Skip to main content
PMC home page
Protein Science : A Publication of the Protein Society logoLink to Protein Science : A Publication of the Protein Society
. 1999 Nov;8(11):2494–2500. doi: 10.1110/ps.8.11.2494

NikR is a ribbon-helix-helix DNA-binding protein.

P T Chivers 1, R T Sauer 1
PMCID: PMC2144182  PMID: 10595554

Abstract

Escherichia coli NikR, a repressor with homologs in other bacteria and archaea, was identified as a potential new member of the ribbon-helix-helix (beta-alpha-alpha) family of transcription factors in profile based sequence searches and in structure prediction experiments. Biophysical and biochemical characterization of the N-terminal domain of NikR show that it has many features expected of a beta-alpha-alpha protein including alpha-helical content, dimeric solution form, concentration dependent thermal stability, and ability to bind DNA in sequence-specific manner. Mutation of a residue predicted to be important for DNA-binding reduces operator affinity but does not affect the secondary structure or stability of the protein.

Full Text

The Full Text of this article is available as a PDF (639.2 KB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Altschul S. F., Madden T. L., Schäffer A. A., Zhang J., Zhang Z., Miller W., Lipman D. J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997 Sep 1;25(17):3389–3402. doi: 10.1093/nar/25.17.3389. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Bairoch A., Apweiler R. The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1998. Nucleic Acids Res. 1998 Jan 1;26(1):38–42. doi: 10.1093/nar/26.1.38. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Bonvin A. M., Vis H., Breg J. N., Burgering M. J., Boelens R., Kaptein R. Nuclear magnetic resonance solution structure of the Arc repressor using relaxation matrix calculations. J Mol Biol. 1994 Feb 11;236(1):328–341. doi: 10.1006/jmbi.1994.1138. [DOI] [PubMed] [Google Scholar]
  4. Bowie J. U., Sauer R. T. Equilibrium dissociation and unfolding of the Arc repressor dimer. Biochemistry. 1989 Sep 5;28(18):7139–7143. doi: 10.1021/bi00444a001. [DOI] [PubMed] [Google Scholar]
  5. Bowie J. U., Sauer R. T. Identifying determinants of folding and activity for a protein of unknown structure. Proc Natl Acad Sci U S A. 1989 Apr;86(7):2152–2156. doi: 10.1073/pnas.86.7.2152. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Bowie J. U., Sauer R. T. TraY proteins of F and related episomes are members of the Arc and Mnt repressor family. J Mol Biol. 1990 Jan 5;211(1):5–6. doi: 10.1016/0022-2836(90)90004-6. [DOI] [PubMed] [Google Scholar]
  7. Brown B. M., Milla M. E., Smith T. L., Sauer R. T. Scanning mutagenesis of the Arc repressor as a functional probe of operator recognition. Nat Struct Biol. 1994 Mar;1(3):164–168. doi: 10.1038/nsb0394-164. [DOI] [PubMed] [Google Scholar]
  8. Brown B. M., Sauer R. T. Tolerance of Arc repressor to multiple-alanine substitutions. Proc Natl Acad Sci U S A. 1999 Mar 2;96(5):1983–1988. doi: 10.1073/pnas.96.5.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Burgering M. J., Boelens R., Gilbert D. E., Breg J. N., Knight K. L., Sauer R. T., Kaptein R. Solution structure of dimeric Mnt repressor (1-76). Biochemistry. 1994 Dec 20;33(50):15036–15045. doi: 10.1021/bi00254a012. [DOI] [PubMed] [Google Scholar]
  10. De Pina K., Desjardin V., Mandrand-Berthelot M. A., Giordano G., Wu L. F. Isolation and characterization of the nikR gene encoding a nickel-responsive regulator in Escherichia coli. J Bacteriol. 1999 Jan;181(2):670–674. doi: 10.1128/jb.181.2.670-674.1999. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Fischer D., Eisenberg D. Protein fold recognition using sequence-derived predictions. Protein Sci. 1996 May;5(5):947–955. doi: 10.1002/pro.5560050516. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Gomis-Rüth F. X., Solá M., Acebo P., Párraga A., Guasch A., Eritja R., González A., Espinosa M., del Solar G., Coll M. The structure of plasmid-encoded transcriptional repressor CopG unliganded and bound to its operator. EMBO J. 1998 Dec 15;17(24):7404–7415. doi: 10.1093/emboj/17.24.7404. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Hausinger R. P. Nickel utilization by microorganisms. Microbiol Rev. 1987 Mar;51(1):22–42. doi: 10.1128/mr.51.1.22-42.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. He Y. Y., McNally T., Manfield I., Navratil O., Old I. G., Phillips S. E., Saint-Girons I., Stockley P. G. Probing met repressor-operator recognition in solution. Nature. 1992 Oct 1;359(6394):431–433. doi: 10.1038/359431a0. [DOI] [PubMed] [Google Scholar]
  15. Jonsson T., Waldburger C. D., Sauer R. T. Nonlinear free energy relationships in Arc repressor unfolding imply the existence of unstable, native-like folding intermediates. Biochemistry. 1996 Apr 16;35(15):4795–4802. doi: 10.1021/bi953056s. [DOI] [PubMed] [Google Scholar]
  16. Kim J., Harter K., Theologis A. Protein-protein interactions among the Aux/IAA proteins. Proc Natl Acad Sci U S A. 1997 Oct 28;94(22):11786–11791. doi: 10.1073/pnas.94.22.11786. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Knight K. L., Sauer R. T. Identification of functionally important residues in the DNA binding region of the mnt repressor. J Biol Chem. 1989 Aug 15;264(23):13706–13710. [PubMed] [Google Scholar]
  18. Lüthy R., Xenarios I., Bucher P. Improving the sensitivity of the sequence profile method. Protein Sci. 1994 Jan;3(1):139–146. doi: 10.1002/pro.5560030118. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Milla M. E., Brown B. M., Sauer R. T. Protein stability effects of a complete set of alanine substitutions in Arc repressor. Nat Struct Biol. 1994 Aug;1(8):518–523. doi: 10.1038/nsb0894-518. [DOI] [PubMed] [Google Scholar]
  20. Milla M. E., Sauer R. T. P22 Arc repressor: folding kinetics of a single-domain, dimeric protein. Biochemistry. 1994 Feb 8;33(5):1125–1133. doi: 10.1021/bi00171a011. [DOI] [PubMed] [Google Scholar]
  21. Navarro C., Wu L. F., Mandrand-Berthelot M. A. The nik operon of Escherichia coli encodes a periplasmic binding-protein-dependent transport system for nickel. Mol Microbiol. 1993 Sep;9(6):1181–1191. doi: 10.1111/j.1365-2958.1993.tb01247.x. [DOI] [PubMed] [Google Scholar]
  22. Pabo C. O., Sauer R. T. Transcription factors: structural families and principles of DNA recognition. Annu Rev Biochem. 1992;61:1053–1095. doi: 10.1146/annurev.bi.61.070192.005201. [DOI] [PubMed] [Google Scholar]
  23. Phillips K., Phillips S. E. Electrostatic activation of Escherichia coli methionine repressor. Structure. 1994 Apr 15;2(4):309–316. doi: 10.1016/s0969-2126(00)00032-0. [DOI] [PubMed] [Google Scholar]
  24. Phillips S. E. The beta-ribbon DNA recognition motif. Annu Rev Biophys Biomol Struct. 1994;23:671–701. doi: 10.1146/annurev.bb.23.060194.003323. [DOI] [PubMed] [Google Scholar]
  25. Raumann B. E., Rould M. A., Pabo C. O., Sauer R. T. DNA recognition by beta-sheets in the Arc repressor-operator crystal structure. Nature. 1994 Feb 24;367(6465):754–757. doi: 10.1038/367754a0. [DOI] [PubMed] [Google Scholar]
  26. Rost B. Twilight zone of protein sequence alignments. Protein Eng. 1999 Feb;12(2):85–94. doi: 10.1093/protein/12.2.85. [DOI] [PubMed] [Google Scholar]
  27. Schildbach J. F., Robinson C. R., Sauer R. T. Biophysical characterization of the TraY protein of Escherichia coli F factor. J Biol Chem. 1998 Jan 16;273(3):1329–1333. doi: 10.1074/jbc.273.3.1329. [DOI] [PubMed] [Google Scholar]
  28. Schägger H., von Jagow G. Tricine-sodium dodecyl sulfate-polyacrylamide gel electrophoresis for the separation of proteins in the range from 1 to 100 kDa. Anal Biochem. 1987 Nov 1;166(2):368–379. doi: 10.1016/0003-2697(87)90587-2. [DOI] [PubMed] [Google Scholar]
  29. Smith T. L., Sauer R. T. P22 Arc repressor: role of cooperativity in repression and binding to operators with altered half-site spacing. J Mol Biol. 1995 Jun 16;249(4):729–742. doi: 10.1006/jmbi.1995.0332. [DOI] [PubMed] [Google Scholar]
  30. Somers W. S., Phillips S. E. Crystal structure of the met repressor-operator complex at 2.8 A resolution reveals DNA recognition by beta-strands. Nature. 1992 Oct 1;359(6394):387–393. doi: 10.1038/359387a0. [DOI] [PubMed] [Google Scholar]
  31. Tam R., Saier M. H., Jr Structural, functional, and evolutionary relationships among extracellular solute-binding receptors of bacteria. Microbiol Rev. 1993 Jun;57(2):320–346. doi: 10.1128/mr.57.2.320-346.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Vershon A. K., Bowie J. U., Karplus T. M., Sauer R. T. Isolation and analysis of arc repressor mutants: evidence for an unusual mechanism of DNA binding. Proteins. 1986 Dec;1(4):302–311. doi: 10.1002/prot.340010404. [DOI] [PubMed] [Google Scholar]
  33. Vershon A. K., Liao S. M., McClure W. R., Sauer R. T. Bacteriophage P22 Mnt repressor. DNA binding and effects on transcription in vitro. J Mol Biol. 1987 May 20;195(2):311–322. doi: 10.1016/0022-2836(87)90652-8. [DOI] [PubMed] [Google Scholar]

Articles from Protein Science : A Publication of the Protein Society are provided here courtesy of The Protein Society

RESOURCES