Arc repressor - Operator DNA interactions and contribution of Phe10 to binding specificity

Biochemistry

Volumn 44, Issue 23, 2005, Pages 8387-8396

  Dostál, Lubomír ^a   Misselwitz, Rolf ^a   Welfle, Heinz ^a  

^a MAX DELBRÜCK CENTER FOR MOLECULAR MEDICINE   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING ENERGY; CONFORMATIONS; ENZYMES; FLUORESCENCE; HYDROGEN BONDS; HYDROPHOBICITY; MONOMERS; RAMAN SPECTROSCOPY;

CIRCULAR DICHROISM; DNA BINDING; RAMAN DIFFERENCE SPECTROSCOPY; VAN DER WAALS INTERACTIONS;

DNA;

AMINO ACID; ARC REPRESSOR PROTEIN; DEOXYRIBOSE; DNA; PHENYLALANINE; REPRESSOR PROTEIN; TRYPTOPHAN; UNCLASSIFIED DRUG;

ARTICLE; BACTERIOPHAGE P22; BINDING AFFINITY; CIRCULAR DICHROISM; COMPLEX FORMATION; CONFORMATION; CRYSTAL STRUCTURE; FLUORESCENCE; HYDROGEN BOND; HYDROPHOBICITY; MOLECULAR INTERACTION; NONHUMAN; OPERATOR GENE; PRIORITY JOURNAL; PROTEIN DNA INTERACTION; RAMAN SPECTROMETRY; REPRESSOR GENE; SALMONELLA;

AMINO ACID SUBSTITUTION; CIRCULAR DICHROISM; CRYSTALLOGRAPHY, X-RAY; DEOXYRIBONUCLEOSIDES; DEOXYRIBOSE; DNA, VIRAL; DNA-BINDING PROTEINS; HISTIDINE; HYDROPHOBICITY; NUCLEIC ACID CONFORMATION; OPERATOR REGIONS (GENETICS); PHENYLALANINE; PURINES; PYRIMIDINES; REPRESSOR PROTEINS; SALMONELLA; SPECTROMETRY, FLUORESCENCE; SPECTRUM ANALYSIS, RAMAN; THERMODYNAMICS; TRYPTOPHAN; TYROSINE; VIRAL PROTEINS;

SALMONELLA BACTERIOPHAGE;

EID: 20444404270     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi0476073     Document Type: Article

References (35)

1. Vershon, A. K., Youderian, P., Susskind, M. M., and Sauer, R. T. (1985) The bacteriophage P22 Arc and Mnt repressors, J. Biol. Chem. 260, 12124-12129.
2. Raumann, B. E., Brown, B. M., and Sauer, R. T. (1994) Major groove DNA recognition by β-sheets: The ribbon-helix-helix family of gene regulatory proteins, Curr. Opin. Struct. Biol. 4, 36-43.
3. Raumann, B. E., Rould, M. A., Pabo, C. O., and Sauer, R. T. (1994) DNA recognition by β-sheets in the Arc repressor-operator crystal structure, Nature 367, 754-757.
4. Schildbach, J. F., Karzai, A. W., Raumann, B. E., and Sauer, R. T. (1999) Origins of DNA-binding specificity: Role of protein contacts with DNA backbone, Proc. Natl. Acad. Sci. U.S.A. 96, 811-817.
5. Milla, M. E., Brown, B. M., and Sauer, R. T. (1994) Protein stability effects of a complete set of alanine substitutions in Arc repressor, Nat. Struct. Biol. 1, 518-523.
6. Brown, B. M., Milla, M. E., Smith, T. L., and Sauer, R. T. (1994) Scanning mutagenesis of the Arc repressor as functional probe of operator recognition, Nat. Struct. Biol. 1, 164-168.
7. Breg, J. N., van Ophesden, J. H. J., Burgering, M. J. M., Boelens, R., and Kaptein, R. (1990) Structure of Arc repressor in solution: Evidence for a family of β-sheet DNA-binding proteins, Nature 346, 586-589.
8. Bonvin, A. M. J. J., Vis, H., Breg, J. N., Burgering, M. J. M., Boelens, R., and Kaptein, R. (1994) Nuclear magnetic resonance solution structure of the Arc repressor using relaxation matrix calculations, J. Mol. Biol. 236, 328-341.
9. Nooren, I. M. A., Bietveld, A. W. M., Melacini, G., Sauer, R. T., Kaptein, R., and Boelens, R. (1999) The solution structure and dynamics of an Arc repressor mutant reveal premelting conformational changes related to DNA binding, Biochemistry 38, 6035-6042.
10. Schildbach, J. F., Milla, M. E., Jeffrey, P. D., Raumann, B. E., and Sauer, R. T. (1995) Crystal structure, folding, and operator binding of the hyperstable Arc repressor mutant PL8, Biochemistry 34, 1405-1412.
11. Bloomfield, V. A., Crothers, D. M., and Tinoco, I., Jr. (1999) Electronic and vibrational spectroscopy, in Nucleic Acids, Structures, Properties, and Functions, pp 165-221, University Science Books, Sausalito, CA.
12. Dostál, L., Khare, D., Bok, J., Heinemann, U., Lanka, E., and Welfle, H. (2003) RP4 repressor protein KorB binds to the major groove of the operator DNA: A Raman study, Biochemistry 42, 14476-14482.
13. -1 in the Raman spectra of tyrosyl residues in proteins and certain model compounds, Biochemistry 14, 4870-4876.
14. Serban, D., Arcineigas, S. F., Vorgias, C. E., and Thomas, G. J., Jr. (2003) Structure and dynamics of the DNA-binding protein HU of B. stearothermophilus investigated by Raman and ultraviolet-resonance Raman spectroscopy, Protein Sci. 12, 861-870.
15. Overman, S. A., and Thomas, G. J., Jr. (1999) Raman markers of nonaromatic side chains in an α-helix assembly: Ala, Asp, Glu, Gly, Ile, Leu, Lys, Ser, and Val residues of phage fd subunits, Biochemistry 38, 4018-4027.
16. 2H labels in coat protein subunits, Biochemistry 37, 5654-5665.
17. Miura, T., Takeuchi, H., and Harada, I. (1989) Tryptophan Raman bands sensitive to hydrogen bonding and side-chain conformation, J. Raman Spectrosc. 20, 667-671.
18. Miura, T., Takeuchi, H., and Harada, I. (1988) Characterization of individual tryptophan side chains in proteins using Raman spectroscopy and hydrogen deuterium exchange kinetics, Biochemistry 27, 88-94.
19. Miura, T., Takeuchi, H., and Harada, I. (1991) Raman spectroscopic characterization of tryptophan side chains in lysozyme bound to inhibitors: Role of hydrophobic box in the enzymatic function, Biochemistry 30, 6074-6080.
20. Thomas, G. J., Jr., and Tsuboi, M. (1993) Raman spectroscopy of nucleic acids and their complexes, Adv. Biophys. Chem. 3, 1-70.
21. Thomas, G. J., Jr., and Wang, A. H.-J. (1988) Laser Raman spectroscopy of nucleic acids, Nucleic Acids Mol. Biol. 2, 1-30.
22. Benevides, J. M., Li, T., Lu, X.-J., Srinivasan, A. R., Olson, W. K., Weiss, M. A., and Thomas, G. J., Jr. (2000) Protein-directed DNA structure II. Raman spectroscopy of a leucine zipper bZIP complex, Biochemistry 39, 548-556.
23. Krafft, C., Hinrichs, W., Orth, P., Saenger, W., and Welfle, H. (1998) Interaction of Tet repressor with operator DNA and with tetracycline studied by infrared and Raman spectroscopy, Biophys. J. 74, 63-71.
24. Dostál, L., Chen, C. Y., Wang, A. H., and Welfle, H. (2004) Partial B-to-A DNA transition upon minor groove binding of protein Sac7d monitored by Raman spectroscopy, Biochemistry 42, 9600-9609.
25. Benevides, J. M., Chan, G., Lu, X.-J., Olson, W. K., Weiss, M. A., and Thomas, G. J., Jr. (2000) Protein-directed DNA structure. I. Raman spectroscopy of a high-mobility-group box with application to human sex reversal, Biochemistry 39, 537-547.
26. Benevides, J. M., Kukolj, G., Autexier, C., Aubrey, K. L., DuBow, M. S., and Thomas, G. J., Jr. (1994) Secondary structure and interaction of phage D108 Ner repressor with a 61-base-pair operator: Evidence for altered protein and DNA structures in the complex, Biochemistry 33, 10701-10710.
27. Movileanu, L., Benevides, J. M., and Thomas, G. J., Jr. (1999) Temperature dependence of the Raman spectrum of DNA. Part I. Raman signatures of premelting and melting transitions of poly-(dA-dT)·poly(dA-dT), J. Raman Spectrosc. 30, 637-649.
28. Prescott, B., Steinmetz, W., and Thomas, G. J., Jr (1984) Characterization of DNA structures by Raman spectroscopy, Biopolymers 23, 235-256.
29. Thomas, G. J., Jr, Benevides, J. M., Overman, S. A., Ueda, T., Ushizawa, K, Saitoh, M., and Tsuboi, M. (1995) Polarized Raman spectra of oriented fibres of A-DNA and B-DNA: Anisotropic and isotropic local Raman tensors of base and backbone vibrations, Biophys. J. 68, 1073-1088.
30. Khare, D., Ziegelin, G., Lanka, E., and Heinemann, U. (2004) Sequence-specific DNA binding determined by contacts outside the helix-turn-helix motif of the ParB homolog KorB, Nat. Struct. Mol. Biol. 11, 656-663.
31. Movileanu, L., Benevides, J. M., and Thomas, G. J., Jr. (2002) Temperature dependence of the Raman spectrum of DNA. II. Raman signatures of premelting and melting transitions of poly-(dA)·poly(dT) and comparison with poly(dA-dT)·poly(dA-dT), Biopolymers 63, 181-194.
32. R3, Biochemistry 30, 5955-5963.
33. Benevides, J. M., Weiss, M. A., and Thomas, G. J., Jr. (1991) Design of the helix-turn-helix motif: Nonlocal effects of quaternary structure in DNA recognition investigated by laser Raman spectroscopy, Biochemistry 30, 4381-4388.
34. Benevides, J. M., Weiss, M. A., and Thomas, G. J., Jr. (1994) An altered specificity mutation in the λ repressor induces global reorganization of the protein-DNA interface, J. Biol. Chem. 269, 10869-10878.
35. Steiner, T., and Koellner, G. (2001) Hydrogen bonds with π-acceptors in proteins: Frequencies and role in stabilizing local 3D structures, J. Mol. Biol. 305, 535-557.