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  • Binding Sites  (73)
  • *Ecosystem
  • Protein Structure, Tertiary
  • American Association for the Advancement of Science (AAAS)  (73)
  • Nature Publishing Group (NPG)
  • 2015-2019
  • 1995-1999
  • 1990-1994  (73)
  • 1994  (73)
Collection
Keywords
Publisher
  • American Association for the Advancement of Science (AAAS)  (73)
  • Nature Publishing Group (NPG)
Years
  • 2015-2019
  • 1995-1999
  • 1990-1994  (73)
Year
  • 1
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    Enhancer point mutation results in a homeotic transformation in Drosophila (1994)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1994-05-13
    Description: In Drosophila, the misexpression or altered activity of genes from the bithorax complex results in homeotic transformations. One of these genes, abd-A, normally specifies the identity of the second through fourth abdominal segments (A2 to A4). In the dominant Hyperabdominal mutations (Hab), portions of the third thoracic segment (T3) are transformed toward A2 as the result of ectopic abd-A expression. Sequence analysis and deoxyribonuclease I footprinting demonstrate that the misexpression of abd-A in two independent Hab mutations results from the same single base change in a binding site for the gap gene Kruppel protein. These results establish that the spatial limits of the homeotic genes are directly regulated by gap gene products.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shimell, M J -- Simon, J -- Bender, W -- O'Connor, M B -- New York, N.Y. -- Science. 1994 May 13;264(5161):968-71.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology and Biochemistry, University of California, Irvine 92717.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7909957" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Base Sequence ; Binding Sites ; DNA-Binding Proteins/genetics/metabolism ; *Drosophila Proteins ; Drosophila melanogaster/embryology/*genetics ; Enhancer Elements, Genetic/*genetics ; Gene Expression Regulation ; *Genes, Homeobox ; Genes, Insect ; Kruppel-Like Transcription Factors ; Molecular Sequence Data ; *Nuclear Proteins ; *Point Mutation ; Proteins/*genetics ; Regulatory Sequences, Nucleic Acid ; *Repressor Proteins ; Transcription Factors/genetics/metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 2
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    Catalytic site components common to both splicing steps of a group II intron (1994)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1994-11-25
    Description: The splicing of group II introns occurs in two steps involving substrates with different chemical configurations. The question of whether these two steps are catalyzed by a single or two separate active sites is a matter of debate. Here, certain bases and phosphate oxygen atoms at conserved positions in domain V of a group II self-splicing intron are shown to be required for catalysis of both splicing steps. These results show that the active sites catalyzing the two steps must, at least, share common components, ruling out the existence of two completely distinct active sites in group II introns.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chanfreau, G -- Jacquier, A -- New York, N.Y. -- Science. 1994 Nov 25;266(5189):1383-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Unite de Genetique Moleculaire des Levures, URA 1149 du CNRS, Departement de Biologie Moleculaire, Institut Pasteur, Paris, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7973729" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; Binding Sites ; Catalysis ; Electron Transport Complex IV/genetics ; Electrophoresis, Polyacrylamide Gel ; Exons ; *Introns ; Molecular Sequence Data ; Nucleic Acid Conformation ; *RNA Splicing ; RNA, Fungal/chemistry/*genetics ; Saccharomyces cerevisiae/enzymology/genetics ; Thionucleotides/genetics
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 3
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    Increased recruitment of TATA-binding protein to the promoter by transcriptional activation domains in vivo (1994)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1994-10-14
    Description: The rate at which the TATA-binding protein (TBP) interacts with the TATA element and promotes transcription by RNA polymerase II was determined in yeast cells. A TBP derivative with altered TATA-element specificity was rapidly induced, and transcription from promoters with appropriately mutated TATA elements was measured. Without a functional activator protein, basal transcription was observed only after a lag of several hours. In contrast, GCN4-activated transcription occurred rapidly upon induction of the TBP derivative. These results suggest that accessibility of TBP to the chromatin template in vivo is rate limiting and that activation domains increase recruitment of TBP to the promoter.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Klein, C -- Struhl, K -- GM30186/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1994 Oct 14;266(5183):280-2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7939664" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; Binding Sites ; Chromatin/metabolism ; Copper/pharmacology ; DNA-Binding Proteins/*metabolism ; Fungal Proteins/metabolism/pharmacology ; Hydro-Lyases/genetics ; Molecular Sequence Data ; Protein Kinases/metabolism/pharmacology ; *Saccharomyces cerevisiae Proteins ; *TATA Box ; TATA-Box Binding Protein ; Templates, Genetic ; Transcription Factors/*metabolism/pharmacology ; *Transcriptional Activation ; Yeasts/genetics
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 4
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    Polymerase structures and mechanism (1994)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1994-12-23
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pelletier, H -- New York, N.Y. -- Science. 1994 Dec 23;266(5193):2025-6.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7801132" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Biological Evolution ; Catalysis ; DNA Polymerase I/*chemistry/metabolism ; Protein Structure, Secondary
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  • 5
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    Structures of ternary complexes of rat DNA polymerase beta, a DNA template-primer, and ddCTP (1994)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1994-06-24
    Description: Two ternary complexes of rat DNA polymerase beta (pol beta), a DNA template-primer, and dideoxycytidine triphosphate (ddCTP) have been determined at 2.9 A and 3.6 A resolution, respectively. ddCTP is the triphosphate of dideoxycytidine (ddC), a nucleoside analog that targets the reverse transcriptase of human immunodeficiency virus (HIV) and is at present used to treat AIDS. Although crystals of the two complexes belong to different space groups, the structures are similar, suggesting that the polymerase-DNA-ddCTP interactions are not affected by crystal packing forces. In the pol beta active site, the attacking 3'-OH of the elongating primer, the ddCTP phosphates, and two Mg2+ ions are all clustered around Asp190, Asp192, and Asp256. Two of these residues, Asp190 and Asp256, are present in the amino acid sequences of all polymerases so far studied and are also spatially similar in the four polymerases--the Klenow fragment of Escherichia coli DNA polymerase I, HIV-1 reverse transcriptase, T7 RNA polymerase, and rat DNA pol beta--whose crystal structures are now known. A two-metal ion mechanism is described for the nucleotidyl transfer reaction and may apply to all polymerases. In the ternary complex structures analyzed, pol beta binds to the DNA template-primer in a different manner from that recently proposed for other polymerase-DNA models.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pelletier, H -- Sawaya, M R -- Kumar, A -- Wilson, S H -- Kraut, J -- CA17374/CA/NCI NIH HHS/ -- ES06839/ES/NIEHS NIH HHS/ -- GM10928/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1994 Jun 24;264(5167):1891-903.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, University of California, San Diego 92093-0317.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7516580" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Base Sequence ; Binding Sites ; Crystallization ; Crystallography, X-Ray ; DNA/chemistry/metabolism ; DNA Polymerase I/*chemistry/metabolism ; DNA Primers/*chemistry/metabolism ; DNA-Directed RNA Polymerases/chemistry/metabolism ; Deoxycytosine Nucleotides/*chemistry/metabolism ; Dideoxynucleotides ; HIV Reverse Transcriptase ; Humans ; Hydrogen Bonding ; Models, Molecular ; Molecular Sequence Data ; RNA-Directed DNA Polymerase/chemistry/metabolism ; Rats ; Recombinant Proteins ; Templates, Genetic ; Thymine Nucleotides/chemistry/metabolism ; Viral Proteins ; Zidovudine/analogs & derivatives/chemistry/metabolism
    Print ISSN: 0036-8075
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  • 6
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    Routes to catalysis: structure of a catalytic antibody and comparison with its natural counterpart (1994)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1994-02-04
    Description: The three-dimensional structure of a catalytic antibody (1F7) with chorismate mutase activity has been determined to 3.0 A resolution as a complex with a transition state analog. The structural data suggest that the antibody stabilizes the same conformationally restricted pericyclic transition state as occurs in the uncatalyzed reaction. Overall shape and charge complementarity between the combining site and the transition state analog dictate preferential binding of the correct substrate enantiomer in a conformation appropriate for reaction. Comparison with the structure of a chorismate mutase enzyme indicates an overall similarity between the catalytic mechanism employed by the two proteins. Differences in the number of specific interactions available for restricting the rotational degrees of freedom in the transition state, and the lack of multiple electrostatic interactions that might stabilize charge separation in this highly polarized metastable species, are likely to account for the observed 10(4) times lower activity of the antibody relative to that of the natural enzymes that catalyze this reaction. The structure of the 1F7 Fab'-hapten complex provides confirmation that the properties of an antibody catalyst faithfully reflect the design of the transition state analog.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Haynes, M R -- Stura, E A -- Hilvert, D -- Wilson, I A -- AI-23498/AI/NIAID NIH HHS/ -- GM-38273/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1994 Feb 4;263(5147):646-52.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, Scripps Research Institute, La Jolla, CA 92037.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8303271" target="_blank"〉PubMed〈/a〉
    Keywords: Antibodies, Catalytic/*chemistry/metabolism ; Bacillus subtilis/enzymology ; Binding Sites ; Binding Sites, Antibody ; Catalysis ; Chorismate Mutase/*chemistry/metabolism ; Chorismic Acid/metabolism ; Crystallization ; Haptens ; Hydrogen Bonding ; Immunoglobulin Fab Fragments/metabolism ; Models, Molecular ; Thermodynamics
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  • 7
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    Receptor and ligand domains for invasion of erythrocytes by Plasmodium falciparum (1994)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1994-06-24
    Description: A 175-kilodalton erythrocyte binding protein, EBA-175, of the parasite Plasmodium falciparum mediates the invasion of erythrocytes. The erythrocyte receptor for EBA-175 is dependent on sialic acid. The domain of EBA-175 that binds erythrocytes was identified as region II with the use of truncated portions of EBA-175 expressed on COS cells. Region II, which contains a cysteine-rich motif, and native EBA-175 bind specifically to glycophorin A, but not to glycophorin B, on the erythrocyte membrane. Erythrocyte recognition of EBA-175 requires both sialic acid and the peptide backbone of glycophorin A. The identification of both the receptor and ligand domains may suggest rational designs for receptor blockade and vaccines.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sim, B K -- Chitnis, C E -- Wasniowska, K -- Hadley, T J -- Miller, L H -- New York, N.Y. -- Science. 1994 Jun 24;264(5167):1941-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Malaria Research, National Institutes of Health, Bethesda, MD 20892.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8009226" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Antigens, Protozoan ; Base Sequence ; Binding Sites ; Carrier Proteins/genetics/*metabolism ; Cell Line ; Erythrocytes/metabolism/*parasitology ; Glycopeptides/chemistry/metabolism ; Glycophorin/chemistry/*metabolism ; Molecular Sequence Data ; Plasmodium falciparum/*metabolism ; Protozoan Proteins/genetics/*metabolism ; Recombinant Fusion Proteins/metabolism ; Sialic Acids/*metabolism
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  • 8
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    The structure of flavocytochrome c sulfide dehydrogenase from a purple phototrophic bacterium (1994)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1994-10-21
    Description: The structure of the heterodimeric flavocytochrome c sulfide dehydrogenase from Chromatium vinosum was determined at a resolution of 2.53 angstroms. It contains a glutathione reductase-like flavin-binding subunit and a diheme cytochrome subunit. The diheme cytochrome folds as two domains, each resembling mitochondrial cytochrome c, and has an unusual interpropionic acid linkage joining the two heme groups in the interior of the subunit. The active site of the flavoprotein subunit contains a catalytically important disulfide bridge located above the pyrimidine portion of the flavin ring. A tryptophan, threonine, or tyrosine side chain may provide a partial conduit for electron transfer to one of the heme groups located 10 angstroms from the flavin.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chen, Z W -- Koh, M -- Van Driessche, G -- Van Beeumen, J J -- Bartsch, R G -- Meyer, T E -- Cusanovich, M A -- Mathews, F S -- GM-20530/GM/NIGMS NIH HHS/ -- GM-21277/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1994 Oct 21;266(5184):430-2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7939681" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Chromatium/*enzymology ; Computer Graphics ; Crystallography, X-Ray ; Cytochrome c Group/*chemistry ; Electron Transport ; Flavin-Adenine Dinucleotide/metabolism ; Hydrogen Bonding ; Models, Molecular ; Oxidoreductases/*chemistry ; Protein Conformation ; Protein Structure, Secondary
    Print ISSN: 0036-8075
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  • 9
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    Channel-like function of the Na,K pump probed at microsecond resolution in giant membrane patches (1994)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1994-03-11
    Description: Ion transporters can be thought of as ion channels that open and close only at one end at a time. As in real channels, ions may cross through an electrical field as they diffuse into and bind within the transporter pore, thereby generating electrical current. Extracellular sodium binding by the sodium potassium (Na,K) pump is associated with ultrafast charge movements in giant cardiac membrane patches. The charge movements are complete within 4 microseconds. They occur only when binding sites are open to the extracellular side, and they are abolished by ouabain and by the removal of extracellular sodium. Fast extracellular ion binding may be the exclusive source of Na,K pump electrogenicity.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hilgemann, D W -- New York, N.Y. -- Science. 1994 Mar 11;263(5152):1429-32.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Physiology, University of Texas Southwestern Medical Center, Dallas 75235.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8128223" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/metabolism ; Animals ; Binding Sites ; Guinea Pigs ; Membrane Potentials ; Models, Biological ; Myocardium/cytology/*metabolism ; Sodium/*metabolism ; Sodium Channels/*metabolism ; Sodium-Potassium-Exchanging ATPase/*metabolism
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  • 10
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    Structure of the allosteric regulatory enzyme of purine biosynthesis (1994)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1994-06-03
    Description: Multi-wavelength anomalous diffraction (MAD) has been used to determine the structure of the regulatory enzyme of de novo synthesis of purine nucleotides, glutamine 5-phosphoribosyl-1-pyrophosphate (PRPP) amidotransferase, from Bacillus subtilis. This allosteric enzyme, a 200-kilodalton tetramer, is subject to end product regulation by purine nucleotides. The metalloenzyme from B. subtilis is a paradigm for the higher eukaryotic enzymes, which have been refractory to isolation in stable form. The two folding domains of the polypeptide are correlated with functional domains for glutamine binding and for transfer of ammonia to the substrate PRPP. Eight molecules of the feedback inhibitor adenosine monophosphate (AMP) are bound to the tetrameric enzyme in two types of binding sites: the PRPP catalytic site of each subunit and an unusual regulatory site that is immediately adjacent to each active site but is between subunits. An oxygen-sensitive [4Fe-4S] cluster in each subunit is proposed to regulate protein turnover in vivo and is distant from the catalytic site. Oxygen sensitivity of the cluster is diminished by AMP, which blocks a channel through the protein to the cluster. The structure is representative of both glutamine amidotransferases and phosphoribosyltransferases.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Smith, J L -- Zaluzec, E J -- Wery, J P -- Niu, L -- Switzer, R L -- Zalkin, H -- Satow, Y -- DK-42303/DK/NIDDK NIH HHS/ -- GM-24658/GM/NIGMS NIH HHS/ -- R37 DK042303/DK/NIDDK NIH HHS/ -- New York, N.Y. -- Science. 1994 Jun 3;264(5164):1427-33.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Sciences, Purdue University, West Lafayette, IN 47907.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8197456" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Monophosphate/metabolism ; Allosteric Regulation ; Amidophosphoribosyltransferase/*chemistry/metabolism ; Amino Acid Sequence ; Animals ; Bacillus subtilis/*enzymology ; Binding Sites ; Computer Graphics ; Crystallography, X-Ray ; Humans ; Models, Molecular ; Molecular Sequence Data ; Oxygen/pharmacology ; Protein Folding ; Protein Structure, Secondary ; Saccharomyces cerevisiae
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