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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
    Publication Date: 2001-12-26
    Description: 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〉
    Keywords: 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
    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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    Structure-function relationships of anaerobic gas-processing metalloenzymes (2009)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2009-08-14
    Description: 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〉
    Keywords: Anaerobiosis ; Biocatalysis ; Catalytic Domain ; Enzymes/*chemistry/*metabolism ; Gases/*metabolism ; Metalloproteins/*chemistry/*metabolism ; Structure-Activity Relationship
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by 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
    Publication Date: 2006-12-23
    Description: 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〉
    Keywords: 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
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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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
    Publication Date: 2008-07-26
    Description: 〈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〉
    Keywords: 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
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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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
    Publication Date: 2016-03-19
    Description: 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〉
    Keywords: 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
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 6
    Electronic Resource
    Electronic Resource
    Rapid access to an updated biological macromolecule crystallization database through artificial intelligence
    Amsterdam : Elsevier
    Journal of Crystal Growth 106 (1990), S. 405-409 
    Details
    ISSN: 0022-0248
    Source: Elsevier Journal Backfiles on ScienceDirect 1907 - 2002
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Type of Medium: Electronic Resource
    URL: http://linkinghub.elsevier.com/retrieve/pii/0022-0248(90)90086-Z
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  • 7
    Electronic Resource
    Electronic Resource
    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
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: 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.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444995009528
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  • 8
    Electronic Resource
    Electronic Resource
    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
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: 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.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444999008410
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  • 9
    Electronic Resource
    Electronic Resource
    ASTEC: an automated system for sitting-drop protein crystallization (1993)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 26 (1993), S. 558-562 
    Details
    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: An automated system for protein crystallization that is based on the vapor diffusion method has been developed using novel sitting-drop supports for standard Linbro plates. Laboratory robotics have been designed for liquid handling of stock solutions, silicone-grease dispensing and coverslip transfer. The system can handle up to four crystallization plates (96 wells) and ten stock solutions, without any user attendance. The software allows specification of several experimental parameters and records experiments, which may be accessed by the use of a bar-code label. Experiments may be conducted according to a user's specific design, a screening test or an incomplete factorial design. The system is capable of pipetting viscous solutions such as polyethylene glycol with good reproducibility. Automatic well-sealing techniques are discussed and preliminary protein-crystallization results are presented.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0021889893001633
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  • 10
    Electronic Resource
    Electronic Resource
    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
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: 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.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444900015274
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