Homeodomain-DNA recognition

Affolter, 1990, DNA binding properties of the purified Antennapedia homeodomain, 87, 4093 Affolter, 1991, Similarities between the homeodomain and the Hin recombinase DNA-binding domain, Cell, 64, 879, 10.1016/0092-8674(91)90311-L Ammerer, 1990, Identification, purification, and cloning of a polypeptide (PRTFGRM) that binds to mating-specific promoter elements in yeast, Genes Dev., 4, 299, 10.1101/gad.4.2.299 Billeter, 1990, Determination of the three-dimensional structure of the Antennapedia homeodomain from Drosophila in solution by 1H nuclear magnetic resonance spectroscopy, J. Mol. Biol., 214, 183, 10.1016/0022-2836(90)90155-F Billeter, 1993, Determination of the NMR solution structure of an Antennapedia homeodomain-DNA complex, J. Mol. Biol., 234, 1084, 10.1006/jmbi.1993.1661 Billeter, 1993, Appendix: model studies relating nuclear magnetic resonance data with the three-dimensional structure of protein-DNA complexes, J. Mol. Biol., 234, 1094, 10.1006/jmbi.1993.1662 Ceska, 1993, The X-ray structure of an atypical homeodomain present in the rat liver transcription factor LFB1HNF1 and implications for DNA binding, EMBO J., 12, 1805, 10.1002/j.1460-2075.1993.tb05828.x Chan, 1993, The segment identity functions of Ultrabithorax are contained within its homeo domain and carboxyterminal sequences, Genes Dev., 7, 796, 10.1101/gad.7.5.796 De Simeone, 1991, Transcriptional regulation of liver-specific gene expression, Curr. Opin. Cell Biol., 3, 960, 10.1016/0955-0674(91)90114-E Dranginis, 1990, Binding of yeast a1 and α2 as a heterodimer to the operator DNA of a haploid-specific gene, Nature, 347, 682, 10.1038/347682a0 Driever, 1989, The bicoid protein is a positive regulator of hunchback transcription in the early Drosophila embryo, Nature, 337, 138, 10.1038/337138a0 Feng, 1994, Hin recombinase bound to DNA: the origin of specificity in major and minor groove interactions, Science, 263, 348, 10.1126/science.8278807 Furukubo-Tokunaga, 1992, In vivo analysis of the helix-turn-helix motif of the fushi tarazu homeo domain of Drosophila melanogaster, Genes Dev., 6, 1082, 10.1101/gad.6.6.1082 Furukubo-Tokunaga, 1993, Functional specificity of the Antennapedia homeodomain, 90, 6360 Gehring, 1987, Homeo boxes in the study of development, Science, 236, 1245, 10.1126/science.2884726 Gehring, 1990, The structure of the homeodomain and its functional implications, Trends Genet., 6, 323, 10.1016/0168-9525(90)90253-3 Gehring, 1994, Homeodomain proteins, Annu. Rev. Biochem., 63, 437, 10.1146/annurev.bi.63.070194.002415 Gibson, 1990, The specificites of Sex combs reduced and Antennapedia are defined by a distinct portion of each protein that includes the homeodomain, Cell, 62, 1087, 10.1016/0092-8674(90)90386-S Goutte, 1993, Yeast a1 and α2 homeodomain proteins form a DNA-binding activity with properties distinct from those of either protein, J. Mol. Biol., 233, 359, 10.1006/jmbi.1993.1517 Güntert, 1991, Structure determination of the Antp(C39←S) homeodomain from nuclear magnetic resonance data in solution using a novel strategy for the programs DIANA, CALIBA, HABAS, and GLOMSA, J. Mol. Biol., 217, 531, 10.1016/0022-2836(91)90755-U Hanes, 1989, DNA specificity of the bicoid activator protein is determined by homeodomain recognition helix residue 9, Cell, 57, 1275, 10.1016/0092-8674(89)90063-9 Hanes, 1991, A genetic model for interaction of the homeodomain recognition helix with DNA, Science, 251, 426, 10.1126/science.1671176 Hiromi, 1987, Regulation and function of the Drosophila segmentation gene fushi tarazu, Cell, 50, 963, 10.1016/0092-8674(87)90523-X Johnson, 1990, Binding of a Drosophila POU domain protein to a sequence element regulating gene expression in specific dopminergic neurons, Nature, 343, 467, 10.1038/343467a0 Johnson, 1992, A combinatorial regulatory circuit in budding yeast, 975 Kalionis, 1993, A universal sequence is bound in vitro by diverse homeodomains, Mech. Dev., 43, 57, 10.1016/0925-4773(93)90023-Q Kamps, 1990, A new homeobox gene contributes the DNA binding domain of the t(1;19) translocation protein in pre-B ALL, Cell, 60, 547, 10.1016/0092-8674(90)90658-2 Kapiloff, 1991, Variable effects of phosphorylation of Pit-1 dictated by the DNA response elements, Science, 253, 786, 10.1126/science.1652153 Keleher, 1988, The yeast cell-type-specific repressor α2 acts cooperatively with a non-cell-type-specific protein, Cell, 53, 927, 10.1016/S0092-8674(88)90449-7 Kissinger, 1990, Crystal structure of an engrailed homeodomain-DNA complex at 2.8 Å resolution: a framework for understanding homeodomain-DNA interactions, Cell, 63, 579, 10.1016/0092-8674(90)90453-L Klemm, 1994, Crystal structure of the Oct-1 POU domain bound to an octamer site: DNA recognition with tethered DNA-binding modules, Cell, 77, 21, 10.1016/0092-8674(94)90231-3 Kornberg, 1993, Understanding the homeodomain, J. Biol. Chem., 268, 26813, 10.1016/S0021-9258(19)74183-0 Laughon, 1991, DNA binding specificity of homeodomains, Biochemistry, 30, 11357, 10.1021/bi00112a001 Leiting, 1993, The three-dimensional NMR-solution structure of the polypeptide fragment 195–286 of the LFB1HNF1 transcription factor from rat liver comprises a non-classical homeodomain, EMBO J., 12, 1797, 10.1002/j.1460-2075.1993.tb05827.x Lin, 1992, Mapping functional specificity in the Dfd and Ubx homeo domains, Genes Dev., 6, 1071, 10.1101/gad.6.6.1071 Mann, 1990, Functional dissection of Ultrabithorax proteins in Drosophila melanogaster, Cell, 60, 597, 10.1016/0092-8674(90)90663-Y McGinnis, 1992, Homeobox genes and axial patterning, Cell, 68, 283, 10.1016/0092-8674(92)90471-N Mendel, 1991, HNF-1, a member of a novel class of dimerizing homeodomain proteins, J. Biol. Chem., 266, 677, 10.1016/S0021-9258(17)35222-5 Monica, 1991, PBX2 and PBX3, new homeobox genes with extensive homology to the human proto-oncogene PBX1, Mol. Cell. Biol., 11, 6149, 10.1128/MCB.11.12.6149 Müller, 1988, Isolation and sequence-specific DNA binding of the Antennapedia homeodomain, EMBO J., 7, 4299, 10.1002/j.1460-2075.1988.tb03328.x Nourse, 1990, Chromosomal translocation t(1;19) results in the synthesis of a homeobox fusion mRNA that codes for the potential chimeric transcription factor, Cell, 60, 535, 10.1016/0092-8674(90)90657-Z Otting, 1990, Protein-DNA contacts in the structure of a homeodomain-DNA complex determined by nuclear magnetic resonance spectroscopy in solution, EMBO J., 9, 3085, 10.1002/j.1460-2075.1990.tb07505.x Otting, 1991, Proton exchange with internal water molecules in the protein BPTI in aqueous solution, J. Am. Chem. Soc., 113, 4363, 10.1021/ja00011a068 Otwinowski, 1988, Crystal structure of trp repressor/operator complex at atomic resolution, Nature, 335, 321, 10.1038/335321a0 Pabo, 1992, Transcription factors: structural families and principles of DNA recognition, Annu. Rev. Biochem., 61, 1053, 10.1146/annurev.bi.61.070192.005201 Passmore, 1989, A protein involved in minichromosome maintenance in yeast binds a transcriptional enhancer conserved in eukaryotes, Genes Dev., 3, 921, 10.1101/gad.3.7.921 Peifer, 1990, Mutations in the Drosophila gene extradenticle affect the way specific homeo domain proteins regulate segmental identity, Genes Dev., 4, 1209, 10.1101/gad.4.7.1209 Percival-Smith, 1990, The interaction with DNA of wild-type and mutant fushi tarazu homeodomains, EMBO J., 9, 3967, 10.1002/j.1460-2075.1990.tb07617.x Pick, 1990, Analysis of the ftz upstream element: germ layer-specific enhancers are independently autoregulated, Genes Dev., 4, 1224, 10.1101/gad.4.7.1224 Qian, 1989, The structure of the Antennapedia homeodomain determined by NMR spectroscopy in solution: comparison with prokaryotic repressors, Cell, 59, 573, 10.1016/0092-8674(89)90040-8 Qian, 1992, NMR structure determination reveals that the homeodomain is connected through a flexible linker to the main body in the Drosophila Antennapedia protein, 89, 10738 Qian, 1993, NMR spectroscopy of a DNA complex with the uniformly 13C-labeled Antennapedia homeodomain and structure determination of the DNA-bound homeodomain, J. Mol. Biol., 234, 1070, 10.1006/jmbi.1993.1660 Qian, 1993, NMR detection of hydration water in the intermolecular interface of a protein-DNA complex, J. Am. Chem. Soc., 115, 1189, 10.1021/ja00056a077 Qian, 1994, Nuclear magnetic resonance solution structure of the fushi tarazu homeodomain from Drosophila and comparison with the Antennapedia homeodomain, J. Mol. Biol., 238, 333, 10.1006/jmbi.1994.1296 Qian, 1994, The des(1–6) Antennapedia homeodomain: comparison of the NMR solution structure and the DNA binding affinity with the intact Antennapedia homeodomain, 91, 4091 Rauskolb, 1993, extradenticle, a regulator of homeotic gene activity, is a homolog of the homeobox-containing human proto-oncogene pbx1, Cell, 74, 1101, 10.1016/0092-8674(93)90731-5 Schier, 1992, Direct homeodomain-DNA interaction in the autoregulation of the fushi tarazu gene, Nature, 356, 804, 10.1038/356804a0 Schier, 1993, Functional specificity of the homeodomain protein fushi tarazu: the role of DNA binding specificity in vivo, 90, 1450 Schier, 1993, Analysis of a fushi tarazu autoregulatory element: multiple sequence elements contribute to enhancer activity, EMBO J., 12, 1111, 10.1002/j.1460-2075.1993.tb05752.x Schulz, 1990, The b alleles of U. maydis, whose combinations program pathogenic development, code for poly-peptides containing a homeodomain-related motif, Cell, 60, 295, 10.1016/0092-8674(90)90744-Y Scott, 1989, The structure and function of the homeodomain, Biochim. Biophys. Acta, 989, 25 Segil, 1991, Mitotic phosphorylation of the Oct-1 homeodomain and regulation of Oct-1 DNA binding activity, Science, 254, 1814, 10.1126/science.1684878 Shakked, 1994, Determinants of repressor/operator recognition from the structure of the trp operator binding site, Nature, 368, 469, 10.1038/368469a0 Sluka, 1987, Synthesis of a sequence-specific DNA-cleaving peptide, Science, 238, 1129, 10.1126/science.3120311 Sluka, 1990, Importance of minor-groove contacts for recognition of DNA by the binding domain of Hin recombinase, Biochemistry, 29, 6551, 10.1021/bi00480a002 Steitz, 1990, Structural studies of protein-nucleic acid interaction: the sources of sequence-specific binding, Quart. Rev. Biophys., 23, 205, 10.1017/S0033583500005552 Suzuki, 1993, Common features in DNA recognition helices of eukaryotic transcription factors, EMBO J., 12, 3221, 10.1002/j.1460-2075.1993.tb05991.x Treacy, 1991, I-POU: a POU domain protein that inhibits neuron-specific gene activation, Nature, 350, 577, 10.1038/350577a0 Treacy, 1992, Twin of I-POU: a two amino acid difference in the I-POU homeodomain distinguishes an activator from an inhibitor of transcription, Cell, 68, 491, 10.1016/0092-8674(92)90186-G Treisman, 1989, A single amino acid can determine the DNA binding specificity of homeodomain proteins, Cell, 59, 553, 10.1016/0092-8674(89)90038-X Vershon, 1993, A short, disordered protein region mediates interactions between the homeodomain of the yeast α2 protein and the MCM1 protein, Cell, 72, 1, 10.1016/0092-8674(93)90054-T Wieschaus, 1986, Specificity of embryonic lethal mutations in Drosophila analysed in germ line clones, Roux's Arch. Dev. Biol., 195, 63, 10.1007/BF00444042 Wolberger, 1991, Crystal structure of a MATα2 homeodomain-operator complex suggests a general model for homeodomain-DNA interactions, Cell, 67, 517, 10.1016/0092-8674(91)90526-5 Wüthrich, 1992, Transcriptional regulation by homeodomain proteins: structural, functional, and genetic aspects, 535 Zeng, 1993, Ectopic expression and function of the Antp and Scr homeotic genes: the N terminus of the homeodomain is critical to functional specificity, Development, 118, 339, 10.1242/dev.118.2.339