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. 1999 Jan;8(1):203–214. doi: 10.1110/ps.8.1.203

The influence of C-terminal extension on the structure of the "J-domain" in E. coli DnaJ.

K Huang 1, J M Flanagan 1, J H Prestegard 1
PMCID: PMC2144109  PMID: 10210198

Abstract

Two different recombinant constructs of the N-terminal domain in Escherichia coli DnaJ were uniformly labeled with nitrogen-15 and carbon-13. One, DnaJ(1-78), contains the complete "J-domain," and the other, DnaJ(1-104), contains both the "J-domain" and a conserved "G/F" extension at the C-terminus. The three-dimensional structures of these proteins have been determined by heteronuclear NMR experiments. In both proteins the "J-domain" adopts a compact structure consisting of a helix-turn-helix-loop-helix-turn-helix motif. In contrast, the "G/F" region in DnaJ(1-104) does not fold into a well-defined structure. Nevertheless, the "G/F" region has been found to have an effect on the packing of the helices in the "J-domain" in DnaJ(1-104). Particularly, the interhelical angles between Helix IV and other helices are significantly different in the two structures. In addition, there are some local conformational changes in the loop region connecting the two central helices. These structural differences in the "J-domain" in the presence of the "G/F" region may be related to the observation that DnaJ (1-78) is incapable of stimulating the ATPase activity of the molecular chaperone protein DnaK despite evidence that sites mediating the binding of DnaJ to DnaK are located in the 1-78 segment.

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Selected References

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  1. Auger I., Roudier J. A function for the QKRAA amino acid motif: mediating binding of DnaJ to DnaK. Implications for the association of rheumatoid arthritis with HLA-DR4. J Clin Invest. 1997 Apr 15;99(8):1818–1822. doi: 10.1172/JCI119348. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Bai Y., Milne J. S., Mayne L., Englander S. W. Primary structure effects on peptide group hydrogen exchange. Proteins. 1993 Sep;17(1):75–86. doi: 10.1002/prot.340170110. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Banecki B., Zylicz M. Real time kinetics of the DnaK/DnaJ/GrpE molecular chaperone machine action. J Biol Chem. 1996 Mar 15;271(11):6137–6143. doi: 10.1074/jbc.271.11.6137. [DOI] [PubMed] [Google Scholar]
  4. Bardwell J. C., Tilly K., Craig E., King J., Zylicz M., Georgopoulos C. The nucleotide sequence of the Escherichia coli K12 dnaJ+ gene. A gene that encodes a heat shock protein. J Biol Chem. 1986 Feb 5;261(4):1782–1785. [PubMed] [Google Scholar]
  5. Bork P., Sander C., Valencia A., Bukau B. A module of the DnaJ heat shock proteins found in malaria parasites. Trends Biochem Sci. 1992 Apr;17(4):129–129. doi: 10.1016/0968-0004(92)90319-5. [DOI] [PubMed] [Google Scholar]
  6. Clore G. M., Bax A., Gronenborn A. M. Stereospecific assignment of beta-methylene protons in larger proteins using 3D 15N-separated Hartmann-Hahn and 13C-separated rotating frame Overhauser spectroscopy. J Biomol NMR. 1991 May;1(1):13–22. doi: 10.1007/BF01874566. [DOI] [PubMed] [Google Scholar]
  7. Connelly G. P., Bai Y., Jeng M. F., Englander S. W. Isotope effects in peptide group hydrogen exchange. Proteins. 1993 Sep;17(1):87–92. doi: 10.1002/prot.340170111. [DOI] [PubMed] [Google Scholar]
  8. Greene M. K., Maskos K., Landry S. J. Role of the J-domain in the cooperation of Hsp40 with Hsp70. Proc Natl Acad Sci U S A. 1998 May 26;95(11):6108–6113. doi: 10.1073/pnas.95.11.6108. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Grzesiek S., Vuister G. W., Bax A. A simple and sensitive experiment for measurement of JCC couplings between backbone carbonyl and methyl carbons in isotopically enriched proteins. J Biomol NMR. 1993 Jul;3(4):487–493. doi: 10.1007/BF00176014. [DOI] [PubMed] [Google Scholar]
  10. Hendrick J. P., Langer T., Davis T. A., Hartl F. U., Wiedmann M. Control of folding and membrane translocation by binding of the chaperone DnaJ to nascent polypeptides. Proc Natl Acad Sci U S A. 1993 Nov 1;90(21):10216–10220. doi: 10.1073/pnas.90.21.10216. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Hill R. B., Flanagan J. M., Prestegard J. H. 1H and 15N magnetic resonance assignments, secondary structure, and tertiary fold of Escherichia coli DnaJ(1-78). Biochemistry. 1995 Apr 25;34(16):5587–5596. doi: 10.1021/bi00016a033. [DOI] [PubMed] [Google Scholar]
  12. Karzai A. W., McMacken R. A bipartite signaling mechanism involved in DnaJ-mediated activation of the Escherichia coli DnaK protein. J Biol Chem. 1996 May 10;271(19):11236–11246. doi: 10.1074/jbc.271.19.11236. [DOI] [PubMed] [Google Scholar]
  13. Kudlicki W., Odom O. W., Kramer G., Hardesty B. Binding of an N-terminal rhodanese peptide to DnaJ and to ribosomes. J Biol Chem. 1996 Dec 6;271(49):31160–31165. doi: 10.1074/jbc.271.49.31160. [DOI] [PubMed] [Google Scholar]
  14. Langer T., Lu C., Echols H., Flanagan J., Hayer M. K., Hartl F. U. Successive action of DnaK, DnaJ and GroEL along the pathway of chaperone-mediated protein folding. Nature. 1992 Apr 23;356(6371):683–689. doi: 10.1038/356683a0. [DOI] [PubMed] [Google Scholar]
  15. Laskowski R. A., Rullmannn J. A., MacArthur M. W., Kaptein R., Thornton J. M. AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR. J Biomol NMR. 1996 Dec;8(4):477–486. doi: 10.1007/BF00228148. [DOI] [PubMed] [Google Scholar]
  16. Liberek K., Marszalek J., Ang D., Georgopoulos C., Zylicz M. Escherichia coli DnaJ and GrpE heat shock proteins jointly stimulate ATPase activity of DnaK. Proc Natl Acad Sci U S A. 1991 Apr 1;88(7):2874–2878. doi: 10.1073/pnas.88.7.2874. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Ohki M., Tamura F., Nishimura S., Uchida H. Nucleotide sequence of the Escherichia coli dnaJ gene and purification of the gene product. J Biol Chem. 1986 Feb 5;261(4):1778–1781. [PubMed] [Google Scholar]
  18. Pellecchia M., Szyperski T., Wall D., Georgopoulos C., Wüthrich K. NMR structure of the J-domain and the Gly/Phe-rich region of the Escherichia coli DnaJ chaperone. J Mol Biol. 1996 Jul 12;260(2):236–250. doi: 10.1006/jmbi.1996.0395. [DOI] [PubMed] [Google Scholar]
  19. Piotto M., Saudek V., Sklenár V. Gradient-tailored excitation for single-quantum NMR spectroscopy of aqueous solutions. J Biomol NMR. 1992 Nov;2(6):661–665. doi: 10.1007/BF02192855. [DOI] [PubMed] [Google Scholar]
  20. Qian Y. Q., Patel D., Hartl F. U., McColl D. J. Nuclear magnetic resonance solution structure of the human Hsp40 (HDJ-1) J-domain. J Mol Biol. 1996 Jul 12;260(2):224–235. doi: 10.1006/jmbi.1996.0394. [DOI] [PubMed] [Google Scholar]
  21. Rice L. M., Brünger A. T. Torsion angle dynamics: reduced variable conformational sampling enhances crystallographic structure refinement. Proteins. 1994 Aug;19(4):277–290. doi: 10.1002/prot.340190403. [DOI] [PubMed] [Google Scholar]
  22. Richards F. M., Kundrot C. E. Identification of structural motifs from protein coordinate data: secondary structure and first-level supersecondary structure. Proteins. 1988;3(2):71–84. doi: 10.1002/prot.340030202. [DOI] [PubMed] [Google Scholar]
  23. Saito H., Uchida H. Initiation of the DNA replication of bacteriophage lambda in Escherichia coli K12. J Mol Biol. 1977 Jun 15;113(1):1–25. doi: 10.1016/0022-2836(77)90038-9. [DOI] [PubMed] [Google Scholar]
  24. Stein E. G., Rice L. M., Brünger A. T. Torsion-angle molecular dynamics as a new efficient tool for NMR structure calculation. J Magn Reson. 1997 Jan;124(1):154–164. doi: 10.1006/jmre.1996.1027. [DOI] [PubMed] [Google Scholar]
  25. Straus D. B., Walter W. A., Gross C. A. Escherichia coli heat shock gene mutants are defective in proteolysis. Genes Dev. 1988 Dec;2(12B):1851–1858. doi: 10.1101/gad.2.12b.1851. [DOI] [PubMed] [Google Scholar]
  26. Straus D., Walter W., Gross C. A. DnaK, DnaJ, and GrpE heat shock proteins negatively regulate heat shock gene expression by controlling the synthesis and stability of sigma 32. Genes Dev. 1990 Dec;4(12A):2202–2209. doi: 10.1101/gad.4.12a.2202. [DOI] [PubMed] [Google Scholar]
  27. Sunshine M., Feiss M., Stuart J., Yochem J. A new host gene (groPC) necessary for lambda DNA replication. Mol Gen Genet. 1977 Feb 28;151(1):27–34. doi: 10.1007/BF00446909. [DOI] [PubMed] [Google Scholar]
  28. Szabo A., Korszun R., Hartl F. U., Flanagan J. A zinc finger-like domain of the molecular chaperone DnaJ is involved in binding to denatured protein substrates. EMBO J. 1996 Jan 15;15(2):408–417. [PMC free article] [PubMed] [Google Scholar]
  29. Szyperski T., Pellecchia M., Wall D., Georgopoulos C., Wüthrich K. NMR structure determination of the Escherichia coli DnaJ molecular chaperone: secondary structure and backbone fold of the N-terminal region (residues 2-108) containing the highly conserved J domain. Proc Natl Acad Sci U S A. 1994 Nov 22;91(24):11343–11347. doi: 10.1073/pnas.91.24.11343. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Tsai J., Douglas M. G. A conserved HPD sequence of the J-domain is necessary for YDJ1 stimulation of Hsp70 ATPase activity at a site distinct from substrate binding. J Biol Chem. 1996 Apr 19;271(16):9347–9354. doi: 10.1074/jbc.271.16.9347. [DOI] [PubMed] [Google Scholar]
  31. Wall D., Zylicz M., Georgopoulos C. The NH2-terminal 108 amino acids of the Escherichia coli DnaJ protein stimulate the ATPase activity of DnaK and are sufficient for lambda replication. J Biol Chem. 1994 Feb 18;269(7):5446–5451. [PubMed] [Google Scholar]
  32. Wall D., Zylicz M., Georgopoulos C. The conserved G/F motif of the DnaJ chaperone is necessary for the activation of the substrate binding properties of the DnaK chaperone. J Biol Chem. 1995 Feb 3;270(5):2139–2144. doi: 10.1074/jbc.270.5.2139. [DOI] [PubMed] [Google Scholar]
  33. Wickner S., Hoskins J., McKenney K. Monomerization of RepA dimers by heat shock proteins activates binding to DNA replication origin. Proc Natl Acad Sci U S A. 1991 Sep 15;88(18):7903–7907. doi: 10.1073/pnas.88.18.7903. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Wishart D. S., Bigam C. G., Yao J., Abildgaard F., Dyson H. J., Oldfield E., Markley J. L., Sykes B. D. 1H, 13C and 15N chemical shift referencing in biomolecular NMR. J Biomol NMR. 1995 Sep;6(2):135–140. doi: 10.1007/BF00211777. [DOI] [PubMed] [Google Scholar]
  35. Wishart D. S., Sykes B. D., Richards F. M. The chemical shift index: a fast and simple method for the assignment of protein secondary structure through NMR spectroscopy. Biochemistry. 1992 Feb 18;31(6):1647–1651. doi: 10.1021/bi00121a010. [DOI] [PubMed] [Google Scholar]
  36. Wishart D. S., Sykes B. D. The 13C chemical-shift index: a simple method for the identification of protein secondary structure using 13C chemical-shift data. J Biomol NMR. 1994 Mar;4(2):171–180. doi: 10.1007/BF00175245. [DOI] [PubMed] [Google Scholar]
  37. Wüthrich K., Billeter M., Braun W. Pseudo-structures for the 20 common amino acids for use in studies of protein conformations by measurements of intramolecular proton-proton distance constraints with nuclear magnetic resonance. J Mol Biol. 1983 Oct 5;169(4):949–961. doi: 10.1016/s0022-2836(83)80144-2. [DOI] [PubMed] [Google Scholar]

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