Succinimide and isoaspartate residues in the crystal structures of hen egg-white lysozyme complexed with tri-N-acetylchitotriose

Journal of Molecular Biology

Volumn 278, Issue 1, 1998, Pages 231-238

  Noguchi, Shuji ^a   Miyawaki, Kazuki ^a   Satow, Yoshinori ^a  

^a TOKYO UNIVERSITY OF SCIENCE   (Japan)

Author keywords

Crystal structure; Hen egg white lysozyme; Isoaspartate; Post translational modification; Succinimide

Indexed keywords

ASPARTIC ACID; EGG WHITE; LIGAND; LYSOZYME; SUCCINIMIDE; TRI N ACETYLCHITOTRIOSE; TRIOSE; UNCLASSIFIED DRUG;

ARTICLE; COMPLEX FORMATION; CRYSTAL STRUCTURE; HYDROGEN BOND; ISOMERISM; NONHUMAN; PH; PRIORITY JOURNAL; PROTEIN PROCESSING;

EID: 0032562736     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1998.1674     Document Type: Article

References (37)

1. Bernstein F.C., Koetzle T.F., Williams G.J.B., Meyer E.F. Jr, Brice M.D., Rodgers J.R., Kennard O., Shimanouchi T., Tasumi M. The Protein Data Bank a computer-based archival file for macromolecular structures. J. Mol. Biol. 112:1977;535-542
2. Bhat T.N., Bentley G.A., Boulot G., Green M.I., Tello D., Dall'acqua W., Sopuchon H., Schwarz F.P., Mariuzza R.A., Poljak R.J. Bound water molecules and conformational stabilization help mediate an antigen-antibody association. Proc. Natl Acad. Sci. USA. 91:1994;1089-1093
3. Bischoff R., Lepage P., Jaquinod M., Cauet G., Acker-Klein M., Clesse D., Laporte M., Bayol A., van Dorsselaer A., Roitsch C. Sequence-specific deamidation Isolation and biochemical characterization of succinimide intermediates of recombinant hirudin. Biochemistry. 32:1993;725-734
4. Braden B.C., Souchon H., Eisele J.-L., Bentley G.A., Bhat T.N., Navaza J., Poljak R.J. Three-dimensional structures of the free and the antigen-complexed Fab form monoclonal anti-lysozyme antibody D44.1. J. Mol. Biol. 243:1994;767-781
5. Brennan T.V., Clarke S. Effect of adjacent histidine and cysteine residues on the spontaneous degradation of asparaginyl- and aspartyl-containing peptides. Int. J. Pept. Protein Res. 45:1995;. 547-533
6. Brennan T.V., Anderson J.W., Jia Z., Waygood E.B., Clarke S. Repair of spontaneously deamidated HPr phosphocarrier protein catalyzed by the L -isoaspartate-(D -aspartate) O -Methyltransferase. J. Biol. Chem. 269:1994;24586-24595
7. Brünger A.T. X-PLOR Version 3. 1 A System for X-ray Crystallography and NMR. 1992;Yale University Press, New Haven
8. Cacia J., Keck R., Presta L.G., Frenz J. Isomerization of an aspartic acid residue in the complementarity-determining regions of a recombinant antibody to human IgE identification and effect on binding affinity. Biochemistry. 35:1996;1897-1903
9. Capasso S., Mazzarella L., Sica F., Zagari A. Solid-state conformations of aminosuccinyl peptides crystal structure of tert -Butyloxycarbonyl- L -leucyl- L -aminosuccinyl- L -phenylalaninamide. Biopolymers. 28:1989;139-147
10. Capasso S., Mazzarella L., Sica F., Zagari A. Solid-state conformations of aminosuccinyl peptides structure of tert -butyloxycarbonyl- L -prolyl- L -aminosuccinyl-glycyl- L -alanine methyl ester (Boc- L -Pro- L -Asu-Gly- L -Ala-OMe). A case of pseudo-translational symmetry. Acta Crystallog. sect. B. 48:1992;285-290
11. Capasso S., Di Donato A., Esposito L., Sica F., Sorrentino G., Vitagliano L., Zagari A., Mazzarella L. Deamidation in proteins the crystal structure of bovine pancreatic ribonuclease with an isoaspartyl residue at position 67. J. Mol. Biol. 257:1996;492-496
12. Davies D.R., Cohen G.H. Interactions of protein antigens with antibodies. Proc. Natl Acad. Sci. USA. 93:1996;7-12
13. Fischmann T.O., Bentley B.A., Bhat T.N., Boulot G., Mariuzza R.A., Phillips S.E.V., Tello D., Poljak R.J. Crystallographic refinement of the three-dimensional structure of the Fab D1.3-lysozyme complex at 2.5 Å resolution. J. Biol. Chem. 266:1991;12915-12920
14. Fujii N., Satoh K., Harada K., Ishibashi Y. Simultaneous stereoinversion and isomerization at specific aspartic acid residues in αA-crystallin from human lens. J. Biochem. 116:1994;663-669
15. Fujii N., Ishibashi Y., Satoh K., Fujino M., Harada K. Simultaneous racemization and isomerization at specific aspartic acid residues in αB-crystallin from the aged human lens. Biochim. Biophys. Acta. 1204:1994;157-163
16. Geiger T., Clarke S. Deamidation, isomerization, and racemization at asparaginyl and aspartyl residues in peptides Succinimide-linked reactions that contribute to protein degradation. J. Biol. Chem. 262:1987;785-794
17. Görbitz C.H. Crystal and molecular structures of the isomeric dipeptides α- L -aspartyl- L -alanine and β- L -aspartyl- L -alanine. Acta Chem. Scand. B 41:1987;679-685
18. Jiang J.-S., Brünger A.T. Protein hydration observed by X-ray diffraction. J. Mol. Biol. 243:1994;100-115
19. Johnson B.A., Shirokawa J.M., Geddens J.W., Choi B.H., Kim R.C., Aswad D.W. Protein L -isoaspartyl methyltransferase in post-mortem brains of aged humans. Neurobiol. Aging. 12:1991;19-24
20. Kraulis P.J. MOLSCRIPT A program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallog. 24:1991;946-950
21. Kurinov I.V., Harrison R.W. The influence of temperature on lysozyme crystals. Structure and dynamics of protein and water. Acta Crystallog. sect. D. 51:1995;98-109
22. Luzzati V. Traitement statistique des erreurs dans la determination des structures cristallines. Acta Crystallog. 5:1952;802-810
23. Maenaka K., Matsushima M., Song H., Sunada F., Watanabe K., Kumagai I. Dissection of protein-carbohydrate interactions in mutant hen egg-white lysozyme complexes and their hydrolytic activity. J. Mol. Biol. 247:1995;281-293
24. Miyawaki K., Noguchi S., Harada S., Satow Y. Crystallography of succinimide hen egg-white lysozyme at low temperatures. J. Cryst. Growth. 168:1996;292-296
25. Najbauer J., Orpiszewski J., Aswad D.W. Molecular aging of tubulin Accumulation of isoaspartyl sites in vitro and in vivo. Biochemistry. 35:1996;5183-5190
26. 2at 1.8 Å resolution. Biochemistry. 34:1995;15583-15591
27. Oliyai C., Borchardt R.T. Chemical pathways of peptide degradation. VI. Effect of the primary sequence on the pathways of degradation of aspartyl residues in model hexapeptides. Pharm. Res. 11:1994;751-758
28. Otwinowski Z. Oscillation data reduction program. Proceedings of the CCP4 Study Weekend. 1993;56-62 SERC Daresbury Laboratory, Warrington, U.K
29. Paranandi M.V., Aswad D.W. Spontaneous alterations in the covalent structure of synapsin I during in vitro aging. Biochem. Biophys. Res. Commun. 212:1995;442-448
30. Roher A.E., Lowenson J.D., Clarke S., Wolkow C., Wang R., Cotter R.J., Reardon I.M., Zürcher-Neely H.A., Heinrikson R.L., Ball M.J., Greenberg B.D. Structural alterations in the peptide backbone of β-amyloid core protein may account for its deposition and stability in Alzheimer's disease. J. Biol. Chem. 268:1993;3072-3083
31. Roussel A., Cambillau C. TURBO-FRODO version 1.1 release b. 1990;Faculté de Medecine Nord, Marseille, France
32. Shao Y., Kent S.B.H. Protein splicing occurrence, mechanisms and related phenomena. Chem. Biol. 4:1997;187-194
33. Shao Y., Xu M.Q., Paulus H. Protein splicing Characterization of the aminosuccinimide residues at the carboxyl terminus of the excised intervening sequence. Biochemistry. 34:1995;10844-10850
34. Shirasawa T., Endoh R., Zeng Y.X., Sakamoto K., Mori H. Protein L -isoaspartyl methyltransferase Developmentally regulated gene expression and protein localization in the central nervous system of aged rat. Neurosci. Letters. 188:1995;37-40
35. Tomizawa H., Yamada H., Ueda T., Imoto T. Isolation and characterization of 101-succinimide lysozyme that possesses the cyclic imide at Asp101-Gly 102. Biochemistry. 33:1994;8770-8774
36. Vaney M.C., Maignan S., Riès-Kautt M., Ducruix A. High-resolution structure (1.33 Å) of a HEW lysozyme tetragonal crystal grown in the APCF apparatus. Data and structural comparison with a crystal grown under microgravity from SpaceHab-01 mission. Acta Crystallog. sect. D. 52:1996;505-517
37. Venkatachalam C.M. Stereochemical criteria for polypeptides and proteins. V. Conformation of a system of three linked peptide units. Biopolymers. 6:1968;1425-1436