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Structural studies of protein–nucleic acid interaction: the sources of sequence-specific binding

Published online by Cambridge University Press:  17 March 2009

Thomas A. Steitz
Affiliation:
Department of Molecular Biophysics and Biochemistry and Howard Hughes Medical Institute at Yale University

Extract

Structural studies of DNA-binding proteins and their complexes with DNA have proceeded at an accelerating pace in recent years due to important technical advances in molecular genetics, DNA synthesis, protein crystallography and nuclear magnetic resonance. The last major review on this subject by Pabo & Sauer (1984) summarized the structural and functional studies of the three sequence-specific DNA-binding proteins whose crystal structures were then known, the E. coli catabolite gene activator protein (CAP) (McKay & Steitz, 1981; McKay et al. 1982; Weber & Steitz, 1987), a cro repressor from phage λ (Anderson et al. 1981), and the DNA-binding proteolytic fragment of λcI repressor protein (Pabo & Lewis, 1982) Although crystallographic studies of the E. coli lac repressor protein were initiated as early as 1971 when it was the only regulatory protein available in sufficient quantities for structural studies (Steitz et al. 1974), little was established about the structural aspects of DNA-binding proteins until the structure of CAP was determined in 1980 followed shortly thereafter by the structure of λcro repressor and subsequently that of the λ repressor fragment. There are now determined at high resolution the crystal structures of seven prokaryotic gene regulatory proteins or fragments [CAP, λcro, λcI repressor fragment, 434 repressor fragment (Anderson et al. 1987), 434 cro repressor (Wolberger et al. 1988), E. coli trp repressor (Schevitz et al. 1985), E. coli met repressor (Rafferty et al. 1989)], EcoR I restriction endonuclease (McClarin et al. 1986), DNAse I (Suck & Ofner, 1986), the catalytic domain of γδ resolvase (Hatfull et al. 1989) and two sequence-independent double-stranded DNA-binding proteins [the Klenow fragment of E. coli DNA polymerase I (Ollis et al. 1985) and the E. coli Hu protein (Tanaka et al., 1984)].

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Research Article
Copyright
Copyright © Cambridge University Press 1990

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References

Abdel-Meguid, S. S., Grindley, N. D. F., Smyth Templeton, N. & Steitz, T. A. (1984). Cleavage of the site-specific recombination protein γδ resolvase: the smaller of two fragments binds DNA specifically. Proc. natn. Acad. Sci. USA 81, 20012005.CrossRefGoogle Scholar
Abdel-Meguid, S. S., Murthy, H. M. K. & Steitz, T. A. (1986). Preliminary X-ray diffraction studies of the putative catalytic domain of γδ resolvase from Escherichia coli. J. biol. Chem. 261, 1593415935.Google Scholar
Adler, K., Beyreuther, K., Fanning, E., Geisler, N., Gronenborn, B., Klemm, A., Müller-Hill, B., Pfahl, M., Schmitz, A. (1972). How Lac repressor binds to DNA. Nature 237, 322326.CrossRefGoogle Scholar
Aggarwal, A. K., Rodgers, D. W., Drottar, M., Ptashne, M. & Harrison, S. C. (1988). Recognition of a DNA operator by the repressor of phage 434: a view at high resolution. Science 242, 99–07.CrossRefGoogle ScholarPubMed
Aiba, H. (1983). Autoregulation of the Escherichia coli crp gene: CRP is a transcriptional repressor for its own gene. Cell 32, 141149.CrossRefGoogle ScholarPubMed
Aiba, H., Fujimoto, S. & Ozaki, N. (1982). Molecular cloning and nucleotide sequencing of the gene for E. coli cAMP receptor protein. Nucl. Acids Res. 10, 1345.CrossRefGoogle ScholarPubMed
Aiba, H., Nakamura, T., Mitani, H. & Mori, H. (1985). Mutations that alter the allosteric nature of cAMP receptor protein of Escherichia coli. EMBO. J. 4, 33293332.Google ScholarPubMed
Anderson, J., Ptashne, M. & Harrison, S. C. (1984). Co-crystals of the DNA-binding domain of phage 434 repressor and a synthetic phage 434 operator. Proc. natn. Acad. Sci. USA 81, 13071311.CrossRefGoogle Scholar
Anderson, J. E., Ptashne, M. & Harrison, S. C. (1985). A phage repressor-operator complex at 7 Å resolution. Nature 316, 596601.CrossRefGoogle ScholarPubMed
Anderson, J. E., Ptashne, M. & Harrison, S. C. (1987). Structure of the repressor-operator complex of bacteriophage 434. Nature 326, 846852.CrossRefGoogle ScholarPubMed
Anderson, W. F., Cygler, M., Vandonselaar, M., Ohlendorf, D. H., Matthews, B. W., Kim, J. & Takeda, Y. (1983). Crystallographic data for complexes of the cro repressor with DNA. J. molec. Biol. 168, 903906.CrossRefGoogle ScholarPubMed
Anderson, W. F., Ohlendorf, D. H., Takeda, Y. & Matthews, B. W. (1981). Structure of the cro repressor from bacteriophage λ and its interaction with DNA. Nature 290, 754758.CrossRefGoogle ScholarPubMed
Anderson, W. F., Takeda, Y., Ohlendorf, D. H. & Matthews, B. W. (1982). Proposed α-helical super-secondary structure associated with protein-DNA recognition. J. molec. Biol. 159, 745751.CrossRefGoogle ScholarPubMed
Benson, N., Sugiono, P. & Yonderian, P. (1988). DNA sequence determinants of λ repressor binding in vivo. Genetics 118, 2129.Google ScholarPubMed
Berg, J. M. (1988). Proposed structure for the zinc-binding domains from transcription factor IIIA and related proteins. Proc. natn. Acad. Sci. USA 85, 99102.CrossRefGoogle ScholarPubMed
Besse, M., Von Wilcken-Bergmann, B. & Müller-Hill, B. (1986). Synthetic lac operator mediates repression through lac repressor when introduced upstream and downstram from lac repressor. EMBO J. 5, 13771381.Google Scholar
Bhat, T. N., Blow, D. M. & Brick, P. (1982). Tyrosyl-tRNA synthetase forms a mononucleotide-binding fold. J. molec. Biol. 158, 699709.CrossRefGoogle ScholarPubMed
Boelens, R., Scheek, R. M., Van Boom, J. H. & Kaptein, R. (1987). Complex of lac repressor headpiece with a 14 base-pair lac operator fragment studied by two-dimensional nuclear magnetic resonance. J. molec. Biol. 193, 213216.CrossRefGoogle ScholarPubMed
Bogenhagen, D. F., Sakonju, S. & Brown, D. D. (1980). A control region in the centre of the 5S RNA gene directs specific initiation of transcription: the 3′ border of the region. Cell 19, 2735.CrossRefGoogle Scholar
Brayer, G. D. & Mcpherson, A. (1983). Refined structure of the gene 5 DNA binding protein from bacteriophage fd. J. molec. Biol. 169, 565596.CrossRefGoogle ScholarPubMed
Brennan, R. G., Takeda, Y., Kim, J., Anderson, W. F. & Matthews, B. W. (1986). Crystallization of a complex of cro repressor with a 17 base-pair operator. J. molec. Biol. 188, 115118.CrossRefGoogle ScholarPubMed
Brick, P., Bhat, T. N. & Blow, D. M. (1989). Structure of tyrosyl-tRNA synthetase refined at 2·3 Å resolution. Interaction of the enzyme with the tyrosyl adenylate intermediate. J. molec. Biol, in press.Google Scholar
Bricogne, G. (1976). Methods and programs for direct-space exploitation of geometric redundancies. Acta Crystallogr. A32, 832.CrossRefGoogle Scholar
Brunie, S., Mellot, P., Zelwer, C., Risler, J.-L., Blanquet, S. & Fayat, G. (1987). Structure-activity relationships of methionyl-tRNA synthetase: graphics modelling and genetic engineering. J. molec. Graphics 5, 1828.CrossRefGoogle Scholar
Brutlag, D., Atkinson, M. R., Setlow, P. & Kornberg, A. (1969). An active fragment of DNA polymerase produced by proteolytic cleavage. Biochem. biophys. Res. Comm. 37, 982989.CrossRefGoogle ScholarPubMed
Brutlag, D. & Kornberg, A. (1972). Enzymatic synthesis of doexyribonucleic acid. J. biol. Chem. 247, 241248.Google Scholar
Burlingame, R. W., Love, W. E., Wang, B.-C., Hamlin, R., Xuong, N. H. & Moudrianankis, E. N. (1985). Crystallographic structure of the octameric histone core of the nucleosome at a resolution of 3·3 Å. Science 228, 546553.CrossRefGoogle Scholar
Carter, C. W. & Kraut, J. (1974). A proposed model for interaction of polypeptides with RNA. Proc. natn. Acad. Sci. USA 71, 283287.CrossRefGoogle ScholarPubMed
Charlier, B. M., Maurizot, J. C. & Zaccui, G. (1980). Neutron scattering studies of lac repressor. Nature (London) 286, 423425.CrossRefGoogle ScholarPubMed
Church, G. M., Sussman, J. L. & Kim, S.-H. (1977). Secondary structure complementarity between DNA and proteins. Proc. natn. Acad. Sci. USA 74, 14581462.CrossRefGoogle Scholar
Coll, M., Frederick, C. A., Wang, A. H.-J. & Rich, A. (1987). A bifurcated hydrogen-bonded conformation in the d(AT) base pairs of the DNA dodecamer d(CGCAAATTTGCG) and its complex with distamycin. Proc. natn. Acad. Sci. USA 84, 83858389.CrossRefGoogle Scholar
Cossart, P. & Gicquel-Sanzey, B. (1982). Cloning and sequence of the crp gene of Escherichia coli K12. Nucl. Acids Res. 10, 13631378.CrossRefGoogle Scholar
La Cour, T. F. M., Nyborg, J., Thirup, S. & Clark, B. F. C. (1985). Structural details of the binding of guanosine diphosphate to elongation factor Tu from E. coli as studies by X-ray crystallography. EMBO J. 4, 23852388.Google Scholar
Crick, F. H. C. & Klug, A. (1975). Kinky helix. Nature 255, 530533.CrossRefGoogle ScholarPubMed
De Crombrugghe, B., Busby, S. & Buc, H. (1984). Cyclic AMP receptor protein: role in transcription activation. Science 224, 831838.CrossRefGoogle ScholarPubMed
Delarue, M. & Moras, D. (1989). RNA structure. In Nucleic Acids and Molecular biology, vol. 3 (ed. Eckstein, F. and Lilley, D. M. J.), pp. 182196. Springer-Verlag.CrossRefGoogle Scholar
Derbyshire, V., Freemont, P. S., Sanderson, M. R., Beese, L. S., Friedman, J. M., Steitz, T. A. & Joyce, C. M. (1988). Genetic and crystallographic studies of the 3′,5′-exonucleolytic site of DNA polymerase I. Science 240, 199201.CrossRefGoogle ScholarPubMed
Diakun, G. P., Fairall, L. & Klug, A. (1986). EXAFS study of the zinc-binding sites in the protein transcription factor IIIA. Nature 324, 698699.CrossRefGoogle ScholarPubMed
Dickerson, R. E. (1983). Base sequence and helix structure variation in B- and A-DNA. J. molec. Biol. 166, 419441.CrossRefGoogle Scholar
Dickerson, R. E. & Drew, H. R. (1981). Structure of a B-DNA dodecamer. II. Influence of base sequence on helix structure. J. molec. Biol. 149, 761786.CrossRefGoogle ScholarPubMed
Dickson, R. C., Abelson, J., Barnes, W. M. & Reznikoff, W. S. (1975). Genetic regulation: the lac control region. Science 187, 2735.CrossRefGoogle ScholarPubMed
Digabriele, A. D., Sanderson, M. R. & Steitz, T. A. (1989). Crystal lattice packing is important in determining the bend of a DNA dodecamer containing an adenine tract. Proc. natn. Acad. Sci. USA 85, 18161820.CrossRefGoogle Scholar
Drew, H. R. & Travers, A. A. (1984). DNA structural variations in the E. coli tyr T promoter. Cell 37, 491502.CrossRefGoogle Scholar
Ebright, R. H., Cossart, P., Gicquel-Sanzey, B. & Beckwith, J. (1984). Mutations that alter the DNA sequence specificity of the catabolite gene activator protein of E. coli. Nature 311, 232235.CrossRefGoogle ScholarPubMed
Ebright, R. H., Kolb, A., Buc, H., Kunkel, T. A., Krakow, J. S. & Beckwith, J. (1987). Role of glutamic acid-181 in DNA-sequence recognition by the catabolite gene activator protein (CAP) of Escherichia coli: altered DNA-sequence-recognition properties of [Val181]CAP and [Leu181]CAP. Proc. natn. Acad. Sci. USA 84, 60836087.CrossRefGoogle Scholar
Ebright, R. H., Le Grice, S. F. J., Miller, J. P. & Krakow, J. S. (1985). Analogs of cyclic AMP that elicit the biochemically defined conformational change in catabolite gene activator protein (CAP) but do not stimulate binding to DNA. J. molec. Biol. 182, 92107.CrossRefGoogle ScholarPubMed
Fersht, A. (1985). Enzyme Structure and Mechanism, 2nd ed.New York: W. H. Freeman & Co.Google Scholar
Files, J. G. & Weber, K. (1976). Limited proteolytic digestion of lac repressor by trypsin. J. biol. Chem. 251, 33863391.Google ScholarPubMed
Frankel, A. D. & Pabo, C. O. (1988). Fingering too many proteins. Cell 53, 675.CrossRefGoogle ScholarPubMed
Frederick, C. A., Grable, J., Melia, M., Samudzi, C., Jen-Jacobson, L., Wang, B.-C., Greene, P. J., Boyer, H. W. & Rosenberg, J. M. (1984). Kinked DNA in crystalline complex with EcoRI endonuclease. Nature 309, 327331.CrossRefGoogle ScholarPubMed
Freemont, P. S., Friedman, J. M., Beese, L. S., Sanderson, M. R. & Steitz, T. A. (1988). Cocrystal structure of an editing complex of Klenow fragment with DNA. Proc. natn. Acad. Sci. USA 85, 89248928.CrossRefGoogle ScholarPubMed
Freemont, P. S., Ollis, D. L., Steitz, T. A. & Joyce, C. M. (1986). A domain of the Klenow fragment of Escherichia coli DNA polymerase I has polymerase but no exonuclease activity. Proteins 1, 6673.CrossRefGoogle ScholarPubMed
Friedman, D. I. (1988). Integration host factor: a protein for all reasons. Cell 55, 545554.CrossRefGoogle ScholarPubMed
Garges, S. & Adhya, S. (1985). Sites of allosteric shift in the structure of the cyclic AMP receptor protein. Cell 41, 745751.CrossRefGoogle ScholarPubMed
Gartenberg, M. R. & Crothers, D. M. (1988). DNA sequence determinants of CAP-induced bending and protein binding affinity. Nature 333, 824829.CrossRefGoogle ScholarPubMed
Gent, M. E., Gronenborn, A. M., Davies, T. W. & Clore, G. M. (1987). Biochem. J. 242, 645653.CrossRefGoogle Scholar
Geisler, N. & Weber, K. (1977). Isolation of the amino-terminal fragment of lactose repressor necessary for DNA binding Biochemistry 16, 938943.CrossRefGoogle ScholarPubMed
Grindley, N. D. F. (1983). Transposition of Tn3 and related transposons. Cell 32, 35.CrossRefGoogle ScholarPubMed
Gronenborn, A. M. & Clore, G. M. (1982). Proton nuclear magnetic resonance studies on cyclic nucleotide binding to the Escherichia coli adenosine cyclic 3′,5′-phosphate receptor protein. Biochemistry 21, 40404048.CrossRefGoogle ScholarPubMed
Gronenborn, A. M., Nermut, M. V., Eason, P. & Clore, G. M. (1984). Visualization of cAMP receptor protein-induced DNA kinking by electron microscopy. J. molec. Biol. 179, 751–575.CrossRefGoogle ScholarPubMed
Hatfull, G. F. & Grindley, N. D. F. (1988). Genetic Recombination (ed. Smith, G. and Kucharlapati, R.), pp. 357564. Washington, D.C.: American Society for Microbiology.Google Scholar
Hatfull, G. F., Sanderson, M. R., Freemont, P. S., Raccuia, P. R., Grindley, N. D. F. & Steitz, T. A. (1989). Preparation of heavy atom derivatives using site-directed mutagenesis: introduction of cysteine residues into γδ resolvase. J. molec. Biol. 208, 661667.CrossRefGoogle Scholar
Hecht, M. H., Nelson, H. C. M. & Sauer, R. T. (1983). Mutations in λ repressor's amino-terminal domain: implications for protein stability and DNA binding. Proc. natn. Acad. Sci. USA 80, 26762680.CrossRefGoogle ScholarPubMed
Hochschild, A. & Ptashne, M. (1986 a). Cooperative binding of λ repressors to sites separated by integral turns of the DNA helix. Cell 44, 681687.CrossRefGoogle ScholarPubMed
Hochschild, A. & Ptashne, M. (1986 b). Homologous interactions of λ repressor and λ cro with the λ operator. Cell 44, 925933.CrossRefGoogle ScholarPubMed
Hol, W. G. S. (1985). The role of the α-helix dipole in protein function and structure. Prog. Biophys. molec. Biol. 45, 149195.CrossRefGoogle ScholarPubMed
Hooper, M. L., Russell, R. L. & Smith, J. D. (1972). Mischarging in mutant tyrosine transfer RNAs. FEBS Lett. 22, 149.CrossRefGoogle ScholarPubMed
Irwin, N. & Ptashne, M. (1987). Mutants of the catabolite activator protein of Escherichia coli that are specifically deficient in the gene-activation function. Proc. natn. Acad. Sci. USA 84, 83158319.CrossRefGoogle ScholarPubMed
Johnson, L. N. & Phillips, D. C. (1965). Structure of some crystalline lysozyme-inhibitor complexes determined by X-ray analysis at 6 Å resolution. Nature 206, 760763.CrossRefGoogle Scholar
Jordan, R. S. & Pabo, C. O. (1988). Structure of the λ complex at 2·5 Å resolution: details of the repressor-operator interactions. Science 242, 893899.CrossRefGoogle ScholarPubMed
Jordan, S. R., Whitcombe, T. V., Berg, J. M. & Pabo, C. O. (1985). Systematic variation in DNA length yields highly ordered repressor-operator co-crystals. Science 230, 1383.CrossRefGoogle Scholar
Joyce, C. M., Ollis, D. L., Rush, J., Steitz, T. A., Konigsberg, W. H. & Grindley, N. D. F. (1986). In: Protein Structure, Folding and Design, UCLA Symposia on Molecular and Cellular Biology (ed. Oxender, D.), pp. 197205. New York: Liss.Google Scholar
Joyce, C. M. & Steitz, T. A. (1987). DNA polymerase. I. From crystal structure to function via genetics. Trends Biochem. Sci. 12, 288292.CrossRefGoogle Scholar
Jurnak, F. (1985). Structure of the GDP domain of EF-Tu and location of the amino acids homologous to ras oncogene proteins. Science 230, 3236.CrossRefGoogle ScholarPubMed
Kaptain, R., Zuiderweg, E. R. P., Scheek, R. M., Boelens, R. & Van Gunsterne, W. F. (1985). A protein structure from nuclear magnetic resonance data. J. molec. Biol. 182, 179182.CrossRefGoogle Scholar
Kennard, O. & Hunter, W. N. (1989). Oligonucleotide structure: a decade of results from single crystal X-ray diffraction studies. Q. Reviews of Biophys. 22, 327379.CrossRefGoogle ScholarPubMed
Kim, R., Modrich, P. & Kim, S.-H. (1984). ‘Interactive’ recognition in EcoR I restriction enzyme-DNA complex. Nucl. Acids Res. 12, 72857292.CrossRefGoogle Scholar
Kim, S. H., Suddath, F. L., Quigley, G. J., McPherson, A., Sussman, J. L., Wang, A. H. J., Seeman, N. C. & Rich, A. (1974). Three-dimensional tertiary structure of yeast phenylalanine transfer RNA. Science 185, 435440.CrossRefGoogle ScholarPubMed
Klenow, H. & Henningson, I. (1970). Selective elimination of the exonuclease activity of the DNA polymerase from E. coli B by a limited proteolysis. Proc. natn. Acad. Sci. USA 65, 168.CrossRefGoogle Scholar
Klug, A., Jack, A., Viswamitra, M. A., Kennard, O., Shakked, Z. & Steitz, T. A. (1979). A hypothesis on a specific sequence-dependent conformation of DNA and its relation to the binding of the lac-repressor protein. J. molec. Biol. 131, 669680.CrossRefGoogle ScholarPubMed
Kolb, A. & Buc, H. (1982). Is DNA unwound by the cyclic AMP receptor protein? Nucl. Acids Res. 10, 473485.CrossRefGoogle ScholarPubMed
Koo, H.-S., Wu, H.-M. & Crothers, D. M. (1986). DNA bending at adenine-thymine tracts. Nature 320, 501506.CrossRefGoogle ScholarPubMed
Koudelka, G. B., Harrison, S. C. & Ptashne, M. (1987). Effect of non-contacted bases on the affinity of 434 operator for 434 repressor and cro. Nature 326, 886888.CrossRefGoogle ScholarPubMed
Koudelka, G. B., Harbury, P., Harrison, S. C. & Ptashne, M. (1988). DNA twisting and the affinity of bacteriophage 434 operator for bacteriophage 434 repressor. Proc. natn. Acad. Sci. USA 85, 46334637.CrossRefGoogle ScholarPubMed
Kramer, H., Niemoller, M., Ampuyal, M., Revet, B., Von Wilcken-Bergmann, B. & Müller-Hill, B. (1987). lac repressor forms loops with linear DNA carrying two suitably spaced lac operators EMBO J. 6, 14811491.Google ScholarPubMed
Landschultz, W. H., Johnson, P. R. & Mcknight, S. L. (1988). The leucine zipper: a hypothetical structure common to a new class of DNA binding proteins. Science 240, 17591764.CrossRefGoogle Scholar
Laughon, A. & Scott, M. P. (1984). Sequence of a Drosophila segmentation gene; protein structure homology with DNA-binding proteins. Nature 310, 2531.CrossRefGoogle ScholarPubMed
Lawson, C. L., Zhang, R.-G., Schevitz, R. W., Otwinowski, Z., Joachimiak, A. & Sigler, P. B. (1988). Flexibility of the DNA-binding domains of trp repressor. Proteins 3, 1831.CrossRefGoogle ScholarPubMed
Leahy, M. C. (1982). The binding of lac repressor to DNA substituted with nucleotide analogs. Ph.D. thesis, Yale University, New Haven, Connecticut.Google Scholar
Lee, M. S., Gippert, G. P., Soman, K. V., Case, D. A., Wright, P. E. (1989). Three-dimensional solution structure of a single zinc finger DNA-binding domain. Science 245, 635637.CrossRefGoogle ScholarPubMed
Lehming, N., Sartorius, J., Niemöller, M., Genenger, G., Wilcken-Bergmann, B.V. & Müller-Hill, B. (1987). The interaction of the recognition helix of lac repressor with lac operator. EMBO J. 6, 31453153.Google ScholarPubMed
Lewis, M., Wang, J. & Pabo, C. (1985). Structure of the operator binding domain of lambda repressor. In: Biological Macromolecules and Assemblies, vol. 2 (ed. Jurnak, F. A. and McPherson, A.), New York: John Wiley & Sons.Google Scholar
Liu-Johnson, H.-N., Gartenberg, M. R. & Grothers, D. M. (1986). The DNA binding domain and bending angle of E. coli CAP protein. Cell 47, 9951005.CrossRefGoogle ScholarPubMed
Lomonossoff, G. P., Butler, P. J. G. & Klug, A. (1981). Sequence-dependent variation in the conformation of DNA. J. molec. Biol. 149, 745760.CrossRefGoogle ScholarPubMed
Majors, J. (1977). Dissertation (Harvard University, Cambridge, MA).Google Scholar
McCall, M., Brown, T., Hunter, W. N. & Kennard, O. (1986). The crystal structure of d(GGATGGGAG) form an essential part of the binding site for TFIIIA. Nature 332, 661664.CrossRefGoogle Scholar
Martin, K., Huo, L. & Schleif, R. F. (1986). 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. natn. Acad. Sci. USA 83, 36543658.CrossRefGoogle ScholarPubMed
Matthews, B. W. (1988). No code for recognition. Nature 335, 294295.CrossRefGoogle ScholarPubMed
Matthews, B. W., Ohlendorf, D. H., Anderson, W. F. & Takeda, Y. (1982). Structure of the DNA-binding region of lac repressor inferred from its homology with cro repressor. Proc. natn. Acad. Sci. USA 79, 1428.CrossRefGoogle ScholarPubMed
McClarin, J. A., Frederick, C. A., Wang, B.-C., Greene, P., Boyer, H. W., Grable, J. & Rosenberg, J. M. (1986). Structure of the DNA-ECoR I endonuclease recognition complex at 3 Å resolution. Science 234, 15261541.CrossRefGoogle ScholarPubMed
Mckay, D. B., Pickover, C. A. & Steitz, T. A. (1982 a). E. coli lac repressor is elongated with its DNA binding domains located at both ends. J. molec. Biol. 156, 175183.CrossRefGoogle Scholar
Mckay, D. B. & Steitz, T. A. (1981). Structure of catabolite gene activator protein at 2·9 Å resolution suggests binding to left-handed B-DNA. Nature 290, 744749.CrossRefGoogle ScholarPubMed
McKay, D. B., Weber, I. T. & Steitz, T. A. (1982 b). Structure of catabolite gene activator protein at 2·9 Å resolution: Incorporation of amino-acid sequence and interactions with c-AMP. J. biol. Chem. 257, 95189524.Google Scholar
Miller, J. H. (1978). The lacI gene: its role in lac operon control and its use as a genetic system. In The Operon (ed. Miller, J. H. and Reznikoff, W. S.). Cold Spring Harbor, New York: Cold Spring Harbor Laboratory.Google Scholar
Miller, J., McLachlan, A. D. & Klug, A. (1985). Repetitive zinc-binding domains in the protein transcription factor IIIA from Xenopus oocytes. EMBO J. 4, 16091614.Google ScholarPubMed
Moore, S. (1981). The Enzymes, 3rd edn, vol. 14 (ed. Boyer, P. D.), pp. 281296. New York: Academic Press.Google Scholar
Moras, D., Comarmond, M. B., Fischer, J., Theirry, J. C., Ebel, J. P. & Giegé, R. (1980). Crystal structure of tRNAAsp. Nature 288, 669674.CrossRefGoogle ScholarPubMed
Müller-Hill, B. (1975). lac repressor and lac operator. Prog. Biophys. molec. Biol. 30, 227252.CrossRefGoogle ScholarPubMed
Müller-Hill, B. (1983). Sequence homology between lac and gal repressors and three sugar-binding periplasmic proteins. Nature 302, 163164.CrossRefGoogle ScholarPubMed
Nelson, H. C. M., Finch, J. T., Luisi, B. F. & Klug, A. (1987). The structure of an oligo(dA)·oligo(dT) tract and its biological implications. Nature 330, 221226.CrossRefGoogle ScholarPubMed
Nelson, H. C. M. & Sauer, R. T. (1986). Interaction of mutant λ repressors with operator and non-operator DNA. J. molec. Biol. 192, 2238.CrossRefGoogle ScholarPubMed
Normanly, J. & Abelson, J. (1989). tRNA Identity. Ann. Rev. Biochem. 58, 10291049.CrossRefGoogle ScholarPubMed
Oefner, C. & Suck, D. (1986). Crystallographic refinement and structure of DNase I at 2 Å resolution. J. molec. Biol. 192, 605632.CrossRefGoogle ScholarPubMed
Ogata, R. T. & Gilbert, W. (1979). DNA-binding site of lac repressor probed by dimethylsulfate methylation of lac operator. J. molec. Biol. 132, 709728.CrossRefGoogle ScholarPubMed
Ohlendorf, D. H., Anderson, W. F., Fisher, R. G., Takeda, Y. & Matthews, B. W. (1982). The molecular basis of DNA-protein recognition inferred from the structure of cro repressor. Nature 298, 718723.CrossRefGoogle ScholarPubMed
Ohlendorf, D. H., Anderson, W. F., Lewis, M., Pabo, C. O. & Matthews, B. W. (1983). Comparison of the structures of cro and λ repressor protein from bacteriophage λ. J. molec. Biol. 169, 757769.CrossRefGoogle ScholarPubMed
Ohlendorf, D. H., Anderson, W. F., Takeda, Y. & Matthews, B. W. (1983). High resolution structural studies of cro repressor protein and implications for DNA recognition. J. biomol. Struct. Design 1, 553563.CrossRefGoogle ScholarPubMed
Ohlendorf, D. H. & Matthews, B. W. (1983). Structural studies of protein-nucleic acid interactions. Ann. Rev. Biophys. Bioeng. 12, 259284.CrossRefGoogle ScholarPubMed
Ollis, D. L., Brick, P., Hamlin, R., Xuong, N. G. & Steitz, T. A. (1985). Structure of large fragment of Escherichia coli DNA polymerase I complexed with dTMP. Nature 313, 762766.CrossRefGoogle ScholarPubMed
O'Shea, E. K., Ruttkowski, R. & Kim, P. S. (1989). Evidence that the leucine zipper is a coiled coil. Science 243, 538542.CrossRefGoogle ScholarPubMed
Otwinowski, Z., Schevitz, R. W., Zhang, R.-G., Lawson, C. L., Joachimiak, A., Marmostein, R. Q., Luisi, B. F. & Sigler, P. B. (1988). Crystal structure of trp repressor/operator complex at atomic resolution. Nature 335, 321329.CrossRefGoogle ScholarPubMed
Pabo, C. O. (1983). DNA-protein interactions. In Proceedings of The Robert A. Welch Foundation Conferences on Chemical Research, XXVII, Stereospecificity in Chemistry and Biochemistry, ch. 7, pp. 223255. Houston, Texas.Google Scholar
Pabo, C. O., Krovatin, W., Jeffrey, A. & Sauer, R. T. (1982). The N-terminal arms of λ repressor wrap around the operator DNA. Nature 298, 441443.CrossRefGoogle ScholarPubMed
Pabo, C. O. & Lewis, M. (1982). The operator-binding domain of λ repressor: structure and DNA recognition. Nature 298, 443447.CrossRefGoogle ScholarPubMed
Pabo, C. O. & Sauer, R. T. (1984). Protein-DNA recognition. Ann. Rev. Biochem. 53, 293321.CrossRefGoogle ScholarPubMed
Pabo, C. O., Sauer, R. T., Sturtevant, J. M. & Ptashne, M. (1979). The λ repressor contains two domains. Proc. natn. Acad. Sci. USA 76, 16081612.CrossRefGoogle ScholarPubMed
Parraga, G., Horvath, S. J., Eisen, A., Taylor, W. E., Hood, L., Young, E. T. & Klevit, R. E. (1988). Zinc-dependent structure of a single-finger domain of yeast ADR1. Science 241, 14891492.CrossRefGoogle ScholarPubMed
Perona, J. J., Swanson, R. N., Rould, M. A., Steitz, T. A. & Söll, D. (1989). Structural basis for misaminoacylation by mutant E. coli glutaminyl-tRNA synthetase enzymes. Science 246, 11521154.CrossRefGoogle ScholarPubMed
Pflugrath, J. W. & Quiocho, F. A. (1985). Sulphate sequestered in the sulphate-binding protein of Salmonella typhimurium is bound solely by hydrogen bonds. Nature 314, 257.CrossRefGoogle ScholarPubMed
Phillips, S. E. V., Manfield, I., Parsons, I., Davidson, B. E., Rafferty, J. B., Somers, W. S., Margarita, D., Cohen, G. N., Saint-Girons, I. & Stockley, P. S. (1989). Cooperative tandem binding of met repressor of Escherichia coli. Nature 341, 711715.CrossRefGoogle ScholarPubMed
Platt, T., Files, J. G. & Weber, K. (1973). lac repressor. J. biol. Chem. 248, 110121.Google ScholarPubMed
Porschke, D., Hillen, W. & Takahashi, M. (1984). The change of DNA structure by specific binding of the cAMP receptor protein from rotation diffusion and dichroism measurements. EMBO J. 3, 28732878.Google ScholarPubMed
Price, P. A. (1975). The essential role of Ca2+ in the activity of bovine pancreatic deoxyribonuclease. J. biol. Chem. 250, 19811986.Google ScholarPubMed
Ptashne, M. (1986). A Genetic Switch. Cambridge, MA: Cell Press.Google Scholar
Ptashne, M. (1986). Gene regulation by proteins acting nearby and at a distance. Nature 322, 697701.CrossRefGoogle ScholarPubMed
Qian, Y. Q., Billeter, M., Otting, G., Müller, M., Gehring, W. J. & Wüthrich, K. (1989). The structure of the Antennapedia homeodomain determined by NMR spectroscopy in solution: Comparison with prokaryotic repressors. Cell 59, 573580.CrossRefGoogle ScholarPubMed
Que, B. G., Downey, K. M. & So, A. (1978). Mechanism of selective inhibition of 3′ to 5′ exonuclease activity of E. coli DNA polymerase I by nucleoside 5′-monophosphates. Biochemistry 17, 1603.CrossRefGoogle Scholar
Rafferty, J. B., Somers, W. S., St.-Girons, I. & Phillips, S. E. V. (1989). Three-dimensional crystal structures of E. coli met repressor with and without corepressor. Nature 341, 705710.CrossRefGoogle ScholarPubMed
Richmond, T. J., Finch, J. T., Rushton, B., Rhodes, D. & Klug, A. (1984). Structure a of the nucleosome core particle at 7 Å resolution. Nature 311, 532537.CrossRefGoogle ScholarPubMed
Richmond, T. J. & Steitz, T. A. (1976). Protein-DNA interaction investigated by binding E. coli lac repressor protein to poly[d(A·U-HgX)]. J. molec. Biol. 103, 2538.CrossRefGoogle Scholar
Robertus, J. D., Ladner, J. E., Finch, J. T., Rhodes, D., Brown, R. S., Clark, B. F. C. & Klug, A. (1974). Structure of yeast phenylalanine tRNA at 3 Å resolution. Nature 250, 546551.CrossRefGoogle ScholarPubMed
Rossman, M. G., Liljas, A., Branden, C.-I. & Banaszak, L. J. (1975). Evolutionary and structural relationships among dehydrogenases. In The Enzymes, vol II (ed. P. Boyer), pp. 61102.CrossRefGoogle Scholar
Rould, M. A., Perona, J. J., Söll, D. & Steitz, T. A. (1989). Structure of E. coli glutaminyl-tRNA synthetase complexed with tRNAGln and ATP at 2·8 Å resolution: implications for tRNA discrimination. Science 246, 11351142.CrossRefGoogle Scholar
Rouvière-Yaniv, J. & Yaniv, M. (1979). E. coli DNA binding protein HU forms nucleosome-like structure with circular double-stranded DNA. Cell 17, 265274.CrossRefGoogle Scholar
Satchwell, S. C., Drew, H. R., Travers, A. A. (1986). Sequence periodicities in chicken nucleosome core DNA. J. molec. Biol. 191, 659675.CrossRefGoogle ScholarPubMed
Sauer, R. T., Jordan, S. R., Pabo, C. O. (1990). λ repressor: A model system for understanding protein-DNA interactions and protein stability. Adv. Prot. Chem. (in the press).CrossRefGoogle Scholar
Sauer, R. T., Pabo, C. O., Meyer, B. J., Ptashne, M. & Backman, K. C. (1979). Regulatory functions of the λ repressor reside in the amino-terminal domain. Nature 279, 396400.CrossRefGoogle ScholarPubMed
Sauer, R. T., Yocum, R. R., Doolittle, R. F., Lewis, M. & Pabo, C. O. (1982). Homology among DNA-binding proteins suggests use of a conserved super-secondary structure. Nature 298, 447451.CrossRefGoogle ScholarPubMed
Scheffler, I. E., Elson, E. L. & Baldwin, R. L. (1968). Helix formation by dAT oligomers. I. Hairpin and straight-chain helices. J. molec. Biol. 36, 291304.CrossRefGoogle ScholarPubMed
Schevitz, R. W., Otwinowski, Z., Joanchimiak, A., Lawson, C. L. & Sigler, P. B. (1985). The three-dimensional structure of trp repressor. Nature 317, 782786.CrossRefGoogle ScholarPubMed
Scholübbers, H.-G., Van Knippenberg, P. H., Baraniak, J., Stec, W. J., Morr, M. & Jastorff, B. (1983). Investigations of stimulation of lac transcription in vivo in Escherichia coli by cAMP analogues. Eur. J. Biochem. 138, 101109.CrossRefGoogle Scholar
Schulman, L. H. & Abelson, J. (1988). Recent exrefment in understanding transfer RNA identity. Science 240, 15911592.CrossRefGoogle ScholarPubMed
Schulman, L. H. & Pelka, H. (1985). In vitro conversion of a methionine to a glutamine-acceptor tRNA. Biochemistry 24, 73097314.CrossRefGoogle ScholarPubMed
Schultz, S. C., Shields, G. C. & Steitz, T. A. (1990). Crystallization of E. coli CAP with its operator DNA: the use of modular DNA. J. molec. Biol (in the press).Google Scholar
Seeman, N. C., Rosenberg, J. M., Rich, A. (1976). Sequence-specific recognition of double helical nucleic acids by proteins. Proc. natn. Acad. Sci. USA 73, 804808.CrossRefGoogle ScholarPubMed
Seong, B. L., Lee, C.-P. & Rajbhandary, U. L. (1989). Supression of amber codons in vivo as evidence that mutants derived fro Escherichia coli initiator tRNA can act at the step of elongation in protein synthesis. J. biol. Chem. 264, 6504.Google Scholar
Shepherd, J. C. W., Mcginnis, W., Carrasco, A. E., De Roberts, E. M., & Gehring, W. J. (1984). Fly and frog homoeo domains show homologies with yeast mating type regulatory proteins. Nature 310, 5972, 7071.CrossRefGoogle ScholarPubMed
Shimura, Y., Aono, H., Ozeki, H., Sarabhai, A., Lamform, H. & Abelson, J. (1972). Mutant tyrosine tRNA of altered amino acid specificity. FEBS Lett. 22, 144148.CrossRefGoogle ScholarPubMed
Simpson, R. B. (1980). Interaction of the cAMP receptor protein with the lac promoter. Nucl. Acids Res. 8, 759.Google ScholarPubMed
Steitz, T. A., Beese, L., Freemont, P. S., Friedman, J. & Sanderson, M. R. (1987). Structural studies of Klenow fragment: an enzyme with two active sites. Cold Spring Harbor Symposia on Quantitative Biology, ch. 52, pp. 465471. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory.Google Scholar
Steitz, T. A., Ohlendorf, D. H., McKay, D. B., Anderson, W. F. & Matthews, B. W. (1982). Structural similarity in the DNA binding domains of catabolite gene activator and cro repressor proteins. Proc. natn. Acad. Sci. USA 79, 30973100.CrossRefGoogle ScholarPubMed
Steitz, T. A., Richmond, T. J., Wise, D. & Engelman, D. M. (1974). The lac repressor protein: molecular shape, subunit structure and proposed model for operator interaction based on structural studies of micro-crystals. Proc. natn. Acad. Sci. USA 72, 53.Google Scholar
Steitz, T. A., Stenkamp, R. E., Geisler, N., Weber, K. & Finch, J. (1979). X-ray and electron microscopic studies of crystals of core lac repressor protein. In Biomolecular Structure, Conformation, Function and Evolution (ed. Srinivasan, R.)., Oxford: Pergamon Press.Google Scholar
Steitz, T. A. & Weber, I. T. (1985). Structure of catabolite gene activator protein. In Biological Macromolecules and Assemblies, 2nd edn (ed. McPherson, A. and Jurnak, F.), pp. 290321. New York: John Wiley.Google Scholar
Steitz, T. A., Weber, I. T., Ollis, D. & Brick, P. (1983). Crystallographic studies of protein-nucleic acid interaction: catabolite gene activator protein and the large fragment of DNA polymerase I. J. biomolec. Struct. Dyn. 1, 10231037.CrossRefGoogle ScholarPubMed
Suck, D., Lahm, A. & Oefner, C. (1988). Structure refined to 2 Å of a nickel DNA octanucleotide complex with DNase I. Nature 332, 6163, 465468.CrossRefGoogle Scholar
Suck, D. & Oefner, C.(1986). Structure of DNase I at 2·0 Å resolution suggests a mechanism for binding to and cutting DNA. Nature 321, 620625.CrossRefGoogle ScholarPubMed
Suck, D., Oefner, C. & Kabsch, W. (1984). Three-dimensional structure of bovine pancreatic DNase I at 2·5 Å resolution. EMBO J. 3, 24232430.Google ScholarPubMed
Sung, M. T. & Dixon, G. H. (1970). Modification of histones during spermiogenesis in trout: a molecular mechanism of altering histone binding to DNA. Proc. natn. Acad. Sci. USA 67, 16161623.CrossRefGoogle Scholar
Takeda, Y., Ohlendorf, D. H., Anderson, W. F. & Matthews, B. W. (1983). DNA-binding proteins. Science 221, 10201026.CrossRefGoogle ScholarPubMed
Tanaka, I., Appelt, K., Dij, K. L., White, S. W. & Wilson, K. S. (1984). 3 Å resolution structure of a protein with histone-like properties in prokaryotes. Nature 310, 376381.CrossRefGoogle ScholarPubMed
Vyas, N. K., Vyas, M. N., & Quiocho, F. A. (1988). Sugar and signal-transducer binding sites of the Escherichia coli galactose chemoreceptor protein. Science 242, 12901295.CrossRefGoogle ScholarPubMed
Wang, B.-C. (1987). Resolution of phase ambiguity in macromolecular crystallography. Methods in Enzymol. 115, 90111.CrossRefGoogle Scholar
Warrant, R. W. & Kim, S. -H. (1978). α-Helix-double helix interaction shown in the structure of a protamine-transfer RNA complex and a nucleoprotamine model. Nature 271, 130135.CrossRefGoogle Scholar
Warwicker, J., Engelman, B. P. & Steitz, T. A. (1987). Electrostatic calculations and model building suggest that DNA bound to CAP is sharply bent. Proteins 2, 283289.CrossRefGoogle ScholarPubMed
Weber, K. & Files, J. G. (1976). Limited proteolytic digestion of lac repressor by trypsin. J. biol. Chem. 251, 33863391.Google Scholar
Weber, I. T. & Steitz, T. Q. (1984). A model for non-specific binding of catabolite gene activator protein to DNA. Nucl. Acids Res. 12, 84758487.CrossRefGoogle ScholarPubMed
Weber, I. T. & Steitz, T. A. (1984). Model of specific complex between CAP and B-DNA suggested by electrostatic complementarity. Proc. natn. Acad. Sci. USA 81, 39733977.CrossRefGoogle ScholarPubMed
Weber, I. T. & Steitz, T. A. (1987). The structure of a complex of catabolite gene activator protein and cyclic AMP refined at 2·5 Å resolution. J. molec. Biol. 198, 311326.CrossRefGoogle ScholarPubMed
Weber, I. T., McKay, D. B. & Steitz, T. A. (1982 a). Two helix DNA binding motif of CAP found in lac repressor and gal repressor Nucl. Acids Res. 10, 50855102.CrossRefGoogle Scholar
Weber, I. T., Steitz, T. A., Bubis, J. & Taylor, S. S. (1987). Predicted structures of cAMP binding domains of type I and II regulatory subunits of cAMP-dependent protein kinase. Biochemistry 26, 343351.CrossRefGoogle ScholarPubMed
Weber, I. T., Takio, K., Titani, K. & Steitz, T. A. (1982 b). The cAMP-binding domains of the regulatory subunit of cAMP-dependent protein kinase and the catabolite gene activator proton are homologous. Proc. natn. Acad. Sci. USA 79, 76797683.CrossRefGoogle Scholar
Weber, P. C., Ollis, D. L., Debrin, W. R., Abdel-Meguid, S. S. & Steitz, T. A. (1982 c). Crystallization of resolvase, a repressor which also catalyzes site-specific DNA recombination. J. biol. Chem. 157, 689690.Google ScholarPubMed
Wharton, R. (1985). Thesis, Harvard University, Cambridge, MA.Google Scholar
Wharton, R. P. & Ptashne, M. (1985). Changing the binding specificity of a repressor by redesigning an α-helix. Nature 316, 601605.CrossRefGoogle ScholarPubMed
Wharton, R. P., Brown, E. L. & Ptashne, M. (1984). Substituting an α-helix switches the sequence-specific DNA interactions of a repressor. Cell 38, 361369.CrossRefGoogle ScholarPubMed
Wolberger, C., Dong, Y., Ptashne, M. & Harrison, S. C. (1988). Structure of a phage 434 cro/DNA complex. Nature 335, 789795.CrossRefGoogle ScholarPubMed
Woo, N. H., Roe, B. A. & Rich, A. (1980). Three-dimensional structure of Escherichia coli initiator tRNAfMet. Nature 286, 346351.CrossRefGoogle ScholarPubMed
Woodbury, C. P., Hagenbüchle, O. & Von Hippel, P. H. (1980). DNA site recognition and reduced specificity of the Ecor I endonuclease. J. biol. Chem. 255, 1153411546.Google Scholar
Wu, H. & Crothers, D. M. (1984). The locus of sequence-directed and protein-induced DNA bending. Nature 308, 509513.CrossRefGoogle ScholarPubMed
Yang, C. -C. & Nash, H. W. (1989). The interaction of E. coli IHF protein with its specific-binding sites. Cell 57, 869880.CrossRefGoogle ScholarPubMed
Yaniv, M., Folk, W., Berg, P. & Soll, L. (1974). A single mutational modification of a tryptophan-specific transfer RNA permits aminoacylation by glutamine and translation of the codon UAG. J. molec. Biol. 86, 245260.CrossRefGoogle ScholarPubMed
Yarus, M. (1988). tRNA identity: a hair of the dogma that bit us. Cell 55, 739741.CrossRefGoogle ScholarPubMed
Yarus, M., Knowlton, R. & Soll, L. (1977). Aminoacylation of the ambivalent Su + 7 amber suppressor tRNA. In Nucleic Acid-Protein Recognition (ed. Vogel, H. J.) pp. 391409. New York: Academic Press.CrossRefGoogle Scholar
Yoon, C., Prive, G. G., Goodsell, D. S. & Dickerson, R. E. (1988). Structure of an alternating-B DNA helix and its relationship to A-tract DNA. Proc. natn. Acad. Sci. USA 85, 63326336.CrossRefGoogle ScholarPubMed
Young, T. -S., Kim, S.-H., Modrich, P., Seth, A. & Jay, E. (1981). Preliminary X-ray diffraction studies of EcoR I restriction endonuclease-DNA complex. J. molec. Biol. 145, 607610.CrossRefGoogle Scholar
Zelwer, C., Risler, J. L. & Brunie, S. (1982). Crystal structure of Escherichia coli methionyl-tRNA synthetase at 2·5 Å resolution. J. molec. Biol. 115, 6381.CrossRefGoogle Scholar
Zhang, R. -G., Joachimiak, A., Lawson, C. L., Schevitz, R. W., Otwinowski, Z. & Sigler, P. G. (1987). The crystal structure of trp aporepressor at 1·8 Å shows how binding tryptophan enhances DNA affinity. Nature 327, 591597.CrossRefGoogle ScholarPubMed
Zubay, G. & Doty, P. J. (1959). The isolation and properties of deoxyribonucleoprotein particles containing single nucleic acid molecules. J. molec. Biol. 7, 120.CrossRefGoogle Scholar

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