The Experts below are selected from a list of 132 Experts worldwide ranked by ideXlab platform

S K Burley - One of the best experts on this subject based on the ideXlab platform.

  • co crystal structure of the hnf 3 fork head dna recognition motif resembles Histone H5
    Nature, 1993
    Co-Authors: Kirk Clark, E D Halay, S K Burley
    Abstract:

    The three-dimensional structure of an HNF-3/fork head DNA-recognition motif complexed with DNA has been determined by X-ray crystallography at 2.5 A resolution. This α/β protein binds B-DNA as a monomer, through interactions with the DNA backbone and through both direct and water-mediated major and minor groove base contacts, inducing a 13° bend. The transcription factor fold is very similar to the structure of Histone H5. In its amino-terminal half, three α-helices adopt a compact structure that presents the third helix to the major groove. The remainder of the protein includes a twisted, antiparallel β-structure and random coil that interacts with the minor groove.

  • co crystal structure of the hnf 3 fork head dna recognition motif resembles Histone H5
    Nature, 1993
    Co-Authors: Kirk Clark, E D Halay, S K Burley, Eseng Lai
    Abstract:

    The three-dimensional structure of an HNF-3/fork head DNA-recognition motif complexed with DNA has been determined by X-ray crystallography at 2.5 A resolution. This alpha/beta protein binds B-DNA as a monomer, through interactions with the DNA backbone and through both direct and water-mediated major and minor groove base contacts, inducing a 13 degrees bend. The transcription factor fold is very similar to the structure of Histone H5. In its amino-terminal half, three alpha-helices adopt a compact structure that presents the third helix to the major groove. The remainder of the protein includes a twisted, antiparallel beta-structure and random coil that interacts with the minor groove.

Kirk Clark - One of the best experts on this subject based on the ideXlab platform.

  • co crystal structure of the hnf 3 fork head dna recognition motif resembles Histone H5
    Nature, 1993
    Co-Authors: Kirk Clark, E D Halay, S K Burley
    Abstract:

    The three-dimensional structure of an HNF-3/fork head DNA-recognition motif complexed with DNA has been determined by X-ray crystallography at 2.5 A resolution. This α/β protein binds B-DNA as a monomer, through interactions with the DNA backbone and through both direct and water-mediated major and minor groove base contacts, inducing a 13° bend. The transcription factor fold is very similar to the structure of Histone H5. In its amino-terminal half, three α-helices adopt a compact structure that presents the third helix to the major groove. The remainder of the protein includes a twisted, antiparallel β-structure and random coil that interacts with the minor groove.

  • co crystal structure of the hnf 3 fork head dna recognition motif resembles Histone H5
    Nature, 1993
    Co-Authors: Kirk Clark, E D Halay, S K Burley, Eseng Lai
    Abstract:

    The three-dimensional structure of an HNF-3/fork head DNA-recognition motif complexed with DNA has been determined by X-ray crystallography at 2.5 A resolution. This alpha/beta protein binds B-DNA as a monomer, through interactions with the DNA backbone and through both direct and water-mediated major and minor groove base contacts, inducing a 13 degrees bend. The transcription factor fold is very similar to the structure of Histone H5. In its amino-terminal half, three alpha-helices adopt a compact structure that presents the third helix to the major groove. The remainder of the protein includes a twisted, antiparallel beta-structure and random coil that interacts with the minor groove.

E D Halay - One of the best experts on this subject based on the ideXlab platform.

  • co crystal structure of the hnf 3 fork head dna recognition motif resembles Histone H5
    Nature, 1993
    Co-Authors: Kirk Clark, E D Halay, S K Burley
    Abstract:

    The three-dimensional structure of an HNF-3/fork head DNA-recognition motif complexed with DNA has been determined by X-ray crystallography at 2.5 A resolution. This α/β protein binds B-DNA as a monomer, through interactions with the DNA backbone and through both direct and water-mediated major and minor groove base contacts, inducing a 13° bend. The transcription factor fold is very similar to the structure of Histone H5. In its amino-terminal half, three α-helices adopt a compact structure that presents the third helix to the major groove. The remainder of the protein includes a twisted, antiparallel β-structure and random coil that interacts with the minor groove.

  • co crystal structure of the hnf 3 fork head dna recognition motif resembles Histone H5
    Nature, 1993
    Co-Authors: Kirk Clark, E D Halay, S K Burley, Eseng Lai
    Abstract:

    The three-dimensional structure of an HNF-3/fork head DNA-recognition motif complexed with DNA has been determined by X-ray crystallography at 2.5 A resolution. This alpha/beta protein binds B-DNA as a monomer, through interactions with the DNA backbone and through both direct and water-mediated major and minor groove base contacts, inducing a 13 degrees bend. The transcription factor fold is very similar to the structure of Histone H5. In its amino-terminal half, three alpha-helices adopt a compact structure that presents the third helix to the major groove. The remainder of the protein includes a twisted, antiparallel beta-structure and random coil that interacts with the minor groove.

James R Davie - One of the best experts on this subject based on the ideXlab platform.

  • in situ footprinting of chicken Histone H5 gene in mature and immature erythrocytes reveals common factor binding sites
    Chromosoma, 1996
    Co-Authors: Jianmin Sun, Rosa Ferraiuolo, James R Davie
    Abstract:

    In vitro DNAase I footprinting and gel mobility shift assays have shown that the activities of several nuclear factors (GATA-1, Sp1) that bind to the promoter and downstream enhancer regions of the chicken Histone H5 gene are reduced in mature erythrocytes relative to those in immature erythrocytes. In this study we investigated site occupancy in the promoter and downstream enhancer regions of the H5 gene in mature and immature erythrocytes. The ligation-mediated polymerase chain reaction was used to detect DNAase I footprints generated in situ. Most of the sites that bound to Sp1 and/or Sp1-like proteins and GATA-1 in the promoter and enhancer were occupied in situ in mature and immature erythrocytes. However, the level of protection at Sp1/Sp1-like binding sites in the H5 enhancer region of mature erythroid cells was generally less than that observed for immature cells, suggesting that for any given mature cell not all of the Sp1/Sp1-like binding sites are occupied. Nevertheless, the results of this study suggest that the enhancer and promoter of the H5 gene in mature erythrocytes should be functional, agreeing with nuclear runon studies showing transcriptional activity of the H5 gene in mature permeabilized cells.

  • repression of Histone H5 gene expression in chicken mature erythrocytes is correlated with reduced dna binding activities of transcription factors sp1 and gata 1
    FEBS Letters, 1993
    Co-Authors: Jianmin Sun, Gail C Penner, James R Davie
    Abstract:

    During the final stages of erythroid maturation, the expression of the chicken Histone H5 gene ceases. The Histone H5 promoter has binding sites for Sp1 and UPE-binding protein. The 3' Histone H5 enhancer has binding sites for Sp1, GATA-1 and NF1. Here, we show that the DNA-binding activities of transcription factors Sp1 and GATA-1 is reduced 5- to 10-fold in mature cells, while the activities of UPE-binding protein and NF1 remain the same in mature and immature erythrocytes. The reduced activities of Sp1 and GATA-1 may contribute to the inactivation of the Histone H5 gene in mature erythrocytes.

  • analysis of erythroid nuclear proteins binding to the promoter and enhancer elements of the chicken Histone H5 gene
    Nucleic Acids Research, 1992
    Co-Authors: Jianmin Sun, Gail C Penner, James R Davie
    Abstract:

    Abstract The chicken erythroid proteins binding to the Histone H5 5' promoter and 3' erythroid-specific enhancer regions were identified. In DNase I footprinting and gel mobility shift experiments with immature adult erythrocyte nuclear extracts, we have demonstrated the binding of proteins to the GC-box, a high affinity Sp1 binding site, and to the upstream promoter element. We have previously demonstrated that a multisubunit complex containing the transcription factor GATA-1 was associated with the enhancer. Here, we show that the enhancer region also has four Sp1 binding sites (one medium and three weak affinity, one of which may also bind the CACCC factor), a potential NF-E4 binding site, and a binding site for a NF1-like factor. The results of gel mobility-shift and competition experiments provide evidence that the Sp1 binding sites are associated with a high molecular mass (greater than 450 kDa), Sp1 containing protein complex. We propose that Sp1 multimers bound at the promoter and enhancer interact to mediate the juxta-positioning of the enhancer and promoter elements, bringing the GATA-1 multisubunit complex next to the initiation site. The GATA-1 complex may contribute to the protein-protein interactions between the enhancer and promoter.

  • nuclear matrix proteins bind very tightly to specific regions of the chicken Histone H5 gene
    Biochemistry and Cell Biology, 1992
    Co-Authors: Jianmin Sun, Michael J Hendzel, James R Davie
    Abstract:

    The nuclear matrix is operationally defined as the structure remaining after nuclease-digested nuclei are extracted with high concentrations of salt. The nuclear matrix is thought to have a role in organizing higher order chromatin into loop domains. We determined whether specific regions of the Histone H5 gene were very tightly bound to protein of erythrocyte and liver nuclear matrices in vitro. We demonstrate that DNA fragments spanning sequences 5' to the promoter and the 3' enhancer region of the Histone H5 gene, but not DNA fragments spanning the promoter, were very tightly bound to protein of nuclear matrices of erythrocytes and liver. The nuclear matrix consists of internal nuclear matrix and nuclear pore-lamina complex. Recently, we demonstrated that Histone deacetylase could be used as a marker enzyme of the internal nuclear matrix. We demonstrate that nuclear pore-lamina complex preparations that were depleted of Histone deacetylase activity, and thus of internal nuclear matrix, retained the protein that bound very tightly to the beta-globin and Histone H5 enhancers. These results provide evidence that specific regions of the Histone H5 gene are very tightly bound to nuclear pore-lamina complex protein.

  • multisubunit erythroid complexes binding to the enhancer element of the chicken Histone H5 gene
    Biochemical Journal, 1992
    Co-Authors: C G Penner, James R Davie
    Abstract:

    We identified the factor(s) that bind to the chicken erythroid-cell-specific Histone H5 enhancer region which is located on the 3' end of the gene. In DNAase I footprinting and u.v. cross-linking experiments with nuclear extracts from adult chicken immature erythrocytes, we determined that the trans-acting factor GATA-1 was the predominating protein interacting with the Histone H5 enhancer. GATA-2 and GATA-3 were not detected. In contrast, gel-mobility-shift assays and competition experiments demonstrated that several specific complexes formed with the Histone H5 enhancer region. Gel-mobility-shift assays with 23 bp oligonucleotides containing the GATA-binding site (AGATAA) of the Histone H5 enhancer or of the beta-globin enhancer showed that the GATA sequence was sufficient for the formation of at least five complexes. Diagonal mobility-shift assays demonstrated that multisubunit complexes were forming with the GATA-1 protein. Our interpretation of the results is that GATA-1 interacts with a protein of approx. 105 kDa which, in turn, can associate with protein or protein complexes of approx. 26 kDa, 146 kDa and a protein(s) of molecular mass greater than 450 kDa. The different multisubunit complexes formed via the trans-acting factor GATA-1 may impart different transcriptional responses to the promoter and enhancer elements of the Histone H5 and globin genes.

Kozo Makino - One of the best experts on this subject based on the ideXlab platform.

  • sigma factors have two dna binding domains which resemble dbds of Histone H5 bira lexa and dtxr
    Proceedings of the Japan Academy. Ser. B: Physical and Biological Sciences, 1995
    Co-Authors: Masashi Suzuki, Kozo Makino
    Abstract:

    Sigma factors introduce sequence-specificity to DNA recognition by eubacterial RNA polymerases. Two domains of the factors, domains 4 and 2, bind, respectively, to the -35 and -10 sites in the promoters. We compare the amino acid sequences of the two domains of the major sigma subfamily (the σ70 subfamily) with those of other DNA-binding proteins (i.e. BirA, Histone H5, LexA, and DtxR) of which the 3D structures are known. It is concluded that each of the two sigma domains probably has three α-helices, and that the third α-helix binds to the DNA. Possible ways in which the two domains are combined along the same DNA and contact patterns between amino acid residues in the two domains and the DNA bases are discussed.

  • the dna binding domains of transcription factors phob and ompr adopt the same folding as that of Histone H5 and bind to rna polymerase using the ends of two alpha helices
    Proceedings of the Japan Academy. Ser. B: Physical and Biological Sciences, 1995
    Co-Authors: Masashi Suzuki, Kozo Makino
    Abstract:

    A possible structure and possible DNA-binding mode of transcription factors in the PhoB/OmpR family are discussed in comparison with those of another DNA-binding protein, Histone H5. The amino acid sequences of the DNA-binding domains of factors in this family strongly resemble that of H5 and thus the former are predicted to adopt the same globular fold as the latter, i.e. a domain which is composed of three α-helices, a β-strand (placed between the first two helices) and a β-hairpin at the C-terminus (the β-strand and the β-hairpin fold into a single β-sheet). The third helix is predicted to contact the DNA bases. The residues which have been identified as contacting RNA polymerase are located at the C-terminus of the second helix and the N-terminus of the third helix.