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The structure of cbb3 cytochrome oxidase provides insights into proton pumping (2010)

S. Buschmann ; E. Warkentin ; H. Xie ; [et al.]

American Association for the Advancement of Science (AAAS)

In: Science. 329(5989): 327-30. doi: 10.1126/science.1187303.

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Publication Date: 2010-06-26

Description: The heme-copper oxidases (HCOs) accomplish the key event of aerobic respiration; they couple O2 reduction and transmembrane proton pumping. To gain new insights into the still enigmatic process, we structurally characterized a C-family HCO--essential for the pathogenicity of many bacteria--that differs from the two other HCO families, A and B, that have been structurally analyzed. The x-ray structure of the C-family cbb3 oxidase from Pseudomonas stutzeri at 3.2 angstrom resolution shows an electron supply system different from families A and B. Like family-B HCOs, C HCOs have only one pathway, which conducts protons via an alternative tyrosine-histidine cross-link. Structural differences around hemes b and b3 suggest a different redox-driven proton-pumping mechanism and provide clues to explain the higher activity of family-C HCOs at low oxygen concentrations.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Buschmann, Sabine -- Warkentin, Eberhard -- Xie, Hao -- Langer, Julian D -- Ermler, Ulrich -- Michel, Hartmut -- New York, N.Y. -- Science. 2010 Jul 16;329(5989):327-30. doi: 10.1126/science.1187303. Epub 2010 Jun 24.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Max-Planck-Institut fur Biophysik, Max-von-Laue-Strasse 3, D-60438 Frankfurt/Main, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20576851" target="_blank"〉PubMed〈/a〉

Keywords: Amino Acid Sequence ; Catalytic Domain ; Crystallography, X-Ray ; Cytoplasm/metabolism ; Electron Transport ; Electron Transport Complex IV/*chemistry/*metabolism ; Heme/chemistry ; Histidine/chemistry ; Hydrogen Bonding ; Models, Molecular ; Molecular Sequence Data ; Oxidation-Reduction ; Oxygen/metabolism ; Periplasm/metabolism ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Proton Pumps/*chemistry/*metabolism ; *Protons ; Pseudomonas stutzeri/*enzymology ; Tyrosine/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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The crystal structure of [Fe]-hydrogenase reveals the geometry of the active site (2008)

S. Shima ; O. Pilak ; S. Vogt ; [et al.]

American Association for the Advancement of Science (AAAS)

In: Science. 321(5888): 572-5. doi: 10.1126/science.1158978.

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Publication Date: 2008-07-26

Description: Biological formation and consumption of molecular hydrogen (H2) are catalyzed by hydrogenases, of which three phylogenetically unrelated types are known: [NiFe]-hydrogenases, [FeFe]-hydrogenases, and [Fe]-hydrogenase. We present a crystal structure of [Fe]-hydrogenase at 1.75 angstrom resolution, showing a mononuclear iron coordinated by the sulfur of cysteine 176, two carbon monoxide (CO) molecules, and the sp2-hybridized nitrogen of a 2-pyridinol compound with back-bonding properties similar to those of cyanide. The three-dimensional arrangement of the ligands is similar to that of thiolate, CO, and cyanide ligated to the low-spin iron in binuclear [NiFe]- and [FeFe]-hydrogenases, although the enzymes have evolved independently and the CO and cyanide ligands are not found in any other metalloenzyme. The related iron ligation pattern of hydrogenases exemplifies convergent evolution and presumably plays an essential role in H2 activation. This finding may stimulate the ongoing synthesis of catalysts that could substitute for platinum in applications such as fuel cells.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shima, Seigo -- Pilak, Oliver -- Vogt, Sonja -- Schick, Michael -- Stagni, Marco S -- Meyer-Klaucke, Wolfram -- Warkentin, Eberhard -- Thauer, Rudolf K -- Ermler, Ulrich -- New York, N.Y. -- Science. 2008 Jul 25;321(5888):572-5. doi: 10.1126/science.1158978.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Max-Planck-Institut fur Terrestrische Mikrobiologie and Laboratorium fur Mikrobiologie, Fachbereich Biologie, Philipps-Universitat Marburg, Karl-von-Frisch-Strasse, D-35043 Marburg, Germany. shima@mpi-marburg.mpg.de〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18653896" target="_blank"〉PubMed〈/a〉

Keywords: Apoenzymes/chemistry ; Binding Sites ; Carbon Monoxide/chemistry ; Catalytic Domain ; Coenzymes/chemistry ; Crystallography, X-Ray ; Cyanides/chemistry/metabolism ; Dimerization ; Evolution, Molecular ; Holoenzymes/chemistry ; Hydrogen/chemistry/*metabolism ; Hydrogenase/*chemistry/isolation & purification/metabolism ; Iron/chemistry ; Ligands ; Methane/biosynthesis ; Methanococcales/*enzymology ; Models, Molecular ; Oxidation-Reduction ; 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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Die Kristallstruktur von Praseodymdiiodid (Modifikation V)Professor Gerhard Fritz zum 60. Geburtstage gewidmet (1979)

Warkentin, E. ; Bärnighausen, H.

Weinheim : Wiley-Blackwell

Zeitschrift für anorganische Chemie 459 (1979), S. 187-200

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ISSN: 0044-2313

Keywords: Chemistry ; Inorganic Chemistry

Source: Wiley InterScience Backfile Collection 1832-2000

Topics: Chemistry and Pharmacology

Description / Table of Contents: Crystal Structure of Praseodymium Diiodide (Modification V)There are at least five different modifications of PrI2, four of which can be assignee to the well-known layer structure types of CuTi2, 2H1-MoS2, 3R-MoS2, and CdCl2 respectively. Thd fifth modification is built from cubane-like [Pr4I4]4+ clusters which are linked by I- ions according to the representation ∞3[Pr4Ii4]Ia-a12/3. Alternatively this arrangement may be visualized by its relationship with the spinel structure AB2X4. Imagine the A-sites vacant, the B-sites occupied by praseodymium and the X-sites by iodine, but mind that the Pr-atoms and half of the I-atoms are noticeably shifted from their ideal positions. The observed distortion results from metal-metal bonds as is known from structurally related compounds like MoSBr or GaMo4S8. The crystal structure of PrI2-V has been determined by single crystal X-ray methods: space group F43m, a = 1236.0(5) pm, diffractometer data taken with MoKα radiation, R = 4.1% for 92 independent reflexions. Crystal data of the other four PrI2 modifications, of PrI3 and PrOI are given in the paper.

Notes: PrI2 tritt in mindestens fünf verschiedenen Modifikationen auf; vier davon können den bekannten Schichtstruktur-Typen CuTi2, 2H1-MoS2, 3R-MoS2 und CdCl2 zugeordnet werden. Die fünfte Modifikation enthält cubanartige Cluster [Pr4I4]4+, die im Sinne der Formulierung ∞3[Pr4Ii4]Ia-a12/3 über I--Ionen miteinander verbrückt sind. Die Anordnung kann anschaulich aus der Spinellstruktur AB2X4 abgeleitet werden. Hierzu denkt man sich die A-Plätze unbesetzt, die B-Plätze mit Pr und die X-Plätze mit I belegt. Die Pr-Atome und die Hälfte der I-Atome sind allerdings erheblich aus den Ideallagen verschoben. Die beobachtete Verzerrung läßt sich wie bei den strukturell recht ähnlichen Substanzen MoSBr und GaMo4S8 auf Metall-Metall-Bindungen zurückführen. Die Kristallstruktur von PrI2—V wurde mit röntgenographischen Einkristallmethoden bestimmt: Raumgruppe F43m, a = 1236,0(5) pm, Diffraktometerdaten (MoKα-Strahlung), R = 4,1% bei 92 unabhängigen Reflexen. Die Kristalldaten der and ren vier Modifikationen von PrI2 sowie entsprechende Daten von PrI3 und PrOI sind im Text angegeben.

Additional Material: 4 Ill.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1002/zaac.19794590120

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Gd10C4Cl18 und Gd10C4Cl17, zwei Seltenerdmetall-Clusterverbindungen mit interstitiellen C2-GruppenProfessor Rudolf Hoppe zum 60. Geburtstage gewidmet (1982)

Warkentin, E. ; Masse, R. ; Simon, A.

Weinheim : Wiley-Blackwell

Zeitschrift für anorganische Chemie 491 (1982), S. 323-336

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ISSN: 0044-2313

Keywords: Chemistry ; Inorganic Chemistry

Source: Wiley InterScience Backfile Collection 1832-2000

Topics: Chemistry and Pharmacology

Description / Table of Contents: Gd10C4Cl18 and Gd10C4Cl17, Two Lanthanoid Cluster Compounds with Interstitial C2 UnitsThe compounds Gd10C4Cl18 (I) and Gd10C4Cl17 (II) are prepared by heating stoichiometric amounts of GdCl3, Gd, and graphite in sealed tantalum tubes at 1070 (I) and 1 120 K (II). Single crystal investigations (I: P21/c, Z = 2, a = 918.2, b = 1 612.0, c = 1 288.6 pm, β = 119.86°; II: P1, Z = 1, a = 849.8, b = 917.4, c = 1 146.2 pm, α = 104.56°, β = 95.98°, γ = 111.35°) revealed the occurrence of novel Gd10C4Cl18 clusters. The metal framework is formed by edge-sharing of two Gd6 octahedra. These are centred by C2 units (dC—C = 147 pm) and Cl atoms bridge all available edges of the octahedra. The structure of I corresponds to a packing of such quasi molecular clusters, in II they are linked to chains via common Cl atoms. Both structures are discussed in terms of a model of close packed spheres as well as in the concept of condensed clusters.

Notes: Die Verbindungen Gd10C4Cl18 (I) und Gd10C4Cl17 (II) werden durch Erhitzen stöchiometrischer Gemenge von GdCl3, Gd und Graphit in verschweißten Tantalkapseln bei 1 070 (I) bzw. 1 120 K (II) dargestellt. Strukturuntersuchungen an Einkristallen (I: P21/c, Z = 2, a = 918,2, b = 1 612,0, c = 1 288,6 pm, β = 119,86°; II: P1, Z = 1, a = 849,8, b = 917,4, c = 1 146,2 pm, α = 104,56°, β = 95,98°, γ = 111,35°) ergeben das Vorliegen von neuartigen Gd10C4Cl18-Clustern. Das Metallgerüst wird von zwei kantenverknüpften Gd6-Oktaedern gebildet. Diese sind jeweils mit C2-Einheiten (dC—C = 147 pm) gefüllt und durch Cl-Atome vor allen freien Kanten umgeben. In der Struktur von I liegen diese Cluster quasi molekular vor; in II sind sie über gemeinsame Cl-Atome zu Ketten verknüpft. Beide Strukturen werden im Konzept dichtester Kugelpackungen sowie im Konzept kondensierter Cluster diskutiert.

Additional Material: 5 Ill.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1002/zaac.19824910142

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Gd12C6I17 - eine Verbindung mit kondensierten, C2-gefüllten Gd6I12-ClusternProfessor Harald Schäfer zum 70. Geburtstage am 10. Februar 1983 gewidmet (1983)

Simon, A. ; Warkentin, E.

Weinheim : Wiley-Blackwell

Zeitschrift für anorganische Chemie 497 (1983), S. 79-92

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ISSN: 0044-2313

Keywords: Chemistry ; Inorganic Chemistry

Source: Wiley InterScience Backfile Collection 1832-2000

Topics: Chemistry and Pharmacology

Description / Table of Contents: Gd12C6I17 - a Compound with Condensed, C2-Containing Gd6I12 ClustersGd12C6I17 was isolated in black shining crystals from a reaction product of Gd, GdI3 and graphite, heated in sealed tantalum capsules at 1170 K. The compound is monoclinic (C2/c; a = 1929.7(9), b = 1220.1(5), c = 1863.5(5) pm, = 90.37(3)°). The crystal structure is composed of linear units of 3 condensed Gd6I12 clusters (connection via trans-edges of the central Gd6 octahedron), which are further linked via cis edges to form zig-zag chains. The centres of the Gd6 octahedra are occupied by C2 units. The distances dC—C ≈ 145 pm correspond to a filling of the antibonding π* orbitals of the C2 group, which, however, interact with empty d-orbitals of the metal atoms especially in the apices of the octahedra and thus loose their pure carbon character. The short Gd—C distances (dGd—C = 222 and 227 pm, respectively) are explained as due to multiple bonds. The occurrence of C2 units and single C atoms, respectively, in lanthanide carbides and carbide halides is coupled to the electron concentration of the metal or cluster framework.

Notes: Gd12C6I17 wurde in schwarzen glänzenden Kristallen aus Gd, GdI3 und Graphit in verschweißten Tantal-Kapseln bei 1170 K (neben anderen Reaktionsprodukten) erhalten. Die Verbindung kristallisiert monoklin (C2/c; a = 1929,7(9), b = 1220,1(5), c = 1863,5(5) pm, β 90,37(3)°). Die Kristallstruktur enthält lineare Einheiten aus 3 kondensierten Gd6I12-Clustern (trans-Kantenverknüpfung für den mittleren Gd6-Oktaeder), welche durch weitere Verknüpfung über cis-ständige Kanten gewinkelte Ketten aufbauen. Die Zentren der Gd6-Oktaeder sind von C2-Einheiten besetzt. Die Abstände dC—C ≈ 145 pm entsprechen einer Besetzung der antibindenden π*-Orbitale der C2-Gruppe, die jedoch durch Wechselwirkung mit leeren d-Zuständen der Metallatome, insbesondere derjenigen an den Oktaederspitzen, den reinen Kohlenstoffcharakter verlieren. Die kurzen Gd—C-Abstände (dGd—C = 222 bzw. 227 pm) werden mit Mehrfachbindungsanteilen erklärt. Das Auftreten von C2-Gruppen bzw. einzelnen C-Atomen bei Lanthanoidcarbiden und -carbidhalogeniden wird von der Elektronenkonzentration im Metall- oder Clustergerüst gesteuert.

Additional Material: 3 Ill.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1002/zaac.19834970208

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