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  • 1
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    Crystal structure of the free radical intermediate of pyruvate:ferredoxin oxidoreductase (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publikationsdatum: 2001-12-26
    Beschreibung: In anaerobic organisms, the decarboxylation of pyruvate, a crucial component of intermediary metabolism, is catalyzed by the metalloenzyme pyruvate: ferredoxin oxidoreductase (PFOR) resulting in the generation of low potential electrons and the subsequent acetylation of coenzyme A (CoA). PFOR is the only enzyme for which a stable acetyl thiamine diphosphate (ThDP)-based free radical reaction intermediate has been identified. The 1.87 A-resolution structure of the radical form of PFOR from Desulfovibrio africanus shows that, despite currently accepted ideas, the thiazole ring of the ThDP cofactor is markedly bent, indicating a drastic reduction of its aromaticity. In addition, the bond connecting the acetyl group to ThDP is unusually long, probably of the one-electron type already described for several cation radicals but not yet found in a biological system. Taken together, our data, along with evidence from the literature, suggest that acetyl-CoA synthesis by PFOR proceeds via a condensation mechanism involving acetyl (PFOR-based) and thiyl (CoA-based) radicals.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chabriere, E -- Vernede, X -- Guigliarelli, B -- Charon, M H -- Hatchikian, E C -- Fontecilla-Camps, J C -- New York, N.Y. -- Science. 2001 Dec 21;294(5551):2559-63.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratoire de Cristallographie et Cristallogenese des Proteines, Institut de Biologie Structurale Jean-Pierre Ebel, Commissariat a l'Energie Atomique, Universite Joseph Fourier, CNRS, 41, rue Jules Horowitz, 38027 Grenoble Cedex 1, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11752578" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Acetyl Coenzyme A/metabolism ; Anaerobiosis ; Binding Sites ; Carbon Dioxide/metabolism ; Catalysis ; Chemistry, Physical ; Coenzymes/*chemistry/metabolism ; Crystallization ; Crystallography, X-Ray ; Desulfovibrio/*enzymology ; Dimerization ; Electron Spin Resonance Spectroscopy ; *Free Radicals/chemistry/metabolism ; Ketone Oxidoreductases/*chemistry/metabolism ; Molecular Conformation ; Molecular Structure ; Oxidation-Reduction ; Physicochemical Phenomena ; Protein Conformation ; Pyruvate Synthase ; Pyruvic Acid/metabolism ; Thiamine Pyrophosphate/*chemistry/metabolism
    Print ISSN: 0036-8075
    Digitale ISSN: 1095-9203
    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
    Publiziert von American Association for the Advancement of Science (AAAS)
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  • 2
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    Structure-function relationships of anaerobic gas-processing metalloenzymes (2009)
    Nature Publishing Group (NPG)
    Details
    Publikationsdatum: 2009-08-14
    Beschreibung: Reactions involving H(2), N(2), CO, CO(2) and CH(4) are likely to have been central to the origin of life. This is indicated by the active-site structures of the enzymes involved, which are often reminiscent of minerals. Through the combined efforts of protein crystallography, various types of spectroscopy, theoretical calculations and model chemistry, it has been possible to put forward plausible mechanisms for gas-based metabolism by extant microorganisms. Although the reactions are based on metal centres, the protein matrix regulates reactivity and substrate and product trafficking through internal pathways, specific ligation and dielectricity.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fontecilla-Camps, Juan C -- Amara, Patricia -- Cavazza, Christine -- Nicolet, Yvain -- Volbeda, Anne -- England -- Nature. 2009 Aug 13;460(7257):814-22. doi: 10.1038/nature08299.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratoire de Cristallographie et Cristallogenese des Proteines, Institut de Biologie Structurale J.P. Ebel, CEA, CNRS, Universite Joseph Fourier, 41 rue J. Horowitz, 38027 Grenoble Cedex 1, France. juan-carlos.fontecilla@ibs.fr〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19675641" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Anaerobiosis ; Biocatalysis ; Catalytic Domain ; Enzymes/*chemistry/*metabolism ; Gases/*metabolism ; Metalloproteins/*chemistry/*metabolism ; Structure-Activity Relationship
    Print ISSN: 0028-0836
    Digitale ISSN: 1476-4687
    Thema: Biologie , Chemie und Pharmazie , Medizin , Allgemeine Naturwissenschaft , Physik
    Publiziert von Nature Publishing Group (NPG)
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  • 3
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    Structure of dual function iron regulatory protein 1 complexed with ferritin IRE-RNA (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publikationsdatum: 2006-12-23
    Beschreibung: Iron regulatory protein 1 (IRP1) binds iron-responsive elements (IREs) in messenger RNAs (mRNAs), to repress translation or degradation, or binds an iron-sulfur cluster, to become a cytosolic aconitase enzyme. The 2.8 angstrom resolution crystal structure of the IRP1:ferritin H IRE complex shows an open protein conformation compared with that of cytosolic aconitase. The extended, L-shaped IRP1 molecule embraces the IRE stem-loop through interactions at two sites separated by approximately 30 angstroms, each involving about a dozen protein:RNA bonds. Extensive conformational changes related to binding the IRE or an iron-sulfur cluster explain the alternate functions of IRP1 as an mRNA regulator or enzyme.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Walden, William E -- Selezneva, Anna I -- Dupuy, Jerome -- Volbeda, Anne -- Fontecilla-Camps, Juan C -- Theil, Elizabeth C -- Volz, Karl -- DK20251/DK/NIDDK NIH HHS/ -- DK47281/DK/NIDDK NIH HHS/ -- GM47522/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2006 Dec 22;314(5807):1903-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbiology and Immunology, University of Illinois at Chicago, Chicago, IL 60612-7344, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17185597" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Apoferritins/*genetics ; Binding Sites ; Crystallography, X-Ray ; Hydrogen Bonding ; Iron/metabolism ; Iron Regulatory Protein 1/*chemistry/*metabolism ; Models, Molecular ; Nucleic Acid Conformation ; Protein Binding ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; RNA, Messenger/chemistry/genetics/metabolism ; *Regulatory Sequences, Ribonucleic Acid ; *Response Elements ; Sulfur/metabolism ; Untranslated Regions/*chemistry/*metabolism
    Print ISSN: 0036-8075
    Digitale ISSN: 1095-9203
    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
    Publiziert von American Association for the Advancement of Science (AAAS)
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  • 4
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    Biochemistry. A natural choice for activating hydrogen (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publikationsdatum: 2008-07-26
    Beschreibung: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Armstrong, Fraser A -- Fontecilla-Camps, Juan C -- New York, N.Y. -- Science. 2008 Jul 25;321(5888):498-9. doi: 10.1126/science.1161326.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QR, UK. fraser.armstrong@chem.ox.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18653870" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Binding Sites ; Carbon Dioxide/metabolism ; Carbon Monoxide/chemistry/metabolism ; Crystallography, X-Ray ; Cyanides/chemistry/metabolism ; Hydrogen/*metabolism ; Hydrogenase/*chemistry/*metabolism ; Iron/chemistry ; Ligands ; Methane/*biosynthesis ; Oxidation-Reduction
    Print ISSN: 0036-8075
    Digitale ISSN: 1095-9203
    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
    Publiziert von American Association for the Advancement of Science (AAAS)
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  • 5
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    Fine-tuning of a radical-based reaction by radical S-adenosyl-L-methionine tryptophan lyase (2016)
    American Association for the Advancement of Science (AAAS)
    Details
    Publikationsdatum: 2016-03-19
    Beschreibung: The radical S-adenosyl-L-methionine tryptophan lyase NosL converts L-tryptophan into 3-methylindolic acid, which is a precursor in the synthesis of the thiopeptide antibiotic nosiheptide. Using electron paramagnetic resonance spectroscopy and multiple L-tryptophan isotopologues, we trapped and characterized radical intermediates that indicate a carboxyl fragment migration mechanism for NosL. This is in contrast to a proposed fragmentation-recombination mechanism that implied Calpha-Cbeta bond cleavage of L-tryptophan. Although NosL resembles related tyrosine lyases, subtle substrate motions in its active site are responsible for a fine-tuned radical chemistry, which selects the Calpha-C bond for disruption. This mechanism highlights evolutionary adaptation to structural constraints in proteins as a route to alternative enzyme function.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sicoli, Giuseppe -- Mouesca, Jean-Marie -- Zeppieri, Laura -- Amara, Patricia -- Martin, Lydie -- Barra, Anne-Laure -- Fontecilla-Camps, Juan C -- Gambarelli, Serge -- Nicolet, Yvain -- New York, N.Y. -- Science. 2016 Mar 18;351(6279):1320-3. doi: 10.1126/science.aad8995.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Universite Grenoble-Alpes, Institut Nanosciences et Cryogenie (INAC)-Service de Chimie Inorganique et Biologique (SCIB)/Laboratoire de Resonance Magnetique (LRM), F-38000 Grenoble, France. Commissariat a l'Energie Atomique et aux Energies Alternatives (CEA), INAC-SCIB/LRM, F-38000 Grenoble, France. ; Metalloproteins Unit, Institut de Biologie Structurale, CEA, CNRS, Universite Grenoble-Alpes, 71, Avenue des Martyrs, 38044 Grenoble Cedex 9, France. ; Laboratoire National des Champs Magnetiques Intenses, UPR CNRS 3228, F-38048 Grenoble, France. ; Universite Grenoble-Alpes, Institut Nanosciences et Cryogenie (INAC)-Service de Chimie Inorganique et Biologique (SCIB)/Laboratoire de Resonance Magnetique (LRM), F-38000 Grenoble, France. Commissariat a l'Energie Atomique et aux Energies Alternatives (CEA), INAC-SCIB/LRM, F-38000 Grenoble, France. yvain.nicolet@ibs.fr serge.gambarelli@cea.fr. ; Metalloproteins Unit, Institut de Biologie Structurale, CEA, CNRS, Universite Grenoble-Alpes, 71, Avenue des Martyrs, 38044 Grenoble Cedex 9, France. yvain.nicolet@ibs.fr serge.gambarelli@cea.fr.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26989252" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Carbon-Carbon Lyases/*chemistry ; Catalytic Domain ; Electron Spin Resonance Spectroscopy ; Indoles/*metabolism ; S-Adenosylmethionine/*chemistry ; Streptomyces/*enzymology ; Tryptophan/*chemistry ; Tryptophanase/*chemistry
    Print ISSN: 0036-8075
    Digitale ISSN: 1095-9203
    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
    Publiziert von American Association for the Advancement of Science (AAAS)
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  • 6
    Digitale Medien
    Digitale Medien
    Combination of methods used in the structure solution of pyruvate:ferredoxin oxidoreductase from two crystal forms (1999)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 1546-1554 
    Details
    ISSN: 1399-0047
    Quelle: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Thema: Chemie und Pharmazie , Geologie und Paläontologie , Physik
    Notizen: The structure of the homodimeric 267 kDa pyruvate:ferredoxin oxidoreductase (PFOR) of Desulfovibrio africanus was solved with data from two crystals forms, both containing two monomers per asymmetric unit. Phases were obtained from multiwavelength anomalous dispersion (MAD), solvent flattening (SF), molecular replacement (MR) using a 5 Å resolution electron-density search model, multiple isomorphous replacement (MIR) and, finally, electron-density averaging (DA) procedures. It is shown how the combination of all these techniques was used to overcome problems arising from incompleteness of MAD data and weak phasing power of MIR data. A real-space refinement (RSR) procedure is described to improve MR solutions and obtain very accurate protein envelopes and non-crystallographic symmetry (NCS) transformations from 5 Å resolution phase information. These were crucial for the phase extension to high resolution by DA methods.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1107/S0907444999008410
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  • 7
    Digitale Medien
    Digitale Medien
    Crystallization and 2.2 Å resolution structure of R-phycoerythrin from Gracilaria chilensis: a case of perfect hemihedral twinning (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 52-60 
    Details
    ISSN: 1399-0047
    Quelle: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Thema: Chemie und Pharmazie , Geologie und Paläontologie , Physik
    Notizen: R-phycoerythrin, a light-harvesting component from the red algae Gracilaria chilensis, was crystallized by vapour diffusion using ammonium sulfate as precipitant agent. Red crystals grew after one week at 293 K and diffracted to 2.70 Å resolution. Three serial macroseeding assays were necessary to grow a second larger crystal to dimensions of 0.68 × 0.16 × 0.16 mm. This crystal diffracted to 2.24 Å resolution using synchrotron radiation at beamline BM14 of the European Synchrotron Radiation Facility (ESRF) at Grenoble, France and was used for structure determination. Data were collected at 100 K to a completeness of 98.6%. The crystal was trigonal, space group R3, with unit-cell parameters a = b = 187.3, c = 59.1 Å, α = β = 90, γ = 120°. Data treatment using the CCP4 suite of programs indicated that the crystal was twinned (〈I2〉/〈I〉2 = 1.41). Molecular replacement was performed with AMoRe using the R-phycoerythrin from Polysiphonia urceolata [Chang et al. (1996), J. Mol. Biol. 249, 424–440] as a search model. In order to overcome the twinning problem, SHELX97 was used for the crystallographic refinement. The twin fraction was 0.48, indicating a nearly perfect hemihedrally twinned crystal. The final Rwork and Rfree factors are 0.16 and 0.25, respectively. All the residues and chromophores of the α- and β-chains are well defined in the electron-density maps. Some residues belonging to the γ-linker are also recognizable.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1107/S0907444900015274
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  • 8
    Digitale Medien
    Digitale Medien
    Ab Initio Structure Determination and Refinement of a Scorpion Protein Toxin (1997)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 53 (1997), S. 551-557 
    Details
    ISSN: 1399-0047
    Quelle: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Thema: Chemie und Pharmazie , Geologie und Paläontologie , Physik
    Notizen: The structure of toxin II from the scorpion Androctonus australis Hector has been determined ab initio by direct methods using SnB at 0.96 Å resolution. For the purpose of this structure redetermination, undertaken as a test of the minimal function and the SnB program, the identity and sequence of the protein was withheld from part of the research team. A single solution obtained from 1 619 random atom trials was clearly revealed by the bimodal distribution of the final value of the minimal function associated with each individual trial. Five peptide fragments were identified from a conservative analysis of the initial E-map, and following several refinement cycles with X-PLOR, a model was built of the complete structure. At the end of the X-PLOR refinement, the sequence was compared with the published sequence and 57 of the 64 residues had been correctly identified. Two errors in sequence resulted from side chains with similar size while the rest of the errors were a result of severe disorder or high thermal motion in the side chains. Given the amino-acid sequence, it is estimated that the initial E-map could have produced a model containing 99% of all main-chain and 81% of side-chain atoms. The structure refinement was completed with PROFFT, including the contributions of protein H atoms, and converged at a residual of 0.158 for 30 609 data with F ≥ 2σ(F) in the resolution range 8.0–0.964 Å. The final model consisted of 518 non-H protein atoms (36 disordered), 407 H atoms, and 129 water molecules (43 with occupancies less than unity). This total of 647 non-H atoms represents the largest light-atom structure solved to date.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1107/S0907444997005386
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  • 9
    Digitale Medien
    Digitale Medien
    Structure of fasciculin 2 from green mamba snake venom: evidence for unusual loop flexibility (1996)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 52 (1996), S. 87-92 
    Details
    ISSN: 1399-0047
    Quelle: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Thema: Chemie und Pharmazie , Geologie und Paläontologie , Physik
    Notizen: The crystal structure of the snake toxin fasciculin 2, a potent acetylcholinesterase inhibitor from the venom of the green mamba (Dendroaspis angusticeps), has been determined by the molecular-replacement method, using the fasciculin 1 model and refined to 2.0 Å resolution. The introduction of an overall anisotropic temperature factor improved significantly the quality of the electron-density map. It suggests, as it was also indicated by the packing, that the thermal motion along the unique axis direction is less pronounced than on the (ab) plane. The final crystallographic R factor is 0.188 for a model having r.m.s. deviations from ideality of 0.016 Å for bond lengths and 2.01° for bond angles. As fasciculin 1, fasciculin 2 belongs to the three-finger class of Elapidae toxins, a structural group that also contains the α-neurotoxins and the cardiotoxins. Although the two fasciculins have, overall, closely related structures, the conformation of loop I differs appreciably in the two molecules. The presence of detergent in crystallization medium in the case of fasciculin 2 appears to be responsible for the displacement of the loop containing Thr9. This conformational change also results in the formation of a crystallographic dimer that displays extensive intermolecular interactions.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1107/S0907444995007517
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  • 10
    Digitale Medien
    Digitale Medien
    How to Escape from Model Bias with a High-Resolution Native Data Set – Structure Determination of the PcpA-S6 Subunit III (1996)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 52 (1996), S. 345-355 
    Details
    ISSN: 1399-0047
    Quelle: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Thema: Chemie und Pharmazie , Geologie und Paläontologie , Physik
    Notizen: The structure of procarboxypeptidase A-S6 subunit III, a truncated zymogen E, has been determined by molecular replacement using as search model porcine elastase 1 which, as revealed by crystallographic analysis, contained about 20% of the amino acids in a radically different orientation. Two monoclinic crystal forms were used: the first one diffracts to 2.3 Å resolution and contains one molecule per asymmetric unit; the second diffracts to 1.7 Å resolution and contains two molecules per asymmetric unit. Molecular replacement and conventional X-PLOR refinement led to a model for which 20% of the chain was ill defined in both crystal forms. To remove the bias introduced by the initial model, an automated refinement procedure [Lamzin & Wilson (1993). Acta Cryst. D49, 129–147] was applied successfully to the second crystal form, which diffracts to high resolution. The resulting dramatic improvement of the electron-density map led to extensive rebuilding of some surface loops. The reliability of the modified model was confirmed by refinement of the first crystal form. For the two forms, the final R factor is 18.8% for data between 8.0 and 2.0 Å resolution, and 18.4% for data between 8.0 and 1.7 Å, respectively.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1107/S0907444995009528
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