltransferase. Deamidation of asparaginyl residues and degradation in Xenopus laevis oocytes (1993) J. Biol. Chem., 268, pp. 13784-1379
Bischoff, R., Lepage, P., Jaquinod, M., Cauet, G., Acker-Klein, M., Clesse, D., Laporte, M., Roitsch, C., Sequencespecific deamidation: Isolation and biochemical characterization of succinimide intermediates of recombinant hirudin (1993) Biochemistry, 32, pp. 725-734
Brennan, T.V., Clarke, S., Spontaneous degradation of polypeptides at aspartyl and asparaginyl residues: Effect of the solvent dielectric (1993) Protein Sci., 2, pp. 331-338
Brünger, A.T., (1992) X-PLOR V3.1 User's Guide. A System for X-ray Crystallography and NMR, , Yale University New Haven
Capasso, S., Mazzarella, L., Sica, F., Zagari, A., Deamidation via cyclic imide in asparaginyl peptides (1989) Pept. Res., 2, pp. 195-200
Capasso, S., Kirby, A.J., Salvadori, S., Sica, F., Zagari, A., Kinetics and mechanism of the reversible isomerization of aspartic acid residues in tetrapeptides (1995) J. Chem. Soc. Perkin Trans. 2, pp. 437-442
Di Donato, A., Galletti, P., D'Alessio, G., Selective deamidation and enzymatic methylation of seminal ribonuclease (1986) Biochemistry, 25, pp. 8361-8368
Di Donato, A., Ciardiello, M.A., De Nigris, M., Piccoli, R., Mazzarella, L., D'Alessio, G., Selective deamidation of ribonuclease A. Isolation and characterization of the resulting isoaspartyl and aspartyl derivatives (1993) J. Biol. Chem., 268, pp. 4745-4751
Engh, R.A., Huber, R., Accurate bond and angle parameters of X-ray protein structure refinement (1991) Acta Crystallog. Sect. A, 47, pp. 392-400
Friedman, A.R., Ichhpurani, A.K., Brown, D.M., Hillman, R.M., Krabill, L.F., Martin, R.A., Zurcher-Neely, H.A., Guido, D.M., Degradation of growth hormone releasing factor analogs in neutral aqueous solution is related to deamidation of asparagine residues (1991) Int. J. Pept. Protein Res., 37, pp. 14-21
Geiger, T., Clarke, S., Deamidation, isomerization, and racemization at asparaginyl and aspartyl residues in peptides: Succinimide-linked reactions that contribute to protein degradation (1987) J. Biol. Chem., 262, pp. 785-794
Hendrickson, W.A., Stereochemically restrained refinement of macromolecular structures (1985) Methods Enzymol., 115, pp. 252-270
Jones, T.A., A graphics model building and refinement system for macromolecules (1978) J. Appl. Crystallog., 11, pp. 268-272
Kossiakoff, A.A., Tertiary structure is a principal determinant to protein deamidation (1988) Science, 240, pp. 191-194
Kraulis, P.J., MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures (1991) J. Appl. Crystallog., 24, pp. 946-950
Laskowski, R.A., McArthur, M.W., Moss, D.S., Thorton, J.M., PROCHECK: A program to check the stereochemical quality of protein structures (1993) J. Appl. Crystallog., 26, pp. 282-291
Luzzati, V., Traitement statistique des erreurs dans la determination des structures cristalline (1952) Acta Crystallog., 5, pp. 802-810
Matthews, B.W., Solvent content of protein crystals (1968) J. Mol. Biol., 33, pp. 491-497
Meinwald, Y.C., Stimson, E.R., Scheraga, H.A., Deamidation of the asparaginyl-glycyl sequence (1986) Int. J. Pept. Protein Res., 28, pp. 79-84
Montelione, G.T., Scheraga, H.A., Formation of local structures in protein folding (1989) Acc. Chem. Res., 22, pp. 70-76
Patel, K., Borchardt, R.T., Chemical pathways of peptide degradation. II. Kinetics of deamidation of an asparaginyl residue in model hexapeptide (1990) Pharm. Res., 7, pp. 703-711
Tyler-Cross, R., Schirch, V., Effects of amino acid sequence, buffers, and ionic strength on the rate and mechanism of deamidation of asparagine residues in small peptides (1991) J. Biol. Chem., 266, pp. 22549-22556
Wlodawer, A., Sjölin, L., Structure of ribonuclease A: Results of joint neutron and X-ray refinement at 2.0 A° resolution (1983) Biochemistry, 22, pp. 2720-2728
Wright, H.T., Non-enzymatic deamidation of asparaginyl and glutaminyl residues in proteins (1991) Crit. Rev. Biochem. Mol. Biol., 26, pp. 1-52
Brennan, T. V., Clarke, S., Spontaneous degradation of polypeptides at aspartyl and asparaginyl residues: Effect of the solvent dielectric (1993) Protein Sci., 2, pp. 331-338
Br nger, A. T., (1992) X-PLOR V3. 1 User's Guide. A System for X-ray Crystallography and NMR, , Yale University New Haven
Engh, R. A., Huber, R., Accurate bond and angle parameters of X-ray protein structure refinement (1991) Acta Crystallog. Sect. A, 47, pp. 392-400
Friedman, A. R., Ichhpurani, A. K., Brown, D. M., Hillman, R. M., Krabill, L. F., Martin, R. A., Zurcher-Neely, H. A., Guido, D. M., Degradation of growth hormone releasing factor analogs in neutral aqueous solution is related to deamidation of asparagine residues (1991) Int. J. Pept. Protein Res., 37, pp. 14-21
Hendrickson, W. A., Stereochemically restrained refinement of macromolecular structures (1985) Methods Enzymol., 115, pp. 252-270
Jones, T. A., A graphics model building and refinement system for macromolecules (1978) J. Appl. Crystallog., 11, pp. 268-272
Kossiakoff, A. A., Tertiary structure is a principal determinant to protein deamidation (1988) Science, 240, pp. 191-194
Kraulis, P. J., MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures (1991) J. Appl. Crystallog., 24, pp. 946-950
Laskowski, R. A., McArthur, M. W., Moss, D. S., Thorton, J. M., PROCHECK: A program to check the stereochemical quality of protein structures (1993) J. Appl. Crystallog., 26, pp. 282-291
Matthews, B. W., Solvent content of protein crystals (1968) J. Mol. Biol., 33, pp. 491-497
Meinwald, Y. C., Stimson, E. R., Scheraga, H. A., Deamidation of the asparaginyl-glycyl sequence (1986) Int. J. Pept. Protein Res., 28, pp. 79-84
Montelione, G. T., Scheraga, H. A., Formation of local structures in protein folding (1989) Acc. Chem. Res., 22, pp. 70-76
Wlodawer, A., Sj lin, L., Structure of ribonuclease A: Results of joint neutron and X-ray refinement at 2. 0 A resolution (1983) Biochemistry, 22, pp. 2720-2728
Wright, H. T., Non-enzymatic deamidation of asparaginyl and glutaminyl residues in proteins (1991) Crit. Rev. Biochem. Mol. Biol., 26, pp. 1-52
Deamidation in proteins: The crystal structure of bovine pancreatic ribonuclease with an isoaspartyl residue at position 67
The non-enzymatic deamidation of asparagine residues in proteins is a widely occurring reaction, both in vivo and in vitro. Although the importance of this process is commonly recognised, only little structural information is available on it. In order to evaluate the structural effects of this reaction in proteins, we have determined the crystal structure of a ribonuclease A derivative in which asparagine 67 has been replaced by an isoaspartyl residue, as a consequence of an in vitro deamidation reaction. The overall structure of the model, refined to a crystallographic X-factor of 0.159 at a resolution of 1.9 Å, is very similar to that of the native protein, but considerable deviations are observed in the region delimited by the disulphide bridge 65-72. In particular, the insertion of an extra methylene group in the main chain at residue 67 breaks up the hydrogen bond network that makes this region rather rigid in ribonuclease A. On the basis of the structure observed, some of the slightly but significantly different properties of this deamidated derivative, with respect to the native enzyme, can be explained.
Deamidation in proteins: The crystal structure of bovine pancreatic ribonuclease with an isoaspartyl residue at position 67