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Adrian J. Lapthorn - One of the best experts on this subject based on the ideXlab platform.

  • the three Dimensional Structure of shikimate kinase
    Journal of Molecular Biology, 1998
    Co-Authors: Tino Krell, John R. Coggins, Adrian J. Lapthorn
    Abstract:

    The three-Dimensional Structure of shikimate kinase from Erwinia chrysanthemi has been determined by multiple isomorphous replacement. Two models are presented: a high resolution 1.9 A model and a 2.6 A model which contains bound Mg-ADP. The enzyme is an alpha/beta protein consisting of a central sheet of five parallel beta-strands flanked by alpha-helices with overall topology similar to adenylate kinase. Evidence is presented that shikimate kinase undergoes major conformational changes on ligand binding. It resembles adenylate kinase in having a P-loop containing core Structure and two flexible domains which undergo induced fit movement on substrate binding. The binding of Mg2+ in the active site of shikimate kinase involves direct interaction with two protein side-chains which is different from the situation found in adenylate kinase. Shikimate kinase has a readily identifiable Walker A-motif and a recognisable but modified Walker B-motif. Comparison of shikimate kinase to adenylate kinase has led to the identification of an adenine-binding motif (I/VDAXQ/NXP). Difference Fourier calculations have revealed the shikimate binding site which corresponds to the location of the AMP-binding site in adenylate kinase. A model for shikimate-binding is presented.

  • Regular articleThe three-Dimensional Structure of shikimate kinase1
    Journal of Molecular Biology, 1998
    Co-Authors: Tino Krell, John R. Coggins, Adrian J. Lapthorn
    Abstract:

    The three-Dimensional Structure of shikimate kinase from Erwinia chrysanthemi has been determined by multiple isomorphous replacement. Two models are presented: a high resolution 1.9 A model and a 2.6 A model which contains bound Mg-ADP. The enzyme is an α/β protein consisting of a central sheet of five parallel β-strands flanked by α-helices with overall topology similar to adenylate kinase. Evidence is presented that shikimate kinase undergoes major conformational changes on ligand binding. It resembles adenylate kinase in having a P-loop containing core Structure and two flexible domains which undergo induced fit movement on substrate binding. The binding of Mg2+ in the active site of shikimate kinase involves direct interaction with two protein side-chains which is different from the situation found in adenylate kinase. Shikimate kinase has a readily identifiable Walker A-motif and a recognisable but modified Walker B-motif. Comparison of shikimate kinase to adenylate kinase has led to the identification of an adenine-binding motif (I/VDAXQ/NXP). Difference Fourier calculations have revealed the shikimate binding site which corresponds to the location of the AMP-binding site in adenylate kinase. A model for shikimate-binding is presented.

Yoshiki Matsuura - One of the best experts on this subject based on the ideXlab platform.

  • three Dimensional Structure of pseudomonas isoamylase at 2 2 a resolution
    Journal of Molecular Biology, 1998
    Co-Authors: Yoshio Katsuya, Yoshihiro Mezaki, Michio Kubota, Yoshiki Matsuura
    Abstract:

    Abstract The three-Dimensional Structure of isoamylase from Pseudomonasamyloderamosa , which hydrolyzes α-1,6-glucosidic linkages of amylopectin and glycogen, has been determined by X-ray Structure analysis. The enzyme has 750 amino acid residues and a molecular mass of 80 kDa, and it can be crystallized from ammonium sulfate solution. The Structure was elucidated by the multiple isomorphous replacement method and refined at 2.2 A resolution, resulting in a final R -factor of 0.161 for significant reflections with a root-mean-square deviation from ideality in bond lengths of 0.009 A. The analysis revealed that in the N-terminal region, isoamylase has a novel extra domain that we call domain N, whose three-Dimensional Structure has not so far been reported. It has a (β/α) 8 -barrel-type supersecondary Structure in the catalytic domain common to the α-amylase family enzymes, though the barrel is incomplete, with a deletion of an α-helix between the fifth and sixth β-strands. A long excursed region is present between the third β-strand and the third α-helix of the barrel but, in contrast to the so-called domain B that has been identified in the other enzymes of α-amylase family, it cannot be considered to be an independent domain, because this loop forms a globular cluster together with the loop between the fourth β-strand and the fourth α-helix. Isoamylase contains a bound calcium ion, but this is not in the same position as the conserved calcium ion that has been reported in other α-amylase family enzymes.

  • regular articlethree Dimensional Structure of pseudomonas isoamylase at 2 2 a resolution1
    Journal of Molecular Biology, 1998
    Co-Authors: Yoshio Katsuya, Yoshihiro Mezaki, Michio Kubota, Yoshiki Matsuura
    Abstract:

    The three-Dimensional Structure of isoamylase from Pseudomonasamyloderamosa, which hydrolyzes α-1,6-glucosidic linkages of amylopectin and glycogen, has been determined by X-ray Structure analysis. The enzyme has 750 amino acid residues and a molecular mass of 80 kDa, and it can be crystallized from ammonium sulfate solution. The Structure was elucidated by the multiple isomorphous replacement method and refined at 2.2 A resolution, resulting in a final R-factor of 0.161 for significant reflections with a root-mean-square deviation from ideality in bond lengths of 0.009 A. The analysis revealed that in the N-terminal region, isoamylase has a novel extra domain that we call domain N, whose three-Dimensional Structure has not so far been reported. It has a (β/α)8-barrel-type supersecondary Structure in the catalytic domain common to the α-amylase family enzymes, though the barrel is incomplete, with a deletion of an α-helix between the fifth and sixth β-strands. A long excursed region is present between the third β-strand and the third α-helix of the barrel but, in contrast to the so-called domain B that has been identified in the other enzymes of α-amylase family, it cannot be considered to be an independent domain, because this loop forms a globular cluster together with the loop between the fourth β-strand and the fourth α-helix. Isoamylase contains a bound calcium ion, but this is not in the same position as the conserved calcium ion that has been reported in other α-amylase family enzymes.

Tino Krell - One of the best experts on this subject based on the ideXlab platform.

  • the three Dimensional Structure of shikimate kinase
    Journal of Molecular Biology, 1998
    Co-Authors: Tino Krell, John R. Coggins, Adrian J. Lapthorn
    Abstract:

    The three-Dimensional Structure of shikimate kinase from Erwinia chrysanthemi has been determined by multiple isomorphous replacement. Two models are presented: a high resolution 1.9 A model and a 2.6 A model which contains bound Mg-ADP. The enzyme is an alpha/beta protein consisting of a central sheet of five parallel beta-strands flanked by alpha-helices with overall topology similar to adenylate kinase. Evidence is presented that shikimate kinase undergoes major conformational changes on ligand binding. It resembles adenylate kinase in having a P-loop containing core Structure and two flexible domains which undergo induced fit movement on substrate binding. The binding of Mg2+ in the active site of shikimate kinase involves direct interaction with two protein side-chains which is different from the situation found in adenylate kinase. Shikimate kinase has a readily identifiable Walker A-motif and a recognisable but modified Walker B-motif. Comparison of shikimate kinase to adenylate kinase has led to the identification of an adenine-binding motif (I/VDAXQ/NXP). Difference Fourier calculations have revealed the shikimate binding site which corresponds to the location of the AMP-binding site in adenylate kinase. A model for shikimate-binding is presented.

  • Regular articleThe three-Dimensional Structure of shikimate kinase1
    Journal of Molecular Biology, 1998
    Co-Authors: Tino Krell, John R. Coggins, Adrian J. Lapthorn
    Abstract:

    The three-Dimensional Structure of shikimate kinase from Erwinia chrysanthemi has been determined by multiple isomorphous replacement. Two models are presented: a high resolution 1.9 A model and a 2.6 A model which contains bound Mg-ADP. The enzyme is an α/β protein consisting of a central sheet of five parallel β-strands flanked by α-helices with overall topology similar to adenylate kinase. Evidence is presented that shikimate kinase undergoes major conformational changes on ligand binding. It resembles adenylate kinase in having a P-loop containing core Structure and two flexible domains which undergo induced fit movement on substrate binding. The binding of Mg2+ in the active site of shikimate kinase involves direct interaction with two protein side-chains which is different from the situation found in adenylate kinase. Shikimate kinase has a readily identifiable Walker A-motif and a recognisable but modified Walker B-motif. Comparison of shikimate kinase to adenylate kinase has led to the identification of an adenine-binding motif (I/VDAXQ/NXP). Difference Fourier calculations have revealed the shikimate binding site which corresponds to the location of the AMP-binding site in adenylate kinase. A model for shikimate-binding is presented.

Yoshio Katsuya - One of the best experts on this subject based on the ideXlab platform.

  • three Dimensional Structure of pseudomonas isoamylase at 2 2 a resolution
    Journal of Molecular Biology, 1998
    Co-Authors: Yoshio Katsuya, Yoshihiro Mezaki, Michio Kubota, Yoshiki Matsuura
    Abstract:

    Abstract The three-Dimensional Structure of isoamylase from Pseudomonasamyloderamosa , which hydrolyzes α-1,6-glucosidic linkages of amylopectin and glycogen, has been determined by X-ray Structure analysis. The enzyme has 750 amino acid residues and a molecular mass of 80 kDa, and it can be crystallized from ammonium sulfate solution. The Structure was elucidated by the multiple isomorphous replacement method and refined at 2.2 A resolution, resulting in a final R -factor of 0.161 for significant reflections with a root-mean-square deviation from ideality in bond lengths of 0.009 A. The analysis revealed that in the N-terminal region, isoamylase has a novel extra domain that we call domain N, whose three-Dimensional Structure has not so far been reported. It has a (β/α) 8 -barrel-type supersecondary Structure in the catalytic domain common to the α-amylase family enzymes, though the barrel is incomplete, with a deletion of an α-helix between the fifth and sixth β-strands. A long excursed region is present between the third β-strand and the third α-helix of the barrel but, in contrast to the so-called domain B that has been identified in the other enzymes of α-amylase family, it cannot be considered to be an independent domain, because this loop forms a globular cluster together with the loop between the fourth β-strand and the fourth α-helix. Isoamylase contains a bound calcium ion, but this is not in the same position as the conserved calcium ion that has been reported in other α-amylase family enzymes.

  • regular articlethree Dimensional Structure of pseudomonas isoamylase at 2 2 a resolution1
    Journal of Molecular Biology, 1998
    Co-Authors: Yoshio Katsuya, Yoshihiro Mezaki, Michio Kubota, Yoshiki Matsuura
    Abstract:

    The three-Dimensional Structure of isoamylase from Pseudomonasamyloderamosa, which hydrolyzes α-1,6-glucosidic linkages of amylopectin and glycogen, has been determined by X-ray Structure analysis. The enzyme has 750 amino acid residues and a molecular mass of 80 kDa, and it can be crystallized from ammonium sulfate solution. The Structure was elucidated by the multiple isomorphous replacement method and refined at 2.2 A resolution, resulting in a final R-factor of 0.161 for significant reflections with a root-mean-square deviation from ideality in bond lengths of 0.009 A. The analysis revealed that in the N-terminal region, isoamylase has a novel extra domain that we call domain N, whose three-Dimensional Structure has not so far been reported. It has a (β/α)8-barrel-type supersecondary Structure in the catalytic domain common to the α-amylase family enzymes, though the barrel is incomplete, with a deletion of an α-helix between the fifth and sixth β-strands. A long excursed region is present between the third β-strand and the third α-helix of the barrel but, in contrast to the so-called domain B that has been identified in the other enzymes of α-amylase family, it cannot be considered to be an independent domain, because this loop forms a globular cluster together with the loop between the fourth β-strand and the fourth α-helix. Isoamylase contains a bound calcium ion, but this is not in the same position as the conserved calcium ion that has been reported in other α-amylase family enzymes.

Lyndon Emsley - One of the best experts on this subject based on the ideXlab platform.

  • Three-Dimensional Structure Determination of Surface Sites
    Journal of the American Chemical Society, 2017
    Co-Authors: Pierrick Berruyer, Moreno Lelli, Matthew P. Conley, Daniel L Silverio, M. Widdifield Cory, Georges Siddiqi, David Gajan, Anne Lesage, Christophe Copéret, Lyndon Emsley
    Abstract:

    The spatial arrangement of atoms is directly linked to chemical function. A fundamental challenge in surface chemistry and catalysis relates to the determination of three-Dimensional Structures with atomic-level precision. Here we determine the three-Dimensional Structure of an organometallic complex on an amorphous silica surface using solid-state NMR measurements, enabled through a dynamic nuclear polarization surface enhanced NMR spectroscopy approach that induces a 200-fold increase in the NMR sensitivity for the surface species. The result, in combination with EXAFS, is a detailed Structure for the surface complex determined with a precision of 0.7 angstrom. We observe a single well-defined conformation that is folded toward the surface in such a way as to include an interaction between the platinum metal center and the surface oxygen atoms.