Conformational variation revealed by the crystal structure of RNase U2A complexed with Ca Ion and 2'-adenylic acid at 1.03 Å resolution

Protein and Peptide Letters

Volumn 17, Issue 12, 2010, Pages 1559-1561

  Noguchi, Shuji ^a  

^a UNIVERSITY OF TOKYO   (Japan)

Author keywords

Asparagine deamidation; Isoaspartate; Isomerization; Ribonuclease U2; Succinimide; Ustilago sphaerogena

Indexed keywords

USTILAGO SPHAEROGENA;

EID: 78650646085     PISSN: 09298665     EISSN: None     Source Type: Journal    
DOI: 10.2174/0929866511009011559     Document Type: Article

References (21)

1. Geiger, T.; Clarke, S. Deamidation, isomerization, and racemiza-tion at asparaginyl and aspartyl residues in peptides. Succinimide-linked reactions that contribute to protein degradation. J. Biol. Chem., 1987, 262, 785-794.
2. Manning, M.C.; Chou, D.K.; Murphy, B.M.; Payne, R.W.; Kata-yama, D.S. Stability of protein pharmaceuticals: an update. Pharm. Res., 2010, 275, 544-575.
3. Shimizu, T.; Watanabe, A.; Ogawara, M.; Mori, H.; Shirasawa, T. Isoaspartate formation and neurodegeneration in Alzheimer's disease. Arch. Biochem. Biophys., 2000, 381, 225-234.
4. Miyawaki, K.; Noguchi, S.; Harada, S.; Satow, Y. Crystallography of succinimide hen egg-white lysozyme at low temperatures. J. Cryst. Growth, 1996, 168, 292-296.
5. Kim, E.; Lowenson, J.D.; MacLaren, D.C.; Clarke, S.; Young, S.G. Deficiency of a protein-repair enzyme results in the accumulation of altered proteins, retardation of growth, and fatal seizures in mice. Proc. Natl. Acad. Sci. USA, 1997, 94, 6132-6137.
6. Stephenson, R.C.; Clarke, S. Succinimide formation from aspartyl and asparaginyl peptides as a model for the spontaneous degradation of proteins. J. Biol. Chem., 1989, 264, 6164-6170.
7. Arima, T.; Uchida, T.; Egami, F. Studies on extracellular ribonu-cleases of Ustilago sphaerogena. Purification and properties. Bio-chem. J., 1968, 106, 601-607.
8. Noguchi, S.; Satow, Y.; Uchida, T.; Sasaki, C.; Matsuzaki, T. Crystal structure of Ustilago sphaerogena ribonuclease U2 at 1.8 Å resolution. Biochemistry, 2010, 34, 15583-15591.
9. Noguchi, S. Isomerization mechanism of aspartate to isoaspartate implied by structures of Ustilago sphaerogena ribonuclease U2 complexed with adenosine 3'-monophosphate. Acta Crystallogr. Sect. D Biol. Crystallogr., 2010, 66, 843-849.
10. Noguchi, S. Structural changes induced by the deamidation and isomerization of asparagine revealed by the crystal structure of Ustilago sphaerogena ribonuclease U2B. Biopolymers, 2010, 93, 1003-1010.
11. Kanaya, S.; Uchida, T. Comparison of the primary structures of ribonuclease U2 isoforms. Biochem. J., 1986, 240, 163-170.
12. Uchida, T; Shibata, Y. An affinity adsorbent, 5'-adenylate-aminohexyl- sepharose. I. Purification and properties of two forms of RNase U2. J. Biochem., 1981, 90, 463-471.
13. Noguchi, S.; Satow, Y.; Uchida, T.; Sasaki, C.; Matsuzaki, T. Crystallization and preliminary X-ray investigation of six new crystal forms of ribonuclease U2 from Ustilago sphaerogena. J. Cryst. Growth, 1996, 168, 270-274.
14. Otwinowski, Z.; Minor, W. Processing of X-ray diffraction data collected in oscillation mode. Method Enzymol., 1997, 276, 307-326.
15. [15] CCP4. The CCP4 suite: programs for protein crystallography. Acta Crystallogr. Sect. D Biol. Crystallogr., 1994, 50, 760-763.
16. Murshudov, G.N.; Vagin, A.A.; Dodson, E.J. Refinement of mac-romolecular structures by the maximum-likelihood method. Acta. Crystallogr. Sect. D Biol. Crystallogr., 1997, 53, 240-255.
17. Emsley, P.; Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D Biol. Crystallogr., 2004, 60, 2126-2132.
18. Lovell, S.C.; Davis, I.W.; Arendall, W.B.; de Bakker, P.I.; Word, J.M.; Prisant, M.G.; Richardson, J.S.; Richardson, D.C. Structure validation by Cα geometry: φ, ψ and Cβ deviation. Proteins, 2003, 50, 437-450.
19. Patel, K.; Borchardt, R.T. Chemical pathways of peptide degradation. II. Kinetics of deamidation of an asparaginyl residue in a model hexapeptide. Pharm. Res., 1990, 7, 703-711.
20. Yasuda, T.; Inoue, Y. Studies of catalysis by ribonuclease U2. Steady-state kinetics for transphosphorylation of oligonucleotide and synthetic substrates. Biochemistry, 1982, 21, 364-369.
21. Granzin, J.; Puras-Lutzke, R.; Landt, O.; Grunert, H.P.; Heine-mann, U.; Saenger, W.; Hahn, U. RNase T1 mutant Glu46Gln binds the inhibitors 2'GMP and 2'AMP at the 3' subsite. J. Mol. Biol., 1992, 225, 533-542.