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  • 1
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    A model for the mechanism of human topoisomerase I (1998)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1998-03-21
    Description: The three-dimensional structure of a 70-kilodalton amino terminally truncated form of human topoisomerase I in complex with a 22-base pair duplex oligonucleotide, determined to a resolution of 2.8 angstroms, reveals all of the structural elements of the enzyme that contact DNA. The linker region that connects the central core of the enzyme to the carboxyl-terminal domain assumes a coiled-coil configuration and protrudes away from the remainder of the enzyme. The positively charged DNA-proximal surface of the linker makes only a few contacts with the DNA downstream of the cleavage site. In combination with the crystal structures of the reconstituted human topoisomerase I before and after DNA cleavage, this information suggests which amino acid residues are involved in catalyzing phosphodiester bond breakage and religation. The structures also lead to the proposal that the topoisomerization step occurs by a mechanism termed "controlled rotation."〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stewart, L -- Redinbo, M R -- Qiu, X -- Hol, W G -- Champoux, J J -- CA65656/CA/NCI NIH HHS/ -- GM16713/GM/NIGMS NIH HHS/ -- GM49156/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1998 Mar 6;279(5356):1534-41.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Biomolecular Structure Center and Department of Biological Structure, School of Medicine, University of Washington, Seattle, WA 98195-7742, USA. emerald_biostructures@rocketmail.com〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9488652" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Arginine/chemistry/metabolism ; Binding Sites ; Catalysis ; Crystallography, X-Ray ; DNA/chemistry/*metabolism ; DNA Topoisomerases, Type I/*chemistry/*metabolism ; Humans ; Hydrogen Bonding ; *Models, Chemical ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; Oligodeoxyribonucleotides/chemistry/metabolism ; *Protein Conformation ; Protein Structure, Secondary ; Tyrosine/chemistry/metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 2
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    The human nuclear xenobiotic receptor PXR: structural determinants of directed promiscuity (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-06-16
    Description: The human nuclear pregnane X receptor (hPXR) activates cytochrome P450-3A expression in response to a wide variety of xenobiotics and plays a critical role in mediating dangerous drug-drug interactions. We present the crystal structures of the ligand-binding domain of hPXR both alone and in complex with the cholesterol-lowering drug SR12813 at resolutions of 2.5 and 2.75 angstroms, respectively. The hydrophobic ligand-binding cavity of hPXR contains a small number of polar residues, permitting SR12813 to bind in three distinct orientations. The position and nature of these polar residues were found to be critical for establishing the precise pharmacologic activation profile of PXR. Our findings provide important insights into how hPXR detects xenobiotics and may prove useful in predicting and avoiding drug-drug interactions.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Watkins, R E -- Wisely, G B -- Moore, L B -- Collins, J L -- Lambert, M H -- Williams, S P -- Willson, T M -- Kliewer, S A -- Redinbo, M R -- New York, N.Y. -- Science. 2001 Jun 22;292(5525):2329-33. Epub 2001 Jun 14.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina (UNC) at Chapel Hill, Chapel Hill, NC 27599, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11408620" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Crystallography, X-Ray ; Diphosphonates/chemistry/*metabolism ; Humans ; Ligands ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Receptors, Cytoplasmic and Nuclear/*chemistry/*metabolism ; Receptors, Steroid/*chemistry/*metabolism ; Rifampin/metabolism ; Xenobiotics/*metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 3
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    Crystal structures of human topoisomerase I in covalent and noncovalent complexes with DNA (1998)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1998-03-21
    Description: Topoisomerases I promote the relaxation of DNA superhelical tension by introducing a transient single-stranded break in duplex DNA and are vital for the processes of replication, transcription, and recombination. The crystal structures at 2.1 and 2.5 angstrom resolution of reconstituted human topoisomerase I comprising the core and carboxyl-terminal domains in covalent and noncovalent complexes with 22-base pair DNA duplexes reveal an enzyme that "clamps" around essentially B-form DNA. The core domain and the first eight residues of the carboxyl-terminal domain of the enzyme, including the active-site nucleophile tyrosine-723, share significant structural similarity with the bacteriophage family of DNA integrases. A binding mode for the anticancer drug camptothecin is proposed on the basis of chemical and biochemical information combined with these three-dimensional structures of topoisomerase I-DNA complexes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Redinbo, M R -- Stewart, L -- Kuhn, P -- Champoux, J J -- Hol, W G -- CA65656/CA/NCI NIH HHS/ -- GM49156/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1998 Mar 6;279(5356):1504-13.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Biomolecular Structure Center and Department of Biological Structure, Box 357742, School of Medicine, University of Washington, Seattle, WA 98195, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9488644" target="_blank"〉PubMed〈/a〉
    Keywords: Antineoplastic Agents, Phytogenic/metabolism/pharmacology ; Binding Sites ; Camptothecin/analogs & derivatives/metabolism/pharmacology ; Crystallography, X-Ray ; DNA/chemistry/*metabolism ; DNA Topoisomerases, Type I/*chemistry/genetics/metabolism ; *DNA-Binding Proteins ; Homeodomain Proteins/chemistry ; Host Cell Factor C1 ; Humans ; Hydrogen Bonding ; Integrases/chemistry ; Models, Molecular ; Mutation ; Nucleic Acid Conformation ; Octamer Transcription Factor-1 ; Oligodeoxyribonucleotides/chemistry/metabolism ; *Protein Conformation ; Protein Structure, Secondary ; Recombinant Proteins/chemistry ; Transcription Factors/chemistry ; Tyrosine/chemistry/metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 4
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    Crystal structure of an ancient protein: evolution by conformational epistasis (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-08-19
    Description: The structural mechanisms by which proteins have evolved new functions are known only indirectly. We report x-ray crystal structures of a resurrected ancestral protein-the approximately 450 million-year-old precursor of vertebrate glucocorticoid (GR) and mineralocorticoid (MR) receptors. Using structural, phylogenetic, and functional analysis, we identify the specific set of historical mutations that recapitulate the evolution of GR's hormone specificity from an MR-like ancestor. These substitutions repositioned crucial residues to create new receptor-ligand and intraprotein contacts. Strong epistatic interactions occur because one substitution changes the conformational position of another site. "Permissive" mutations-substitutions of no immediate consequence, which stabilize specific elements of the protein and allow it to tolerate subsequent function-switching changes-played a major role in determining GR's evolutionary trajectory.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2519897/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2519897/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ortlund, Eric A -- Bridgham, Jamie T -- Redinbo, Matthew R -- Thornton, Joseph W -- F32-GM074398/GM/NIGMS NIH HHS/ -- R01 GM081592/GM/NIGMS NIH HHS/ -- R01 GM081592-01/GM/NIGMS NIH HHS/ -- R01 GM081592-02/GM/NIGMS NIH HHS/ -- R01-DK622229/DK/NIDDK NIH HHS/ -- R01-GM081592/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2007 Sep 14;317(5844):1544-8. Epub 2007 Aug 16.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17702911" target="_blank"〉PubMed〈/a〉
    Keywords: Aldosterone/metabolism ; Amino Acid Sequence ; Amino Acid Substitution ; Animals ; Crystallography, X-Ray ; Epistasis, Genetic ; *Evolution, Molecular ; Humans ; Hydrocortisone/metabolism ; Ligands ; Likelihood Functions ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Phylogeny ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Receptors, Glucocorticoid/*chemistry/*genetics/metabolism ; Receptors, Mineralocorticoid/*chemistry/*genetics/metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 5
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    Alleviating cancer drug toxicity by inhibiting a bacterial enzyme (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-11-06
    Description: The dose-limiting side effect of the common colon cancer chemotherapeutic CPT-11 is severe diarrhea caused by symbiotic bacterial beta-glucuronidases that reactivate the drug in the gut. We sought to target these enzymes without killing the commensal bacteria essential for human health. Potent bacterial beta-glucuronidase inhibitors were identified by high-throughput screening and shown to have no effect on the orthologous mammalian enzyme. Crystal structures established that selectivity was based on a loop unique to bacterial beta-glucuronidases. Inhibitors were highly effective against the enzyme target in living aerobic and anaerobic bacteria, but did not kill the bacteria or harm mammalian cells. Finally, oral administration of an inhibitor protected mice from CPT-11-induced toxicity. Thus, drugs may be designed to inhibit undesirable enzyme activities in essential microbial symbiotes to enhance chemotherapeutic efficacy.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3110694/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3110694/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wallace, Bret D -- Wang, Hongwei -- Lane, Kimberly T -- Scott, John E -- Orans, Jillian -- Koo, Ja Seol -- Venkatesh, Madhukumar -- Jobin, Christian -- Yeh, Li-An -- Mani, Sridhar -- Redinbo, Matthew R -- CA127231/CA/NCI NIH HHS/ -- CA98468/CA/NCI NIH HHS/ -- R01 CA127231/CA/NCI NIH HHS/ -- R01 CA127231-01A2/CA/NCI NIH HHS/ -- R01 CA127231-02/CA/NCI NIH HHS/ -- R01 CA127231-03/CA/NCI NIH HHS/ -- R01 CA161879/CA/NCI NIH HHS/ -- R01 DK073338/DK/NIDDK NIH HHS/ -- New York, N.Y. -- Science. 2010 Nov 5;330(6005):831-5. doi: 10.1126/science.1191175.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21051639" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antineoplastic Agents, Phytogenic/metabolism/*toxicity ; Bacteria, Anaerobic/drug effects ; Camptothecin/*analogs & derivatives/metabolism/toxicity ; Cell Line, Tumor ; Colon/drug effects/microbiology/pathology ; Crystallography, X-Ray ; Diarrhea/prevention & control ; Drug Evaluation, Preclinical ; Enzyme Inhibitors/chemistry/metabolism/*pharmacology ; Escherichia coli/enzymology ; Escherichia coli Proteins/antagonists & inhibitors/chemistry/isolation & ; purification/metabolism ; Female ; Glucuronidase/*antagonists & inhibitors/chemistry/isolation & ; purification/metabolism/*pharmacology ; Humans ; Intestinal Mucosa/drug effects/microbiology/pathology ; Mice ; Mice, Inbred BALB C ; Models, Molecular ; Prodrugs/metabolism/toxicity ; Protein Conformation
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 6
    Electronic Resource
    Electronic Resource
    Structure determination of plastocyanin from a specimen with a hemihedral twinning fraction of one-half (1993)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 49 (1993), S. 375-380 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The structure determination of a macromolecule from a hemihedrally twinned crystal specimen with a twinning fraction of one-half is described. Twinning was detected by analysis of crystal-packing density and intensity statistics. The structure was solved using molecular replacement, and the positioned search model was used to overcome the twinning by a novel method of `detwinning' the observed data. Estimates of the unobservable crystallographic intensities from each of the twin domains were obtained and used to refine the model. The structure of a new algal plastocyanin from Chlamydomonas reinhardtii was determined by this method to 1.6 Å resolution with a `twinned' R factor of 15.6%. Additional data from a crystal specimen with a low twinning fraction were used to establish the accuracy of the structure solution from the perfectly twinned data, and to finalize the refinement to 1.5 Å resolution and a true R factor of 16.8%. Methods for detecting twinning and obtaining a molecular-replacement solution in the presence of twinning are discussed.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S090744499300294X
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    Paper (German National Licenses)
    Fulltext
  • 7
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    8-Oxoguanine rearranges the active site of human topoisomerase I (2002)
    National Academy of Sciences
    Details
    Publication Date: 2002-09-03
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 8
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    Molecular basis for pH-dependent mucosal dehydration in cystic fibrosis airways (2013)
    National Academy of Sciences
    Details
    Publication Date: 2013-09-16
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 9
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    Molecular basis of antibiotic multiresistance transfer in Staphylococcus aureus (2013)
    National Academy of Sciences
    Details
    Publication Date: 2013-01-28
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 10
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    Interplay between RsmA and RsmF [Microbiology] (2013)
    National Academy of Sciences
    Details
    Publication Date: 2013-09-11
    Description: Members of the CsrA family of prokaryotic mRNA-binding proteins alter the translation and/or stability of transcripts needed for numerous global physiological processes. The previously described CsrA family member in Pseudomonas aeruginosa (RsmA) plays a central role in determining infection modality by reciprocally regulating processes associated with acute (type III secretion...
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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