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. 1992 Jul;1(7):843–849. doi: 10.1002/pro.5560010702

Structural homology between rbs repressor and ribose binding protein implies functional similarity.

C A Mauzy 1, M A Hermodson 1
PMCID: PMC2142147  PMID: 1304370

Abstract

The deduced amino acid sequence of the rbs repressor, RbsR, of Escherichia coli is homologous over its C-terminal 272 residues to the entire sequence of the periplasmic ribose binding protein. RbsR is also homologous to a family of bacterial repressor proteins including LacI. This implies that the structure of the repressor consists of a two-domain binding protein portion attached to a DNA-binding domain having the four-helix structure of the LacI headpiece. The implications of these relationships to the mechanism of this class of repressors are discussed.

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Selected References

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  1. Aggarwal A. K., Rodgers D. W., Drottar M., Ptashne M., Harrison S. C. Recognition of a DNA operator by the repressor of phage 434: a view at high resolution. Science. 1988 Nov 11;242(4880):899–907. doi: 10.1126/science.3187531. [DOI] [PubMed] [Google Scholar]
  2. Alberti S., Oehler S., von Wilcken-Bergmann B., Krämer H., Müller-Hill B. Dimer-to-tetramer assembly of Lac repressor involves a leucine heptad repeat. New Biol. 1991 Jan;3(1):57–62. [PubMed] [Google Scholar]
  3. Anraku Y. Transport of sugars and amino acids in bacteria. II. Properties of galactose- and leucine-binding proteins. J Biol Chem. 1968 Jun 10;243(11):3123–3127. [PubMed] [Google Scholar]
  4. Argos P., Mahoney W. C., Hermodson M. A., Hanei M. Structural prediction of sugar-binding proteins functional in chemotaxis and transport. J Biol Chem. 1981 May 10;256(9):4357–4361. [PubMed] [Google Scholar]
  5. Bowie J. U., Lüthy R., Eisenberg D. A method to identify protein sequences that fold into a known three-dimensional structure. Science. 1991 Jul 12;253(5016):164–170. doi: 10.1126/science.1853201. [DOI] [PubMed] [Google Scholar]
  6. Chakerian A. E., Tesmer V. M., Manly S. P., Brackett J. K., Lynch M. J., Hoh J. T., Matthews K. S. Evidence for leucine zipper motif in lactose repressor protein. J Biol Chem. 1991 Jan 25;266(3):1371–1374. [PubMed] [Google Scholar]
  7. Devereux J., Haeberli P., Smithies O. A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Res. 1984 Jan 11;12(1 Pt 1):387–395. doi: 10.1093/nar/12.1part1.387. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Farabaugh P. J. Sequence of the lacI gene. Nature. 1978 Aug 24;274(5673):765–769. doi: 10.1038/274765a0. [DOI] [PubMed] [Google Scholar]
  9. Gilliland G. L., Quiocho F. A. Structure of the L-arabinose-binding protein from Escherichia coli at 2.4 A resolution. J Mol Biol. 1981 Mar 5;146(3):341–362. doi: 10.1016/0022-2836(81)90392-2. [DOI] [PubMed] [Google Scholar]
  10. Gordon A. J., Burns P. A., Fix D. F., Yatagai F., Allen F. L., Horsfall M. J., Halliday J. A., Gray J., Bernelot-Moens C., Glickman B. W. Missense mutation in the lacI gene of Escherichia coli. Inferences on the structure of the repressor protein. J Mol Biol. 1988 Mar 20;200(2):239–251. doi: 10.1016/0022-2836(88)90237-9. [DOI] [PubMed] [Google Scholar]
  11. Jordan S. R., Pabo C. O. Structure of the lambda complex at 2.5 A resolution: details of the repressor-operator interactions. Science. 1988 Nov 11;242(4880):893–899. doi: 10.1126/science.3187530. [DOI] [PubMed] [Google Scholar]
  12. Kleina L. G., Miller J. H. Genetic studies of the lac repressor. XIII. Extensive amino acid replacements generated by the use of natural and synthetic nonsense suppressors. J Mol Biol. 1990 Mar 20;212(2):295–318. doi: 10.1016/0022-2836(90)90126-7. [DOI] [PubMed] [Google Scholar]
  13. Lipman D. J., Pearson W. R. Rapid and sensitive protein similarity searches. Science. 1985 Mar 22;227(4693):1435–1441. doi: 10.1126/science.2983426. [DOI] [PubMed] [Google Scholar]
  14. Luck L. A., Falke J. J. Open conformation of a substrate-binding cleft: 19F NMR studies of cleft angle in the D-galactose chemosensory receptor. Biochemistry. 1991 Jul 2;30(26):6484–6490. doi: 10.1021/bi00240a019. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Matthews B. W., Rossmann M. G. Comparison of protein structures. Methods Enzymol. 1985;115:397–420. doi: 10.1016/0076-6879(85)15029-9. [DOI] [PubMed] [Google Scholar]
  16. Mauzy C. A., Hermodson M. A. Structural and functional analyses of the repressor, RbsR, of the ribose operon of Escherichia coli. Protein Sci. 1992 Jul;1(7):831–842. doi: 10.1002/pro.5560010701. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Otwinowski Z., Schevitz R. W., Zhang R. G., Lawson C. L., Joachimiak A., Marmorstein R. Q., Luisi B. F., Sigler P. B. Crystal structure of trp repressor/operator complex at atomic resolution. Nature. 1988 Sep 22;335(6188):321–329. doi: 10.1038/335321a0. [DOI] [PubMed] [Google Scholar]
  18. Platt T., Files J. G., Weber K. Lac repressor. Specific proteolytic destruction of the NH 2 -terminal region and loss of the deoxyribonucleic acid-binding activity. J Biol Chem. 1973 Jan 10;248(1):110–121. [PubMed] [Google Scholar]
  19. Reidl J., Römisch K., Ehrmann M., Boos W. MalI, a novel protein involved in regulation of the maltose system of Escherichia coli, is highly homologous to the repressor proteins GalR, CytR, and LacI. J Bacteriol. 1989 Sep;171(9):4888–4899. doi: 10.1128/jb.171.9.4888-4899.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Richarme G. Associative properties of the Escherichia coli galactose-binding protein and maltose-binding protein. Biochim Biophys Acta. 1983 Oct 17;748(1):99–108. doi: 10.1016/0167-4838(83)90032-8. [DOI] [PubMed] [Google Scholar]
  21. Rolfes R. J., Zalkin H. Autoregulation of Escherichia coli purR requires two control sites downstream of the promoter. J Bacteriol. 1990 Oct;172(10):5758–5766. doi: 10.1128/jb.172.10.5758-5766.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Rolfes R. J., Zalkin H. Escherichia coli gene purR encoding a repressor protein for purine nucleotide synthesis. Cloning, nucleotide sequence, and interaction with the purF operator. J Biol Chem. 1988 Dec 25;263(36):19653–19661. [PubMed] [Google Scholar]
  23. Rolfes R. J., Zalkin H. Purification of the Escherichia coli purine regulon repressor and identification of corepressors. J Bacteriol. 1990 Oct;172(10):5637–5642. doi: 10.1128/jb.172.10.5637-5642.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Sams C. F., Vyas N. K., Quiocho F. A., Matthews K. S. Predicted structure of the sugar-binding site of the lac repressor. Nature. 1984 Aug 2;310(5976):429–430. doi: 10.1038/310429a0. [DOI] [PubMed] [Google Scholar]
  25. Valentin-Hansen P., Larsen J. E., Højrup P., Short S. A., Barbier C. S. Nucleotide sequence of the CytR regulatory gene of E. coli K-12. Nucleic Acids Res. 1986 Mar 11;14(5):2215–2228. doi: 10.1093/nar/14.5.2215. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Vyas N. K., Vyas M. N., Quiocho F. A. Comparison of the periplasmic receptors for L-arabinose, D-glucose/D-galactose, and D-ribose. Structural and Functional Similarity. J Biol Chem. 1991 Mar 15;266(8):5226–5237. [PubMed] [Google Scholar]
  27. Vyas N. K., Vyas M. N., Quiocho F. A. Sugar and signal-transducer binding sites of the Escherichia coli galactose chemoreceptor protein. Science. 1988 Dec 2;242(4883):1290–1295. doi: 10.1126/science.3057628. [DOI] [PubMed] [Google Scholar]
  28. Vyas N. K., Vyas M. N., Quiocho F. A. The 3 A resolution structure of a D-galactose-binding protein for transport and chemotaxis in Escherichia coli. Proc Natl Acad Sci U S A. 1983 Apr;80(7):1792–1796. doi: 10.1073/pnas.80.7.1792. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Weber I. T., McKay D. B., Steitz T. A. Two helix DNA binding motif of CAP found in lac repressor and gal repressor. Nucleic Acids Res. 1982 Aug 25;10(16):5085–5102. doi: 10.1093/nar/10.16.5085. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Weber I. T., Steitz T. A. Model of specific complex between catabolite gene activator protein and B-DNA suggested by electrostatic complementarity. Proc Natl Acad Sci U S A. 1984 Jul;81(13):3973–3977. doi: 10.1073/pnas.81.13.3973. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Wolberger C., Dong Y. C., Ptashne M., Harrison S. C. Structure of a phage 434 Cro/DNA complex. Nature. 1988 Oct 27;335(6193):789–795. doi: 10.1038/335789a0. [DOI] [PubMed] [Google Scholar]
  32. Zhang R. G., Joachimiak A., Lawson C. L., Schevitz R. W., Otwinowski Z., Sigler P. B. The crystal structure of trp aporepressor at 1.8 A shows how binding tryptophan enhances DNA affinity. Nature. 1987 Jun 18;327(6123):591–597. doi: 10.1038/327591a0. [DOI] [PubMed] [Google Scholar]
  33. von Wilcken-Bergmann B., Müller-Hill B. Sequence of galR gene indicates a common evolutionary origin of lac and gal repressor in Escherichia coli. Proc Natl Acad Sci U S A. 1982 Apr;79(8):2427–2431. doi: 10.1073/pnas.79.8.2427. [DOI] [PMC free article] [PubMed] [Google Scholar]

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