The structure of the Antennapedia homeodomain determined by NMR spectroscopy in solution: Comparison with prokaryotic repressors

The structure of the Antennapedia homeodomain from Drosophila melanogaster was determined by nuclear magnetic resonance spectroscopy in solution. It includes three well-defined helices (residues 10-21, 28-38, and 42-52) and a more flexible fourth helix (residues 53-59). Residues 30-50 form a helix-turn-helix motif virtually identical to those observed in various prokaryotic repressors. Further comparisons of the homeodomain with prokaryotic repressors showed that there are also significant differences in the molecular architectures. Overall, these studies support the view that the third helix of the homeodomain may function as the DNA recognition site. The elongation of the third helix by the fourth helix is a structured element that so far appears to be unique to the Antennapedia homeodomain.

[1]  R. Brüschweiler,et al.  Combined use of hard and soft pulses for ω1 decoupling in two-dimensional NMR spectroscopy , 1988 .

[2]  J. Gillis,et al.  Crystal Structure Analysis , 1960 .

[3]  G. Rubin,et al.  Human DNA sequences homologous to a protein coding region conserved between homeotic genes of Drosophila , 1984, Cell.

[4]  M. Billeter,et al.  Spatial arrangement of the three α helices in the solution conformation of E. coli lac represser DNA‐binding domain , 1984, FEBS letters.

[5]  M. Scott,et al.  The structure and function of the homeodomain. , 1989, Biochimica et biophysica acta.

[6]  K. Wüthrich,et al.  Secondary structure determination for the Antennapedia homeodomain by nuclear magnetic resonance and evidence for a helix‐turn‐helix motif. , 1988, The EMBO journal.

[7]  N Go,et al.  Calculation of protein conformations by proton-proton distance constraints. A new efficient algorithm. , 1985, Journal of molecular biology.

[8]  Jordan,et al.  Structure of the lambda complex at 2.5 A resolution: details of the repressor-operator interactions , 1988, Science.

[9]  M Ptashne,et al.  Recognition of a DNA operator by the repressor of phage 434: a view at high resolution , 1988, Science.

[10]  William McGinnis,et al.  Cloning of an X. laevis gene expressed during early embryogenesis coding for a peptide region homologous to Drosophila homeotic genes , 1984, Cell.

[11]  A. Laughon,et al.  Sequence of a Drosophila segmentation gene: protein structure homology with DNA-binding proteins , 1984, Nature.

[12]  W. Gehring,et al.  Homeo boxes in the study of development. , 1987, Science.

[13]  A. Joachimiak,et al.  Crystal structure of trp represser/operator complex at atomic resolution , 1988, Nature.

[14]  S W Lin,et al.  Vectors for selective expression of cloned DNAs by T7 RNA polymerase. , 1987, Gene.

[15]  F. Studier,et al.  Use of bacteriophage T7 RNA polymerase to direct selective high-level expression of cloned genes. , 1986, Journal of molecular biology.

[16]  B. Matthews,et al.  Comparison of the structures of Cro and λ repressor proteins from bacteriophage λ , 1983 .

[17]  W. Gehring,et al.  Structural organization and sequence of the homeotic gene Antennapedia of Drosophila melanogaster. , 1986, The EMBO journal.

[18]  C. Pabo,et al.  The operator-binding domain of λ repressor: structure and DNA recognition , 1982, Nature.

[19]  P. Tsonis,et al.  Modeling of the homoeo domain suggests similar structure to repressors. , 1988, Biochemical and Biophysical Research Communications - BBRC.

[20]  S Subbiah,et al.  Structure of the amino-terminal domain of phage 434 repressor at 2.0 A resolution. , 1989, Journal of molecular biology.

[21]  W. McGinnis,et al.  Isolation of a homoeo box-containing gene from the engrailed region of Drosophila and the spatial distribution of its transcripts , 1985, Nature.

[22]  G. A. van der Marel,et al.  H NMR study of a complex between the lac repressor headpiece and a 22 base pair symmetric lac operator. , 1989, Biochemistry.

[23]  W. J. Gehring,et al.  A conserved DNA sequence in homoeotic genes of the Drosophila Antennapedia and bithorax complexes , 1984, Nature.

[24]  S. Harrison,et al.  Structure of a phage 434 Cro/DNA complex , 1988, Nature.

[25]  William McGinnis,et al.  Fly and frog homoeo domains show homologies with yeast mating type regulatory proteins , 1984, Nature.

[26]  Michael B. Smith,et al.  Homoeo-domain homology in yeast MATα2 is essential for repressor activity , 1986, Nature.

[27]  William McGinnis,et al.  Molecular cloning and chromosome mapping of a mouse DNA sequence homologous to homeotic genes of drosophila , 1984, Cell.

[28]  A. Mclachlan.  Gene duplications in the structural evolution of chymotrypsin. , 1979, Journal of molecular biology.

[29]  L. Kauvar,et al.  The engrailed locus of drosophila: Structural analysis of an embryonic transcript , 1985, Cell.

[30]  J. Richardson,et al.  The anatomy and taxonomy of protein structure. , 1981, Advances in protein chemistry.

[31]  K Wüthrich,et al.  Polypeptide secondary structure determination by nuclear magnetic resonance observation of short proton-proton distances. , 1984, Journal of molecular biology.

[32]  M. Scott,et al.  Structural relationships among genes that control development: sequence homology between the Antennapedia, Ultrabithorax, and fushi tarazu loci of Drosophila. , 1984, Proceedings of the National Academy of Sciences of the United States of America.

[33]  K. Wüthrich,et al.  Isolation and sequence‐specific DNA binding of the Antennapedia homeodomain. , 1988, The EMBO journal.

[34]  K. Wüthrich,et al.  Studies of J-connectives and selective 1H-1H Overhauser effects in H2O solutions of biological macromolecules by two-dimensional NMR experiments. , 1980, Biochemical and biophysical research communications.

[35]  Werner Braun,et al.  Automated stereospecific 1H NMR assignments and their impact on the precision of protein structure determinations in solution , 1989 .

[36]  B. Matthews,et al.  The helix-turn-helix DNA binding motif. , 1989, The Journal of biological chemistry.

[37]  M. Billeter,et al.  Three‐dimensional structure of the neurotoxin ATX Ia from Anemonia sulcata in aqueous solution determined by nuclear magnetic resonance spectroscopy , 1989, Proteins.

[38]  Z Otwinowski,et al.  Flexibility of the DNA‐binding domains of trp repressor , 1988, Proteins.

[39]  K. Wüthrich,et al.  Secondary structure of the lac repressor DNA-binding domain by two-dimensional 1H nuclear magnetic resonance in solution. , 1983, Proceedings of the National Academy of Sciences of the United States of America.

[40]  M. Ptashne,et al.  Repressor structure and the mechanism of positive control , 1983, Cell.

[41]  T. Steitz,et al.  Structure of catabolite gene activator protein at 2.9-A resolution. Incorporation of amino acid sequence and interactions with cyclic AMP. , 1982, The Journal of biological chemistry.

[42]  K. G. Coleman,et al.  The invected gene of Drosophila: sequence analysis and expression studies reveal a close kinship to the engrailed gene. , 1987, Genes & development.

[43]  T. Steitz,et al.  Structural similarity in the DNA-binding domains of catabolite gene activator and cro repressor proteins. , 1982, Proceedings of the National Academy of Sciences of the United States of America.

[44]  B. Matthews,et al.  Comparison of the structures of cro and lambda repressor proteins from bacteriophage lambda. , 1989, Journal of molecular biology.

[45]  K Wüthrich,et al.  Determination of the complete three-dimensional structure of the alpha-amylase inhibitor tendamistat in aqueous solution by nuclear magnetic resonance and distance geometry. , 1988, Journal of molecular biology.

[46]  K Wüthrich,et al.  Comparison of the high-resolution structures of the alpha-amylase inhibitor tendamistat determined by nuclear magnetic resonance in solution and by X-ray diffraction in single crystals. , 1989, Journal of molecular biology.