Crystal Structure and Functional Analysis of the Protein Disulfide Isomerase-Related Protein ERp29

Journal of Molecular Biology

Volumn 385, Issue 5, 2009, Pages 1630-1642

  Barak, Naomi N ^a   Neumann, Piotr ^b   Sevvana, Madhumati ^c   Schutkowski, Mike ^d   Naumann, Kai ^e   Malešević, Miroslav ^a   Reichardt, Heike ^a   Fischer, Gunter ^a   Stubbs, Milton T ^b   Ferrari, David M ^a  

^a MAX PLANCK RESEARCH UNIT FOR ENZYMOLOGY OF PROTEIN FOLDING   (Germany)

^b MARTIN LUTHER UNIVERSITY HALLE WITTENBERG   (Germany)

^c UNIVERSITY OF GÖTTINGEN   (Germany)

^d JPT Peptide Technologies GmbH   (Germany)

^e LEIBNIZ INSTITUTE OF PLANT BIOCHEMISTRY   (Germany)

Author keywords

chaperone; endoplasmic reticulum; ERp28; PDI D; Protein disulfide isomerase

Indexed keywords

PROTEIN DISULFIDE ISOMERASE; THYROGLOBULIN;

ARTICLE; BINDING SITE; CONTROLLED STUDY; CRYSTAL STRUCTURE; DROSOPHILA; ENDOPLASMIC RETICULUM; HUMAN; IN VITRO STUDY; IN VIVO STUDY; MUTANT; NONHUMAN; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN STRUCTURE; SEQUENCE HOMOLOGY;

EID: 58549114165     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2008.11.052     Document Type: Article

References (46)

1. Anken E., Braakman I., and Craig E. Versatility of the endoplasmic reticulum protein folding factory. Crit. Rev. Biochem. Mol. Biol. 40 (2005) 191-228
2. Freedman R.B., Klappa P., and Ruddock L.W. Protein disulfide isomerases exploit synergy between catalytic and specific binding domains. EMBO Rep. 3 (2002) 136-140
3. Trombetta E.S., and Parodi A.J. Quality control and protein folding in the secretory pathway. Annu. Rev. Cell Dev. Biol. 19 (2003) 649-676
4. Ellgaard L., and Ruddock L.W. The human protein disulphide isomerase family: substrate interactions and functional properties. EMBO Rep. 6 (2005) 28-32
5. Hatahet F., and Ruddock L.W. Substrate recognition by the protein disulfide isomerases. FEBS J. 274 (2007) 5223-5234
6. Ferrari D.M., Nguyen Van P., Kratzin H.D., and Söling H.D. ERp28, a human endoplasmic-reticulum-lumenal protein, is a member of the protein disulfide isomerase family but lacks a CXXC thioredoxin-box motif. Eur. J. Biochem. 255 (1998) 570-579
7. Ferrari D.M., and Söling H.D. The protein disulphide isomerase family-unravelling a string of folds. Biochem. J. 339 (1999) 1-10
8. Baryshev M., Sargsyan E., and Mkrtchian S. ERp29 is an essential endoplasmic reticulum factor regulating secretion of thyroglobulin. Biochem. Biophys. Res. Commun. 340 (2006) 617-624
9. Magnuson B., Rainey E.K., Benjamin T., Baryshev M., Mkrtchian S., and Tsai B. ERp29 triggers a conformational change in polyomavirus to stimulate membrane binding. Mol. Cell 20 (2005) 289-300
10. Mkrtchian S., Fang C., Hellman U., and Ingelman-Sundberg M. A stress-inducible rat liver endoplasmic reticulum protein, ERp29. Eur. J. Biochem. 251 (1998) 304-313
11. Nilson L.A., and Schupbach T. Localized requirements for windbeutel and pipe reveal a dorsoventral prepattern within the follicular epithelium of the Drosophila ovary. Cell 93 (1998) 253-262
12. Stein D., Roth S., Vogelsang E., and Nusslein-Volhard C. The polarity of the dorsoventral axis in the Drosophila embryo is defined by an extracellular signal. Cell 65 (1991) 725-735
13. Sen J., Goltz J.S., Konsolaki M., Schupbach T., and Stein D. Windbeutel is required for function and correct subcellular localization of the Drosophila patterning protein Pipe. Development 127 (2000) 5541-5550
14. Barnewitz K., Guo C., Sevvana M., Ma Q., Sheldrick G.M., Söling H.-D., and Ferrari D.M. Mapping of a substrate-binding site in the protein disulfide isomerase-related chaperone Wind based on protein function and crystal structure. J. Biol. Chem. 279 (2004) 39829-39837
15. Ma Q., Guo C., Barnewitz K., Sheldrick G.M., Söling H.-D., Usón I., and Ferrari D.M. Crystal structure and functional analysis of Drosophila Wind, a protein-disulfide isomerase-related protein. J. Biol. Chem. 278 (2003) 44600-44607
16. Liepinsh E., Baryshev M., Sharipo A., Ingelman-Sundberg M., Otting G., and Mkrtchian S. Thioredoxin fold as homodimerization module in the putative chaperone ERp29: NMR structures of the domains and experimental model of the 51 kDa dimer. Structure 9 (2001) 457-471
17. Hermann V.M., Cutfield J.F., and Hubbard M.J. Biophysical characterization of ERp29: evidence for a key structural role of cysteine 125. J. Biol. Chem. 280 (2005) 13529-13537
18. Lippert U., Diao D., Barak N.N., and Ferrari D.M. Conserved structural and functional properties of D-domain containing redox-active and -inactive protein disulfide isomerase-related protein chaperones. J. Biol. Chem. 282 (2007) 11213-11220
19. Rainey-Barger E.K., Mkrtchian S., and Tsai B. Dimerization of ERp29, a PDI-like protein, is essential for its diverse functions. Mol. Biol. Cell 18 (2007) 1253-1260
20. Brunger A.T., Adams P.D., Clore G.M., DeLano W.L., Gros P., Grosse-Kunstleve R.W., et al. Crystallography and NMR system (CNS): a new software system for macromolecular structure determination. Acta Crystallogr., Sect. D: Biol. Crystallogr. 54 (1998) 905-921
21. Teng T.-Y. Mounting of crystals for macromolecular crystallography in a free-standing thin film. J. Appl. Crystallogr. 23 (1990) 387-391
22. 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
23. Kozlov G., Maattanen P., Schrag J.D., Pollock S., Cygler M., Nagar B., et al. Crystal structure of the bb′ domains of the protein disulfide isomerase ERp57. Structure 14 (2006) 1331-1339
24. Konsolaki M., and Schupbach T. windbeutel, a gene required for dorsoventral patterning in Drosophila, encodes a protein that has homologies to vertebrate proteins of the endoplasmic reticulum. Genes Dev. 12 (1998) 120-131
25. Ferrari D.M. Isolation and Characterisation of a Novel Protein Disulphide Isomerase (PDI)-Related Protein, ERp28: Implications for the PDI Family (1999), Cuvillier Verlag, Goettingen, Germany
26. Klappa P., Stromer T., Zimmermann R., Ruddock L.W., and Freedman R.B. A pancreas-specific glycosylated protein disulphide-isomerase binds to misfolded proteins and peptides with an interaction inhibited by oestrogens. Eur. J. Biochem. 254 (1998) 63-69
27. Klappa P., Freedman R.B., Langenbuch M., Lan M.S., Robinson G.K., and Ruddock L.W. The pancreas-specific protein disulphide-isomerase PDIp interacts with a hydroxyaryl group in ligands. Biochem. J. 354 (2001) 553-559
28. Ruddock L.W., Freedman R.B., and Klappa P. Specificity in substrate binding by protein folding catalysts: tyrosine and tryptophan residues are the recognition motifs for the binding of peptides to the pancreas-specific protein disulfide isomerase PDIp. Protein Sci. 9 (2000) 758-764
29. Hashimoto S., Okada K., and Imaoka S. Interaction between bisphenol derivatives and protein disulfide isomerase (PDI) and inhibition of PDI functions: requirement of chemical structure for binding to PDI. J. Biochem. 144 (2008) 335-342
30. Hiroi T., Okada K., Imaoka S., Osada M., and Funae Y. Bisphenol A binds to protein disulfide isomerase and inhibits its enzymatic and hormone-binding activities. Endocrinology 147 (2006) 2773-2780
31. McPherson A. Two approaches to the rapid screening of crystallization conditions. J. Cryst. Growth 122 (1992) 161-167
32. Leslie A.G.W. In: Moras V.D., Podjarny A.D., and Thierry J.C. (Eds). Crystallographic Computing (1990), Oxford University Press, Oxford, UK
33. Evans, P. R. (1997). Proceedings of CCP4 Study Weekend, 1997, on Recent Advances in Phasing, Warrington, UK.
34. Schwarzenbacher R., Godzik A., Grzechnik S.K., and Jaroszewski L. The importance of alignment accuracy for molecular replacement. Acta Crystallogr. 60 (2004) 1229-1236
35. Altschul S.F., and Koonin E.V. Iterated profile searches with PSI-BLAST-a tool for discovery in protein databases. Trends Biochem. Sci. 23 (1998) 444-447
36. Kissinger C.R., Gehlhaar D.K., and Fogel D.B. Rapid automated molecular replacement by evolutionary search. Acta Crystallogr., Sect. D: Biol. Crystallogr. 55 (1999) 484-491
37. Vagin A., and Teplyakov A. MOLREP: an automated program for molecular replacement. J. Appl. Crystallogr. 30 (1997) 1022-1025
38. McCoy A.J., Grosse-Kunstleve R.W., Storoni L.C., and Read R.J. Likelihood-enhanced fast translation functions. Acta Crystallogr. 61 (2005) 458-464
39. Read R. Improved Fourier coefficients for maps using phases from partial structures with errors. Acta Crystallogr. 42 (1986) 140-149
40. Jones T.A. Interactive electron-density map interpretation: from INTER to O. Acta Crystallogr. 60 (2004) 2115-2125
41. Emsley P., and Cowtan K. Coot: model-building tools for molecular graphics. Acta Crystallogr. 60 (2004) 2126-2132
42. Laskowski 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. Crystallogr. 26 (1993) 283-291
43. Murshudov G.N., Vagin A.A., and Dodson E.J. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr., Sect. D: Biol. Crystallogr. 53 (1997) 240-255
44. Delano W.L. The PyMOL Molecular Graphics System (2002), DeLano Scientific LLC, San Carlos, CA
45. Baker N.A., Sept D., Joseph S., Holst M.J., and McCammon J.A. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl Acad. Sci. USA 98 (2001) 10037-10041
46. Vaguine A.A., Richelle J., and Wodak S.J. SFCHECK: a unified set of procedures for evaluating the quality of macromolecular structure-factor data and their agreement with the atomic model. Acta Crystallogr., Sect. D: Biol. Crystallogr. 55 (1999) 191-205