Solution structure of the DNA binding domain of AraC protein

Proteins: Structure, Function and Bioinformatics

Volumn 77, Issue 1, 2009, Pages 202-208

  Rodgers, Michael E ^a   Schleif, Robert ^a  

^a JOHNS HOPKINS UNIVERSITY   (United States)

Author keywords

Gene regulation; NMR; Transcription factor

Indexed keywords

ARAC PROTEIN; DNA BINDING PROTEIN; MARA PROTEIN; ROB PROTEIN; UNCLASSIFIED DRUG;

ALPHA HELIX; ARTICLE; ENERGY; NONHUMAN; PRIORITY JOURNAL; PROTEIN DNA BINDING; PROTEIN DOMAIN; PROTEIN MOTIF; PROTEIN STRUCTURE; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY;

ARAC TRANSCRIPTION FACTOR; DNA; ESCHERICHIA COLI PROTEINS; MAGNETIC RESONANCE SPECTROSCOPY; MODELS, BIOLOGICAL; PROTEIN BINDING; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY;

ESCHERICHIA COLI;

EID: 70349313266     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.22431     Document Type: Article

References (46)

1. Gallegos M, Schleif R, Bairoch A, Hofmann K, Ramos J. AraC/XylS family of transcriptional regulators. Microbiol Mol Biol Rev 1997;61:393-410.
2. Egan SM. Growing repertoire of AraC/XylS activators. J Bacteriol 2002;184:5529-5532.
3. Soisson S, MacDougall-Shackleton B, Schleif R, Wolberger C. Structural basis for ligand-regulated oligomerization of AraC. Science 1997;276:421-425. (Pubitemid 27180705)
4. Bustos S, Schleif R. Functional domains of AraC protein. Proc Natl Acad Sci USA 1993;90:5638-5642.
5. Rodgers ME, Holder N, Dirla S, Schleif R. Functional modes of the regulatory arm of AraC. Proteins 2009;74:81-90.
6. Saviola B, Seabold R, Schleif R. Arm-domain interactions in AraC. J Mol Biol 1998;278:539-548.
7. Wu M, Schleif R. Mapping arm-DNA-binding domain interactions in AraC. J Mol Biol 2001;307:1001-1009. (Pubitemid 33029949)
8. Lobel R, Schleif R. DNA looping and unlooping by AraC protein. Science 1990;250:528-532. (Pubitemid 120031777)
9. Carra J, Schleif R. Variation of half-site organization and DNA looping by AraC protein. EMBO J 1993;12:35-44. (Pubitemid 23042380)
10. Seabold R, Schleif R. Apo-AraC actively seeks to loop. J Mol Biol 1998;278:529-538.
11. Harmer T, Wu M, Schleif R. The role of rigidity in DNA looping-unlooping by AraC. Proc Natl Acad Sci USA 2001;98:427-431. (Pubitemid 32105057)
12. Schleif R. Regulation of the L-arabinose operon of Escherichia coli. Trends Genet 2000;16:559-565. (Pubitemid 30843834)
13. Schleif R. The AraC protein: a love-hate relationship. Bio Essays 2003;25:274-282.
14. Martin K, Huo L, Schleif R. The DNA loop model for ara repression: AraC protein occupies the proposed loop sites in vivo and repression-negative mutations lie in these same sites. Proc Nat Acad Sci USA 1986;83:3654-3658. (Pubitemid 16062343)
15. Grainger DC, Belyaeva TA, Lee DJ, Hyde EI, Busby SJW. Binding of the Escherichia coli MelR protein to the melAB promoter: orientation of MelR subunits and investigation of MelR-DNA contacts. Mol Microbiol 2003;48:335-348.
16. Egan S, Schleif R. DNA-dependent renaturation of an insoluble DNA binding protein. J Mol Biol 1994;243:821-829.
17. Domínguez-Cuevas P, Marín P, Busby S, Ramos JL, Marqués S. Roles of effectors in XylS-dependent transcription activation: intramolecular domain derepression and DNA binding. J Bacteriol 2008;190:3118-3128. (Pubitemid 351581406)
18. Yamazaki H, Tomono A, Ohnishi Y, Horinouchi S. DNA-binding specificity of AdpA, a transcriptional activator in the A-factor regulatory cascade in Streptomyces griseus. Mol Microbiol 2004;53:555-572. (Pubitemid 38998175)
19. Rhee S, Martin RG, Rosner JL, Davies DR. A novel DNA-binding motif in MarA: the first structure for an AraC family transcriptional activator. Proc Natl Acad Sci USA 1998;95:10413-10418. (Pubitemid 28413081)
20. Kwon HJ, Bennik MH, Demple B, Ellenberger T. Crystal structure of the Escherichia coli Rob transcription factor in complex with DNA. Nat Struct Biol 2000;7:424-430. (Pubitemid 30250008)
21. Spolar RS, Record MT Jr. Coupling of local folding to site-specific binding of proteins to DNA. Science 1994;263:777-784.
22. Schleif RF, Wensink PC. Practical methods in molecular biology. New York: Springer-Verlag; 1981. pp 196-198.
23. Marley J, Lu M, Bracken C. A method for efficient isotopic labeling of recombinant proteins. J Biomol NMR 2001;20:71-75. (Pubitemid 32519656)
24. Pace CN, Vajdos F, Lee L, Grimsley G, Gray T. How to measure and predict the molar absorption coefficient of a protein. Protein Sci 1995;4:2411-2423.
25. Timmes A, Rodgers ME, Schleif R. Biochemical and physiological properties of the DNA binding domain of AraC protein. J Mol Biol 2004;340:731-738. (Pubitemid 38829634)
26. 2O mixtures. J Phys Chem 1960;64:632-637.
27. Delaglio F, Grzesiek S, Vuister GW, Zhu G, Pfeifer J, Bax A. NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J Biomol NMR 1995;6:277-293.
28. Johnson BA, Blevins RA. NMRView: a computer program for the visualization and analysis of NMR data. J Biomol NMR 1994;4:603-614.
29. Keller R. The computer aided resonance assignment tutorial, 1st ed. Switzerland: Cantina-Verlag; 2004. ISBN 3-85600-112-3.
30. Herrmann T, Güntert P, Wüthrich K. Protein NMR structure determination with automated NOE-identification in the NOESY spectra using the new software ATNOS. J Biomol NMR 2002;24:171-189. (Pubitemid 36113646)
31. Herrmann T, Güntert P, Wüthrich K. Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA. J Mol Biol 2002;319:209-227. (Pubitemid 34729497)
32. Lopez-Mendez B, Jee J-G, Pantoja-Uceda D, Güntert P. Improved automated NMR structure calculation with CYANA 20 NMR. Toronkai Koen Yoshishu 2003;42:282-283.
33. Güntert P. Automated NMR structure calculation with CYANA. Meth Mol Biol 2004;278:353-378.
34. Cornilescu G, Delaglio F, Bax A. Protein backbone angle restraints from searching a database for chemical shift and sequence homology. J Biomol NMR 1999;13:289-302. (Pubitemid 29143535)
35. Nederveen AJ, Doreleijers JF, Vranken W, Miller Z, Spronk CAEM, Nabuurs SB, Güntert P, Livny M, Markley JL, Nilges M, Ulrich EL, Kaptein R, Bonvin AMJJ. RECOORD: a REcalculated COORdinates Database of 5001 proteins from the PDB using restraints from the BioMagResBank. Proteins 2005;59:662-672. (Pubitemid 40695843)
36. Laskowski RA, Rullmann JAC, MacArthur MW, Kaptein R, Thornton JM. AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR. J Biomol NMR 1996;8:477-486. (Pubitemid 126706801)
37. Koradi R, Billeter M, Wüthrich K. MOLMOL: a program for display and analysis of macromolecular structures. J Mol Graphics 1996;14:51-55. (Pubitemid 26152976)
38. Humphrey W, Dalke A, Schulten K. VMD - visual molecular dynamics. J Mol Graphics 1996;14:33-38.
39. Eustance R, Bustos S, Schleif R. Reaching out: locating and lengthening the interdomain linker in AraC protein. J Mol Biol 1994;242:330-338. (Pubitemid 2134849)
40. Liu Y, Eisenberg D. 3D domain swapping: as domains continue to swap. Protein Sci 2002;11:1285-1298. (Pubitemid 34547201)
41. Stejskal EO, Tanner JE. Spin diffusion measurements: spin echos in the presence of a time-dependent field gradient. J Chem Phys 42 1965;42:288-291.
42. Gibbs SJ, Johnson CSJ. A PFG experiment for accurate diffusion and flow studies in the presence of eddy currents. J Magn Reson 1991;93:395-402.
43. Niland P, Huhne R, Müller-Hill B. How AraC interacts specifically with its target DNAs. J Mol Biol 1996;264:667-674. (Pubitemid 27013552)
44. Saviola B, Seabold R, Schleif R. DNA bending by AraC: a negative mutant. J Bacteriol 1998;180:4227-4232. (Pubitemid 28373529)
45. Jair K, Yu X, Skarstad K, Thöny B, Fujita N, Ishihama A, Wolf R Jr. Transcriptional activation of promoters of the superoxide and multiple antibiotic resistance regulons by Rob, a binding protein of the Escherichia coli origin of chromosomal replication. J Bacteriol 1996;178:2507-2513. (Pubitemid 26134472)
46. Harmer T, Schleif R. The C-terminal end of AraC tightly binds to the rest of its domain. J Biol Chem 2001;276:4886-4888. (Pubitemid 37371376)