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  • 1
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    Crystal structure of an initiation factor bound to the 30S ribosomal subunit (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-03-03
    Description: Initiation of translation at the correct position on messenger RNA is essential for accurate protein synthesis. In prokaryotes, this process requires three initiation factors: IF1, IF2, and IF3. Here we report the crystal structure of a complex of IF1 and the 30S ribosomal subunit. Binding of IF1 occludes the ribosomal A site and flips out the functionally important bases A1492 and A1493 from helix 44 of 16S RNA, burying them in pockets in IF1. The binding of IF1 causes long-range changes in the conformation of H44 and leads to movement of the domains of 30S with respect to each other. The structure explains how localized changes at the ribosomal A site lead to global alterations in the conformation of the 30S subunit.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Carter, A P -- Clemons, W M Jr -- Brodersen, D E -- Morgan-Warren, R J -- Hartsch, T -- Wimberly, B T -- Ramakrishnan, V -- GM 44973/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2001 Jan 19;291(5503):498-501.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11228145" target="_blank"〉PubMed〈/a〉
    Keywords: Base Pairing ; Binding Sites ; Crystallography, X-Ray ; Eukaryotic Initiation Factor-1/*chemistry/metabolism ; Hydrogen Bonding ; Models, Molecular ; Nucleic Acid Conformation ; Protein Conformation ; Protein Structure, Secondary ; RNA, Ribosomal, 16S/*chemistry/metabolism ; RNA, Transfer/metabolism ; Ribosomal Proteins/*chemistry/metabolism ; Ribosomes/*chemistry/metabolism ; Thermus thermophilus/*chemistry
    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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    Recognition of cognate transfer RNA by the 30S ribosomal subunit (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-05-08
    Description: Crystal structures of the 30S ribosomal subunit in complex with messenger RNA and cognate transfer RNA in the A site, both in the presence and absence of the antibiotic paromomycin, have been solved at between 3.1 and 3.3 angstroms resolution. Cognate transfer RNA (tRNA) binding induces global domain movements of the 30S subunit and changes in the conformation of the universally conserved and essential bases A1492, A1493, and G530 of 16S RNA. These bases interact intimately with the minor groove of the first two base pairs between the codon and anticodon, thus sensing Watson-Crick base-pairing geometry and discriminating against near-cognate tRNA. The third, or "wobble," position of the codon is free to accommodate certain noncanonical base pairs. By partially inducing these structural changes, paromomycin facilitates binding of near-cognate tRNAs.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ogle, J M -- Brodersen, D E -- Clemons , W M Jr -- Tarry, M J -- Carter, A P -- Ramakrishnan, V -- F31 GM019384/GM/NIGMS NIH HHS/ -- GM 44973/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2001 May 4;292(5518):897-902.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11340196" target="_blank"〉PubMed〈/a〉
    Keywords: Anti-Bacterial Agents/metabolism/pharmacology ; Anticodon/chemistry/metabolism ; Base Pairing ; Binding Sites ; Codon/chemistry/metabolism ; Crystallography, X-Ray ; Guanosine Triphosphate/metabolism ; Hydrogen Bonding ; Models, Molecular ; Nucleic Acid Conformation ; Paromomycin/metabolism/pharmacology ; Peptide Chain Elongation, Translational ; Peptide Elongation Factor Tu/metabolism ; Protein Biosynthesis ; RNA, Bacterial/chemistry/metabolism ; RNA, Messenger/chemistry/*metabolism ; RNA, Ribosomal, 16S/chemistry/*metabolism ; RNA, Transfer/chemistry/*metabolism ; RNA, Transfer, Amino Acid-Specific/chemistry/*metabolism ; RNA, Transfer, Phe/chemistry/metabolism ; Ribosomes/chemistry/*metabolism/ultrastructure ; Thermodynamics ; Thermus thermophilus/chemistry/metabolism/*ultrastructure
    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 structure of the long-chain fatty acid transporter FadL (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-06-05
    Description: The mechanisms by which hydrophobic molecules, such as long-chain fatty acids, enter cells are poorly understood. In Gram-negative bacteria, the lipopolysaccharide layer in the outer membrane is an efficient barrier for fatty acids and aromatic hydrocarbons destined for biodegradation. We report crystal structures of the long-chain fatty acid transporter FadL from Escherichia coli at 2.6 and 2.8 angstrom resolution. FadL forms a 14-stranded beta barrel that is occluded by a central hatch domain. The structures suggest that hydrophobic compounds bind to multiple sites in FadL and use a transport mechanism that involves spontaneous conformational changes in the hatch.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉van den Berg, Bert -- Black, Paul N -- Clemons, William M Jr -- Rapoport, Tom A -- New York, N.Y. -- Science. 2004 Jun 4;304(5676):1506-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA. lvandenberg@hms.harvard.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15178802" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacterial Outer Membrane Proteins/*chemistry/metabolism ; Binding Sites ; Biological Transport ; Crystallization ; Crystallography, X-Ray ; Escherichia coli/chemistry/metabolism ; Escherichia coli Proteins/*chemistry/metabolism ; Fatty Acid Transport Proteins ; Fatty Acids/*metabolism ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Models, Biological ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary
    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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