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  • 1
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    Structure of a peptide inhibitor bound to the catalytic subunit of cyclic adenosine monophosphate-dependent protein kinase (1991)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1991-07-26
    Description: The structure of a 20-amino acid peptide inhibitor bound to the catalytic subunit of cyclic AMP-dependent protein kinase, and its interactions with the enzyme, are described. The x-ray crystal structure of the complex is the basis of the analysis. The peptide inhibitor, derived from a naturally occurring heat-stable protein kinase inhibitor, contains an amphipathic helix that is followed by a turn and an extended conformation. The extended region occupies the cleft between the two lobes of the enzyme and contains a five-residue consensus recognition sequence common to all substrates and peptide inhibitors of the catalytic subunit. The helical portion of the peptide binds to a hydrophobic groove and conveys high affinity binding. Loops from both domains converge at the active site and contribute to a network of conserved residues at the sites of magnesium adenosine triphosphate binding and catalysis. Amino acids associated with peptide recognition, nonconserved, extend over a large surface area.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Knighton, D R -- Zheng, J H -- Ten Eyck, L F -- Xuong, N H -- Taylor, S S -- Sowadski, J M -- RR01644/RR/NCRR NIH HHS/ -- T32CA09523/CA/NCI NIH HHS/ -- T32DK07233/DK/NIDDK NIH HHS/ -- New York, N.Y. -- Science. 1991 Jul 26;253(5018):414-20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, University of California, San Diego, La Jolla 92093-0654.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1862343" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Carrier Proteins/*chemistry/metabolism ; Computer Simulation ; Enzyme Inhibitors/*chemistry ; *Intracellular Signaling Peptides and Proteins ; Macromolecular Substances ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Kinases/*chemistry/metabolism ; X-Ray Diffraction
    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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    Crystal structure of the catalytic subunit of cyclic adenosine monophosphate-dependent protein kinase (1991)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1991-07-26
    Description: The crystal structure of the catalytic subunit of cyclic adenosine monophosphate-dependent protein kinase complexed with a 20-amino acid substrate analog inhibitor has been solved and partially refined at 2.7 A resolution to an R factor of 0.212. The magnesium adenosine triphosphate (MgATP) binding site was located by difference Fourier synthesis. The enzyme structure is bilobal with a deep cleft between the lobes. The cleft is filled by MgATP and a portion of the inhibitor peptide. The smaller lobe, consisting mostly of amino-terminal sequence, is associated with nucleotide binding, and its largely antiparallel beta sheet architecture constitutes an unusual nucleotide binding motif. The larger lobe is dominated by helical structure with a single beta sheet at the domain interface. This lobe is primarily involved in peptide binding and catalysis. Residues 40 through 280 constitute a conserved catalytic core that is shared by more than 100 protein kinases. Most of the invariant amino acids in this conserved catalytic core are clustered at the sites of nucleotide binding and catalysis.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Knighton, D R -- Zheng, J H -- Ten Eyck, L F -- Ashford, V A -- Xuong, N H -- Taylor, S S -- Sowadski, J M -- RR01644/RR/NCRR NIH HHS/ -- T32CA09523/CA/NCI NIH HHS/ -- T32DK07233/DK/NIDDK NIH HHS/ -- New York, N.Y. -- Science. 1991 Jul 26;253(5018):407-14.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, University of California, San Diego, La Jolla 92093-0654.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1862342" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/metabolism ; Animals ; Binding Sites ; Computer Simulation ; Fourier Analysis ; Macromolecular Substances ; Mice ; Models, Molecular ; Protein Kinases/*chemistry/metabolism ; Recombinant Proteins/chemistry/metabolism ; X-Ray Diffraction
    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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    Structural basis of the intrasteric regulation of myosin light chain kinases (1992)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1992-10-02
    Description: The smooth muscle myosin light chain kinase (smMLCK) catalytic core was modeled by using the crystallographic coordinates of the cyclic AMP-dependent protein kinase catalytic subunit (cAPK) and a bound pseudosubstrate inhibitor peptide, PKI(5-24). Despite only 30% identity in amino acid sequence, the MLCK sequence can be readily accommodated in this structure. With the exception of the short B-helix, all major elements of secondary structure in the core are very likely conserved. The active site of the modeled MLCK complements the known requirements for peptide substrate recognition. MLCK contains a pseudosubstrate sequence that overlaps the calmodulin binding domain and has been proposed to act as an intrasteric inhibitor and occupy the substrate binding site in the absence of Ca(2+)-calmodulin. The pseudosubstrate sequence can be modeled easily into the entire backbone of PKI(5-24). The results demonstrate that the intrasteric model for regulation of MLCK by intramolecular competitive inhibition is structurally plausible.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Knighton, D R -- Pearson, R B -- Sowadski, J M -- Means, A R -- Ten Eyck, L F -- Taylor, S S -- Kemp, B E -- T32CA09523/CA/NCI NIH HHS/ -- T32DK07233/DK/NIDDK NIH HHS/ -- New York, N.Y. -- Science. 1992 Oct 2;258(5079):130-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, University of California San Diego, La Jolla 92093-0654.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1439761" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Chromosome Mapping ; Crystallography ; *Gene Expression Regulation, Enzymologic ; Models, Molecular ; Molecular Sequence Data ; Molecular Structure ; Myosin-Light-Chain Kinase/*chemistry ; Oligopeptides/genetics/metabolism ; Peptide Fragments ; Peptides/genetics/metabolism ; Protein Binding/physiology ; Protein Kinases/chemistry ; Sequence Alignment ; Sequence Homology
    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
    Electronic Resource
    Electronic Resource
    Structural Framework for the Protein Kinase Family (1992)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Cell and Developmental Biology 8 (1992), S. 429-462 
    Details
    ISSN: 0743-4634
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.cb.08.110192.002241
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  • 5
    Electronic Resource
    Electronic Resource
    A method of obtaining a stereochemically acceptable protein model which fits a set of atomic coordinates (1976)
    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 32 (1976), S. 349-350 
    Details
    ISSN: 1600-5724
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: A method is proposed by which a protein model with acceptable stereochemistry can be fitted to a set of atomic coordinates. By expressing all constraints in terms of distances between pairs of atoms it is possible to enforce any desired stereochemistry in a physically realistic manner, and at the same time to substantially reduce computing time. Application of the technique to thermolysin is described. The method has been independently developed and applied to insulin by E. J. Dodson, N. W. Isaacs & J. S. Rollett [Acta Cryst. (1976). A32, 311-315].
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0567739476000806
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  • 6
    Electronic Resource
    Electronic Resource
    2.2 Å refined crystal structure of the catalytic subunit of cAMP-dependent protein kinase complexed with MnATP and a peptide inhibitor (1993)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 49 (1993), S. 362-365 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: . The crystal structure of a ternary complex containing the catalytic subunit of cAMP-dependent protein kinase, ATP and a 20-residue inhibitor peptide was refined at a resolution of 2.2 Å to an R value of 0.177. In order to identify the metal binding sites, the crystals, originally grown in the presence of low concentrations of Mg2+, were soaked in Mn2+. Two Mn2+ ions were identified using an anomalous Fourier map. One Mn2+ ion bridges the γ- and β-phosphates and interacts with Asp184 and two water molecules. The second Mn2+ ion interacts with the side chains of Asn171 and Asp l84 as well as with a water molecule. Modeling a serine into the P site of the inhibitor peptide suggests a mechanism for phosphotransfer.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444993000423
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  • 7
    Electronic Resource
    Electronic Resource
    2.0 Å refined crystal structure of the catalytic subunit of cAMP-dependent protein kinase complexed with a peptide inhibitor and detergent (1993)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 49 (1993), S. 357-361 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: . A mutant (Serl39Ala) of the mouse recombinant catalytic (C) subunit of cAMP-dependent protein kinase was co-crystallized with a peptide inhibitor, PKI(5–24), and MEGA-8 (octanoyl-N-methylglucamide) detergent. This structure was refined using all observed data (30 248 reflections) between 30 and 1.95 Å resolution to an R factor of 0.186. R.m.s. deviations of bond lengths and bond angles are 0.013 Å and 2.3°, respectively. The final model has 3075 atoms (207 solvent) with a mean B factor of 31.9 Å2. The placement of invariant protein-kinase residues and most C:PKI(5–24) interactions were confirmed, but register errors affecting residues 55–64 and 309–339 were corrected during refinement by shifting the affected sequences toward the C terminus along the previously determined backbone path. New details of C:PKI(5–24) interactions and the Ser338 autophosphorylation site are described, and the acyl group binding site near the catalytic subunit NH2 terminus is identified.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444993000502
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  • 8
    Electronic Resource
    Electronic Resource
    Crystallographic fast Fourier transforms (1973)
    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 29 (1973), S. 183-191 
    Details
    ISSN: 1600-5724
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: This paper presents methods for incorporating crystallographic symmetry properties into complex Fourier transforms in a form particularly well suited for use with the Cooley-Tukey fast Fourier transform algorithm. The crystallographic transforms are expressed in terms of a small number of one-dimensional special cases. The algebra presented here has been used to write computer programs for both Fourier syntheses and Fourier inversions. Even for some quite large problems (7000 structure factors and 149000 grid points in the asymmetric unit) the rate-limiting step is output of the answers.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0567739473000458
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  • 9
    Electronic Resource
    Electronic Resource
    An efficient general-purpose least-squares refinement program for macromolecular structures (1987)
    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 43 (1987), S. 489-501 
    Details
    ISSN: 1600-5724
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: A package of programs has been developed for efficient restrained least-squares refinement of macromolecular crystal structures. The package has been designed to be as flexible and general purpose as possible. The process of refinement is divided into basic units and an independent computer program handles each task. Each functional unit communicates with other programs in the package by way of files of well defined format. To modify or replace any program, the user need only understand the function of that particular element. Stereochemical restraints are defined in a general way that can be applied to proteins, nucleic acids, prosthetic groups, solvent atoms and so on. Guide values for bond lengths and bond angles are specified in a straightforward direct manner. Designated groups of atoms can be held constant or constrained to behave as a rigid body during refinement. In order to make the package as efficient as possible, the fast Fourier transform algorithm is used for all the crystallographic transformations. To highlight potential errors in the refined structure the user can list those atoms that have the worst bond lengths and angles, or have the largest positional, temperature-factor or occupancy gradients. It is also possible to check that protein and solvent atoms do not sterically clash with symmetry-related neighbors. Applications of the program package to a bacteriochlorophyll-containing protein, thermolysin-inhibitor complexes and mutants of bacteriophage T4 lysozyme are described.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0108767387099124
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  • 10
    Electronic Resource
    Electronic Resource
    Efficient structure-factor calculation for large molecules by the fast Fourier transform (1977)
    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 33 (1977), S. 486-492 
    Details
    ISSN: 1600-5724
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: A method is presented for calculating structure factors by Fourier inversion of a model electron density map. The cost of this method and of the standard methods are analyzed as a function of number of atoms, resolution, and complexity of space group. The cost functions were scaled together by timing both methods on the same problem, with the same computer. The FFT method is 3½ to 7 times less expensive than conventional methods for non-centrosymmetric space groups.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0567739477001211
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