Opposite allosteric mechanisms in TetR and CAP

Protein Science

Volumn 18, Issue 4, 2009, Pages 775-781

  Seedorff, Jennifer E ^a   Rodgers, Michael E ^b   Schleif, Robert ^b  

^a JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b JOHNS HOPKINS UNIVERSITY   (United States)

Author keywords

CAP; CRP: allostery; DNA binding protein; Extrinsic allosteric mechanism; Half site operator; Intrinsic allosteric mechanism; Tet Repressor

Indexed keywords

CYCLIC AMP BINDING PROTEIN; DNA BINDING PROTEIN; GENE PRODUCT; PROTEIN TETR; UNCLASSIFIED DRUG;

ALLOSTERISM; ARTICLE; DNA BINDING; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN PURIFICATION; REPRESSOR GENE;

ALLOSTERIC REGULATION; CYCLIC AMP; CYCLIC AMP RECEPTOR PROTEIN; DNA; DNA-BINDING PROTEINS; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; PROTEIN BINDING; REPRESSOR PROTEINS; TETRACYCLINE;

EID: 63449119299     PISSN: 09618368     EISSN: 1469896X     Source Type: Journal    
DOI: 10.1002/pro.88     Document Type: Article

References (43)

1. Monod J, Wyman J, Changeux JP (1965) On the nature of allosteric transitions: a plausible model. J Mol Biol 12: 88-118.
2. Koshland DE, Né;emethy G, Filmer D (1966) Comparison of experimental binding data and theoretical models in proteins containing subunits. Biochemistry 5:365-385.
3. Hill AV (1913) The combinations of haemoglobin with oxygen and with carbon monoxide. I. Biochem J 5: 471-480.
4. Adair GS (1925) The hemoglobin system VI. The oxygen dissociation curve of hemoglobin. J Biol Chem 63: 529-545
5. Perutz MF (1970) Stereochemistry of cooperative effects in haemoglobin. Nature 228:726-734.
6. Perutz MF, Wilkinson AJ, Paoli M, Dodson GG (1998) The stereochemical mechanism of the cooperative effects in hemoglobin revisited. Annu Rev Biophys Biomol Struct 27:1-34.
7. Hillen W, Klockan G, Kaffenberger I, Wray LV, Reznikoff WS (1982) Purification of the Tet repressor and Tet operator from the transposon Tn1o and characterization of their interaction. J Biol Chem 257:6605-6613.
8. Adhya S, Garges S (1990) Positive control. J Biol Chem 265:10797-10800.
9. Kolb A, Bushy S, Buc H, Garges S, Adhya S (1993) Transcriptional regulation by cAMP and its receptor protein. Annu Rev Biochem 62:749-795.
10. Reznikoff W (1992) Catabolite gene activator protein activation of lac transcription. J Bacteriol 174:655-658.
11. 1. Identification of base-pairs involved in Tet repressor recognition. J Mol Biol 202:397-406.
12. Sizemore C, Wissmann A, Gülland U, Hillen W (1990) Quantitative analysis of Tn1o Tet repressor binding to a complete set of tet operator mutants. Nucleic Acids Res 18:2875-2880.
13. Orth P, Schnappinger D, Hillen W, Saenger W, Hinrichs W (2000) Structural basis of gene regulation by the tetracycline inducible Tet repressor-operator system. Nat Struct Biol 7:215-219.
14. Passner J, Steitz T (1997) The structure of a CAP-DNA complex having two cAMP molecules bound to each monomer. Proc Natl Acad Sci 94:2843-2847.
15. Timmes A, Rodgers M, Schleif R (2004) Biochemical and physiological properties of the DNA binding domain of AraC protein. J Mol Bio 340:731-738.
16. Kamionka A, Bogdanska-Urbaniak J, Scholz O, Hillen W (2004) Two mutations in the tetracycline repressor change the inducer anhydrotetracycline to a corepressor. Nucleic Acids Res 32:842-847.
17. Lederer T, Takahashi M, Hillen W (1995) Thermodynamic analysis of tetracycline-mediated induction of Tet repressor by a quantitative methylation protection assay. Anal Biochem 232:190-196.
18. Orth P, Cordes F, Schnappinger D, Hillen W, Saenger W, Hinrichs W (1998) Conformational changes of the Tet repressor induced by tetracycline trapping. J Mol Biol 279:439-447.
19. Hinrichs W, Kisker C, Duvel M, Muller A, Tovar K, Hillen W, Saenger W (1994) Structure of the Tet repressor-tetracycline complex and regulation of antibiotic resistance. Science 264:418-420.
20. Tiebel B, Aung-Hilbrich LM, Schnappinger D, Hillen W (1998) Conformational changes necessary for gene regulation by Tet repressor assayed by reversible disulfide bond formation. EMBO J 17:5112-5119.
21. Tiebel B, Radzwill N, Aung-Hilbrich LM, Helbl V, Steinhoff HJ, Hillen W (1999) Domain motions accompanying Tet repressor induction defined by changes of interspin distances at selectively labeled sites. J Mol Biol 290:229-240.
22. Tiebel B, Garke K, Hillen W (2000) Observing conformational and activity changes of Tet repressor in vivo, Nat Struct Biol 7:479-481.
23. Antonini SP, Hillen W, Ettner N, Hinrichs W, Fantucci P, Doglia SM, Bousquet JA, Chabbert M (1997) Molecular mechanics analysis of Tet repressor TRP-43 fluorescence. Biophys J 72:1800-1811.
24. Reichheld SE, Davidson AR (2006) Two-way interdomain signal transduction in tetracycline repressor. J Mol Biol 361:382-389
25. Alexsandrov A, Schuldt L, Hinrichs W, Simonson T (2008) Tet repressor induction by tetracycline: a molecular dynamics, continuum electrostatics, and crystallo- graphic study. J Mol Biol 378:898-912.
26. Garges S, Adhya S (1985) Sites of allosteric shift in the structure of the cyclic AMP receptor protein. Cell 41: 745-751.
27. Garges S, Adhya S (1988) Cyclic AMP-induced conformational change of cyclic AMP receptor protein (CRP): intragenic suppressors of cyclic AMP-independent CRP mutations. J Bacteriol 170:1417-1422.
28. Kim J, Adhya S, Garges S (1992) Allosteric changes in the cAMP receptor protein of Escherichia coli: hinge reorientation. Proc Natl Acad Sci 89:9700-9704.
29. Cheng X, Lee JC (1998) Differential perturbation of inter- subunit and interdomain communications by glycine 141 mutation in Escherichia coli CRP. Biochemistry 37: 51-60.
30. Baichoo N, Heyduk T (1999) Mapping cyclic nucleo-tide-induced conformational changes in cyclicAMP receptor protein by a protein footprinting technique using different chemical proteases. Protein Sci 8: 518-528.
31. Won H, Yamazaki T, Lee T, Yoon M, Park S, Kyogoku Y, Lee B (2000) Structural understanding of the allosteric conformational change of cyclic AMP receptor protein by cyclic AMP binding. Biochemistry 39:13953-13962.
32. Passner JM, Schultz SC, Steitz TA (2000) Modeling the cAMP-induced allosteric transition using the crystal structure of CAP-cAMP at 2,1 Å resolution. J Mol Biol 304:847-859.
33. Dong AC, Malecki JM, Lee L, Carpenter JF, Lee JC (2002) Ligand-induced conformational and structural dynamics changes in Escherichia coli cyclic AMP receptor protein. Biochemistry 41:6660-6667.
34. Harmer T, Wu M, Schleif R (2001) The role of rigidity in DNA looping-unlooping by AraC, Proc Natl Acad Sci 98: 427-431.
35. Ettner N, Müller G, Berens C, Backes H, Schnappinger D, Schreppel T, Pfteiderer K, Hillen W (1996) Fast large-scale purification of tetracycline repressor variants from overproducing Escherichia coli strains. J Chromatogr A 742:95-105
36. Schleif R, Wens ink P (1981) Practical methods in molecular biology. New York: Springer-Verlag.
37. Gill SC, von Hippel PH (1989) Calculation of protein extinction coefficients from amino acid sequence data. Anal Biochem 182:319-326.
38. Zhou Y, Zhang X, Ebright R (1991) Random mutagenesis of gene-sized DNA molecules by use of PGR with Taq DNA polymerase. Nucleic Acids Res 19:6052.
39. Burgess RR, Jendrisak JJ (1975) A procedure for the rapid, large-scale purification of Escherichia coli DNA- dependent RNA polymerase involving Polymin P precipitation and DNA-cellulose chromatography. Biochemistry 14:4634-4638.
40. Carra J, Schleif R (1993) Variation of half-site organization and DNA looping by AraC protein. EMBO J 12: 35-44-
41. Boothe JH, Morton J, Petisi JP, Wilkinson RG, Williams JH (1953) Tetracycline J Am Chem Soc 75:4621.
42. Rodgers M, Schleif R (2008) DNA tape measurements of AraC. Nucleic Acids Res 36:404-410.
43. Abramoff MD, Magelhaes PJ, Ram SJ (2004) Image processing with ImageJ. Biophoton Int 11:36-42.