An accessory DNA binding motif in the zinc finger protein Adr1 assists stable binding to DNA and can be replaced by a third finger

Biochemistry

Volumn 39, Issue 3, 2000, Pages 567-574

  Young, Elton T ^a   Kacherovsky, Nataly ^a   Cheng, Cheng ^a,b  

^a UNIVERSITY OF WASHINGTON SCHOOL OF MEDICINE   (United States)

^b NOVARTIS PHARMA AG   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

ALCOHOL DEHYDROGENASE; SINGLE STRANDED DNA; ZINC FINGER PROTEIN;

ARTICLE; BINDING AFFINITY; BINDING SITE; DNA BINDING; DNA STRUCTURE; ELECTROPHORETIC MOBILITY; ENZYME ACTIVITY; GENE EXPRESSION; GENE MUTATION; PRIORITY JOURNAL; PROTEIN ANALYSIS; REGULATOR GENE; YEAST;

ALCOHOL DEHYDROGENASE; BASE SEQUENCE; BINDING SITES; CONSENSUS SEQUENCE; DNA; DNA, SINGLE-STRANDED; DNA-BINDING PROTEINS; GENES, REGULATOR; KINETICS; OLIGONUCLEOTIDE PROBES; PLASMIDS; RECOMBINANT PROTEINS; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; SURFACE PLASMON RESONANCE; TRANSCRIPTION FACTORS; TRANSCRIPTION, GENETIC; ZINC FINGERS;

RICKETTSIA SP. PAR;

EID: 0034711731     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi992049r     Document Type: Article

References (43)

1. Klug, A., and Rhodes, D. (1987) Zinc fingers: a novel protein motif for DNA recognition, Trends Biochem. Sci. 1, 464-469.
2. Berg, J. M., and Godwin, H. A. (1997) Lessons from zinc-binding peptides, Annu. Rev. Biophys. Biomol. Struct. 26: 357-71.
3. Berg, J. M., and Shi, Y. (1996) The galvanization of biology: a growing appreciation for the roles of zinc. Science 271 (5252), 1081-5.
4. 1H nuclear magnetic resonance spectroscopy. A zinc finger structure with a third strand of beta-sheet, J. Mol. Biol. 228, 637-651.
5. Omichinski, J. G., et al. (1990) High-resolution three-dimensional structure of a single zinc finger from a human enhancer binding protein in solution, Biochemistry 29 (40), 9324-34.
6. Pavletich, N. P., and Pabo, C. O. (1991) Zinc finger-DNA recognition: crystal structure of a Zif268-DNA complex at 2.1 Å. Science 252, 809-817.
7. Pavletich, N. P., and Pabo, C. O. (1993) Crystal structure of a five-finger GLI-DNA complex: new perspectives on zinc fingers, Science 261, 1701-1707.
8. Wright, P. E. (1993) Structural basis for recognition of DNA by zinc finger and POU domain transcription factors, Nucleic Acids Symp. Ser. 29, 199.
9. Klevit, R. E., Herriott, J. R., and Horvath, S. J. (1990) Solution structure of a zinc finger domain of yeast ADR1, Proteins: Struct., Funct., Genet. 7(3), 215-26.
10. Fairall, L., et al. (1993) The crystal structure of a two zinc-finger peptide reveals an extension to the rules for zinc-finger/ DNA recognition, Nature 366, 483-487.
11. Nardelli, J., et al. (1991) Base sequence discrimination by zinc-finger DNA binding domains. Nature 349, 175-178.
12. Thukral, S. K. Morrison, M. L., and Young, E. T. (1992) Mutations in the zinc fingers of ADR1 that change the specificity of DNA binding and transactivation, Mol. Cell. Biol. 12 (6), 2784-92.
13. Thiesen, H. J., and Schroder, B. (1991) Amino acid substitutions in the SP1 zinc finger domain alter the DNA binding affinity to cognate SP1 target site. Biochem. Biophys. Res. Commun. 175 (1), 333-8.
14. Jamieson, A. C., Kim, S. H., and Wells, J. A. (1994) In vitro selection of zinc fingers with altered DNA-binding specificity, Biochemistry 33 (19), 5689-95.
15. Choo, Y., and Klug, A. (1997) Physical basis of a protein-DNA recognition code, Curr. Opin. Struct. Biol 7 (1), 117-25.
16. Taylor, W. E., and Young, E. T. (1990) cAMP-dependent phosphorylation and inactivation of yeast transcription factor ADRl does not affect DNA binding, Proc. Natl. Acad. Sci. U.S.A. 87 (11), 4098-102.
17. Rebar, E. J., and Pabo, C. O. (1994) Zinc finger phage: affinity selection of fingers with new DNA-binding specificities, Science 263 (5147), 671-3.
18. Desjarlais, J. R., and Berg, J. M. (1992) Redesigning the DNA-binding specificity of a zinc finger protein: a database-guided approach, Proteins: Struct., Funct., Genet. 12 (2), p 101-4.
19. Choo, Y., Sanchez-Garcia, I., and Klug, A. (1994) In vivo repression by a site-specific DNA-binding protein designed against an oncogenic sequence, Nature (London) 372, 642-645.
20. Beerli, R. R., et al. (1998) Toward controlling gene expression at will: specific regulation of the erbB-2/HER-2 promoter by using polydactyl zinc finger proteins constructed from modular building blocks, Proc. Natl. Acad. Sci. U.S.A 95(25), 14628-33.
21. Kim, J. S., and Pabo, C. O. (1998) Getting a handhold on DNA: design of poly-zinc finger proteins with femtomolar dissociation constants, Proc. Natl. Acad. Sci. U.S.A 95 (6), 2812-7.
22. Pomerantz, J. L., Wolfe, S. A., and Pabo, C. O. (1998) Structure-based design of a dimeric zinc finger protein, Biochemistry 37 (4), 965-70.
23. Smith, J., Berg, J. M., and Chandrasegaran, S. (1999) A detailed study of the substrate specificity of a chimeric restriction enzyme, Nucleic Acids Res. 27 (2), 674-81.
24. Ciriacy, M. (1975) Genetics of alcohol dehydrogenase in Saccharomyces cerevisiae. II. Two loci controlling synthesis of the glucose-repressible ADH II, Mol. Gen. Genet. 138 (2), 157-64.
25. Thukral, S. K., Eisen, A., and Young, E. T. (1991) Two monomers of yeast transcription factor ADR1 bind a palindromic sequence symmetrically to activate ADH2 expression, Mol Cell. Biol. 11 (3), 1566-77.
26. Thukral, S. K., Morrison, M. L., and Young, E. T. (1991) Alanine scanning site-directed mutagenesis of the zinc fingers of transcription factor ADR1: residues that contact DNA and that transactivate, Proc. Natl. Acad. Sci. U.S.A. 88 (20), 9188-92 [published erratum appears in (1993) Proc. Natl. Acad. Sci. U.S.A. 90 (16), 7908].
27. Thukral, S. K., et al. (1989) Localization of a minimal binding domain and activation regions in yeast regulatory protein ADR1, Mol. Cell. Biol. 9 (6), 2360-9.
28. Blumberg, H., et al. (1987) Two zinc fingers of a yeast regulatory protein shown by genetic evidence to be essential for its function, Nature 328 (6129), 443-5.
29. Bowers, P. M., Schaufler, L. E., and Klevit, R. E. (1999) A folding transition and novel zinc finger accessory domain in the transcription factor ADR1, Nat. Struct. Biol. 6 (5), 478-85 [in process citation].
30. Camier, S, Kacherovsky, N., and Young, E. T. (1992) A mutation outside the two zinc fingers of ADR1 can suppress defects in either finger, Mol. Cell. Biol. 12 (12), 5758-67.
31. Dutnall, R. N., Neuhaus, D., and Rhodes, D. (1996) The solution structure of the first zinc finger domain of SWI5: a novel structural extension to a common fold, Structure 4 (5), 599-611.
32. Omichinski, J. G., et al. (1997) The solution structure of a specific GAGA factor-DNA complex reveals a modular binding mode, Nat. Struct. Biol. 4 (2), 122-32 [see comments].
33. Schmiedeskamp, M., and Klevit, R. E. (1997) Paramagnetic cobalt as a probe of the orientation of an accessory DNA-binding region of the yeast ADR1 zinc-finger protein, Biochemistry 36 (46), 14003-11.
34. Hyre, D. E., and Klevit, R. E. (1998) A disorder-to-order transition coupled to DNA binding in the essential zinc-finger DNA-binding domain of yeast ADR1, J. Mol. Biol. 279 (4), 929-43.
35. Young, E. T., et al. (1998) Characterization of a p53-related activation domain in Adr1p that is sufficient for ADR1-dependent gene expression, J. Biol. Chem. 273 (48), 32080-7.
36. Sherman, F., Fink, G. R., and Lawrence, C. W. (1974) Methods of yeast genetics, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
37. Blackwell, T. K., and Weintraub, H. (1990) Differences and similarities in DNA binding preference of MyoD and E2A protein complexes revealed by binding site selection, Science 250, 1104-1110.
38. Baker, R. E., Gabrielsen, O., and Hall, B. D. (1986) Effects of tRNATyr point mutations on the binding of yeast RNA polymerase III transcription factor C, J. Biol. Chem. 261 (12), 5275-82.
39. Guarente, L., Yocum, R. R., and Gifford, P. (1982) A Gal10-Cyc 1 Hybrid yeast promotor identifies the GAL4 regulatory region as an upstream site, Proc. Natl. Acad. Sci. U.S.A. 79, 7410-7414.
40. Cheng, C., et al. (1994) Identification of potential target genes for Adrlp through characterization of essential nucleotides in UAS1, Mol. Cell. Biol. 14 (6), 3842-3852.
41. Blumberg, H., Hartshorne, T. A., and Young, E. T. (1988) Regulation of expression and activity of the yeast transcription factor ADR1, Mol. Cell. Biol. 8 (5), 1868-76.
42. Verdone, L., et al. (1996) Chromatin remodeling during Saccharomyces cerevisiae ADH2 gene activation. Mol. Cell. Biol. 16 (5), 1978-88.
43. Verdone, L., et al. (1997) Factors affecting Saccharomyces cerevisiae ADH2 chromatin remodeling and transcription, J. Biol. Chem. 272 (49), 30828-34.