Chaperone Binding at the Ribosomal Exit Tunnel

Structure

Volumn 11, Issue 12, 2003, Pages 1547-1556

  Kristensen, Ole ^a   Gajhede, Michael ^a  

^a UNIVERSITY OF COPENHAGEN   (Denmark)

Author keywords

[No Author keywords available]

Indexed keywords

CHAPERONE; SIGNAL RECOGNITION PARTICLE;

ARTICLE; BINDING SITE; CRYSTALLIZATION; ESCHERICHIA COLI; MOLECULE; NONHUMAN; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN MOTIF; PROTEIN STRUCTURE; RIBOSOME;

ESCHERICHIA COLI; NEGIBACTERIA;

EID: 0344665607     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.str.2003.11.003     Document Type: Article

References (54)

1. Albanese V., Frydman J. Where chaperones and nascent polypeptides meet. Nat. Struct. Biol. 9:2002;716-718.
2. Al-Karadaghi S., Kristensen O., Liljas A. A decade of progress in understanding the structural basis of protein synthesis. Prog. Biophys. Mol. Biol. 73:2000;167-193.
3. Bang H., Pecht A., Raddatz G., Scior T., Solbach W., Brune K., Pahl A. Prolyl isomerases in a minimal cell. Catalysis of protein folding by trigger factor from Mycoplasma genitalium. Eur. J. Biochem. 267:2000;3270-3280.
4. Barton G.J. Alscript. a tool to format multiple sequence alignments Protein Eng. 6:1993;37-40.
5. Bashan A., Agmon I., Zarivach R., Schluenzen F., Harms J., Berisio R., Bartels H., Franceschi F., Auerbach T., Hansen H.A.et al. Structural basis of the ribosomal machinery for peptide bond formation, translocation, and nascent chain progression. Mol. Cell. 11:2003;91-102.
6. Beck K., Wu L.F., Brunner J., Muller M. Discrimination between SRP- and SecA/SecB-dependent substrates involves selective recognition of nascent chains by SRP and trigger factor. EMBO J. 19:2000;134-143.
7. Beckmann R., Spahn C.M.T., Eswar N., Helmers J., Penczek P.A., Sali A., Frank J., Blobel G. Architecture of the protein-conducting channel associated with the translating 80S ribosome. Cell. 107:2001;361-372.
8. Berisio R., Schluenzen F., Harms J., Bashan A., Auerbach T., Baram D., Yonath A. Structural insight into the role of the ribosomal tunnel in cellular regulation. Nat. Struct. Biol. 10:2003;366-370.
9. Blaha G., Wilson D.N., Stoller G., Fischer G., Willumeit R., Nierhaus K.H. Localization of the trigger factor binding site on the ribosomal 50S subunit. J. Mol. Biol. 326:2003;887-897.
10. Brodersen D.E., Clemons W.M. Jr., Carter A.P., Wimberly B.T., Ramakrishnan V. Crystal structure of the 30 S ribosomal subunit from Thermus thermophilus. structure of the proteins and their interactions with 16 S RNA J. Mol. Biol. 316:2002;725-768.
11. Brunger A.T., Adams P.D., Clore G.M., DeLano W.L., Gros P., Grosse-Kunstleve R.W., Jiang J.S., Kuszewski J., Nilges M., Pannu N.S.et al. Crystallography & NMR system. a new software suite for macromolecular structure determination Acta Crystallogr. D. 54:1998;905-921.
12. Callebaut I., Mornon J.P. Trigger factor, one of the Escherichia coli chaperone proteins, is an original member of the FKBP family. FEBS Lett. 374:1995;211-215.
13. CCP4 The CCP4 (Collaborative Computational Project 4) suite. programs for protein crystallography Acta Crystallogr. D. 50:1994;760-763.
14. Davies C., Gerstner R.B., Draper D.E., Ramakrishnan V., White S.W. The crystal structure of ribosomal protein S4 reveals a two-domain molecule with an extensive RNA-binding surface. one domain shows structural homology to the ETS DNA-binding motif EMBO J. 17:1998;4545-4558.
15. DeLano W.L. The PyMOL Molecular Graphics System. 2002;DeLano Scientific, San Carlos, CA.
16. Deuerling E., Patzelt H., Vorderwulbecke S., Rauch T., Kramer G., Schaffitzel E., Mogk A., Schulze-Specking A., Langen H., Bukau B. Trigger Factor and DnaK possess overlapping substrate pools and binding specificities. Mol. Microbiol. 47:2003;1317-1328.
17. Driessen A.J., Manting E.H., van der Does C. The structural basis of protein targeting and translocation in bacteria. Nat. Struct. Biol. 8:2001;492-498.
18. Feldman D.E., Frydman J. Protein folding in vivo. the importance of molecular chaperones Curr. Opin. Struct. Biol. 10:2000;26-33.
19. de La Fortelle, Bricogne G. Maximum-likelihood heavy-atom parameter refinement for multiple isomorphous replacement and multiwavelength anomalous diffraction methods. Macromolecular Crystallography Part A., Carter C.W., Sweet R.M. Methods in Enzymology. 1997;472-494 Academic Press, San Diego, CA.
20. Gu S.Q., Peske F., Wieden H.J., Rodnina M.V., Wintermeyer W. The signal recognition particle binds to protein L23 at the peptide exit of the Escherichia coli ribosome. RNA. 9:2003;566-573.
21. Hesterkamp T., Deuerling E., Bukau B. The amino-terminal 118 amino acids of Escherichia coli trigger factor constitute a domain that is necessary and sufficient for binding to ribosomes. J. Biol. Chem. 272:1997;21865-21871.
22. Holm L., Sander C. Protein structure comparison by alignment of distance matrices. J. Mol. Biol. 233:1993;123-138.
23. Honig B., Nicholls A. Classical electrostatics in biology and chemistry. Science. 268:1995;1144-1149.
24. Jones S., Thornton J.M. Principles of protein-protein interactions. Proc. Natl. Acad. Sci. USA. 93:1996;13-20.
25. Jones T.A., Bergdoll M., Kjeldgaard M. O. a macromolecular modeling environment Bugg C., Ealick S. Crystallographic and Modeling Methods in Molecular Design. 1990;189-195 Springer-Verlag Press, New York.
26. Kandror O., Sherman M., Goldberg A. Rapid degradation of an abnormal protein in Escherichia coli proceeds through repeated cycles of association with GroEL. J. Biol. Chem. 274:1999;37743-37749.
27. Katchalski-Katzir E., Shariv I., Eisenstein M., Friesem A.A., Aflalo C., Vakser I.A. Molecular surface recognition. determination of geometric fit between proteins and their ligands by correlation techniques Proc. Natl. Acad. Sci. USA. 89:1992;2195-2199.
28. Kim S.J., Jeong D.G., Chi S.W., Lee J.S., Ryu S.E. Crystal structure of proteolytic fragments of the redox-sensitive Hsp33 with constitutive chaperone activity. Nat. Struct. Biol. 8:2001;459-466.
29. Kleywegt G.J., Jones T.A. xdlMAPMAN and xdlDATAMAN - programs for reformatting, analysis and manipulation of biomacromolecular electron-density maps and reflection data sets. Acta Crystallogr. D. 52:1996;826-828.
30. Kleywegt G.J., Jones T.A. Databases in protein crystallography. Acta Crystallogr. D. 54:1998;1119-1131.
31. Kramer G., Rauch T., Rist W., Vorderwulbecke S., Patzelt H., Schulze-Specking A., Ban N., Deuerling E., Bukau B. L23 protein functions as a chaperone docking site on the ribosome. Nature. 419:2002;171-174.
32. Kraulis P.J. Molscript. a program to produce both detailed and schematic plots of protein structures J. Appl. Crystallogr. 24:1991;946-950.
33. Lamzin V.S., Perrakis A., Wilson K.S. The ARP/wARP suite for automated construction and refinement of protein models. Rossmann M.G., Arnold E. International Tables for Crystallography. 2001;720-722 Kluwer Academic Publishers, Dordrecht, Netherlands.
34. Laskowski R.A., MacArthur M.W., Moss D.S., Thornton J.M. Procheck. a program to check the stereochemical quality of protein structures J. Appl. Crystallogr. 26:1993;283-291.
35. Li Z.Y., Liu C.P., Zhu L.Q., Jing G.Z., Zhou J.M. The chaperone activity of trigger factor is distinct from its isomerase activity during co-expression with adenylate kinase in Escherichia coli. FEBS Lett. 506:2001;108-112.
36. Maier R., Eckert B., Scholz C., Lilie H., Schmid F.X. Interaction of trigger factor with the ribosome. J. Mol. Biol. 326:2003;585-592.
37. Morgan D.G., Ménétret J.F., Neuhof A., Rapoport T.A., Akey C.W. Structure of the mammalian ribosome-channel complex at 17 Å resolution. J. Mol. Biol. 324:2002;871-886.
38. Nissen P., Hansen J., Ban N., Moore P.B., Steitz T.A. The structural basis of ribosome activity in peptide bond synthesis. Science. 289:2000;920-930.
39. Patzelt H., Kramer G., Rauch T., Schonfeld H.J., Bukau B., Deuerling E. Three-state equilibrium of Escherichia coli trigger factor. Biol. Chem. 383:2002;1611-1619.
40. Patzelt H., Rudiger S., Brehmer D., Kramer G., Vorderwulbecke S., Schaffitzel E., Waitz A., Hesterkamp T., Dong L., Schneider-Mergener J.et al. Binding specificity of Escherichia coli trigger factor. Proc. Natl. Acad. Sci. USA. 98:2001;14244-14249.
41. Pool M.R., Stumm J., Fulga T.A., Sinning I., Dobberstein B. Distinct modes of signal recognition particle interaction with the ribosome. Science. 297:2002;1345-1348.
42. Ramakrishnan V., White S.W. The structure of ribosomal protein S5 reveals sites of interaction with 16S rRNA. Nature. 358:1992;768-771.
43. Richardson A., Landry S.J., Georgopoulos C. The ins and outs of a molecular chaperone machine. Trends Biochem. Sci. 23:1998;138-143.
44. Scholz C., Stoller G., Zarnt T., Fischer G., Schmid F.X. Cooperation of enzymatic and chaperone functions of trigger factor in the catalysis of protein folding. EMBO J. 16:1997;54-58.
45. Staker B.L., Korber P., Bardwell J.C., Saper M.A. Structure of Hsp15 reveals a novel RNA-binding motif. EMBO J. 19:2000;749-757.
46. Stoller G., Rucknagel K.P., Nierhaus K.H., Schmid F.X., Fischer G., Rahfeld J.U. A ribosome-associated peptidyl-prolyl cis/trans isomerase identified as the trigger factor. EMBO J. 14:1995;4939-4948.
47. Terwilliger T.C. Maximum-likelihood density modification. Acta Crystallogr. D. 56:2000;965-972.
48. Terwilliger T.C., Berendzen J. Automated MAD and MIR structure solution. Acta Crystallogr. D. 55:1999;849-861.
49. Ullers R.S., Houben E.N., Raine A., Ten Hagen-Jongman C.M., Ehrenberg M., Brunner J., Oudega B., Harms N., Luirink J. Interplay of signal recognition particle and trigger factor at L23 near the nascent chain exit site on the Escherichia coli ribosome. J. Cell Biol. 161:2003;679-684.
50. Van Duyne G.D., Standaert R.F., Karplus P.A., Schreiber S.L., Clardy J. Atomic structures of the human immunophilin FKBP-12 complexes with FK506 and rapamycin. J. Mol. Biol. 229:1993;105-124.
51. Vogtherr M., Jacobs D.M., Parac T.N., Maurer M., Pahl A., Saxena K., Ruterjans H., Griesinger C., Fiebig K.M. NMR solution structure and dynamics of the peptidyl-prolyl cis-trans isomerase domain of the trigger factor from Mycoplasma genitalium compared to FK506-binding protein. J. Mol. Biol. 318:2002;1097-1115.
52. Wimberly B.T., Brodersen D.E., Clemons W.M. Jr., Morgan-Warren R.J., Carter A.P., Vonrhein C., Hartsch T., Ramakrishnan V. Structure of the 30S ribosomal subunit. Nature. 407:2000;327-339.
53. Yonath A. High-resolution structures of large ribosomal subunits from mesophilic eubacteria and halophilic archaea at various functional states. Curr. Protein Pept. Sci. 3:2002;67-78.
54. Yusupov M.M., Yusupova G.Z., Baucom A., Lieberman K., Earnest T.N., Cate J.H., Noller H.F. Crystal structure of the ribosome at 5.5 Å resolution. Science. 292:2001;883-896.