Prof. Dr. rer. nat. Holger Dobbek

Profil

• CL Katalyse II: E1/E2

  Quelle ↗

  Förderer: DFG Exzellenzinitiative Cluster Zeitraum: 11/2012 - 10/2017 Projektleitung: Prof. Dr. rer. nat. Holger Dobbek

• Cluster: Integrale Konzepte der Katalyse (Professur)

  Quelle ↗

  Förderer: DFG Exzellenzinitiative Cluster Zeitraum: 07/2009 - 10/2012 Projektleitung: Prof. Dr. rer. nat. Holger Dobbek

• CooC2/AcsF und Cfd1/Nbp35: Reifung komplexer Fe/S-Zentren durch MinD-Typ ATpasen (SPP 1927 – Iron/Sulfur for Life)

  Quelle ↗

  Förderer: DFG Schwerpunktprogramm Zeitraum: 01/2017 - 12/2021 Projektleitung: Prof. Dr. rer. nat. Holger Dobbek

• Die Aufdeckung des photo-induzierten Assemblierungsmechanismus des lichtgetriebenen Wasseroxidationskomplexes in Photosystem II

  Quelle ↗

  Förderer: DFG Exzellenzinitiative Cluster Zeitraum: 11/2017 - 12/2018 Projektleitung: Prof. Dr. Athina Zouni

• Dioxygenase-Reaktivität von Hämoproteinen, die mit Nicht-Hem-Eisenkatalysatoren in asummetrischen cis-Dihydroxylierungs- und Indol-Oxidationsreaktionen rekonstituiert wurden

  Quelle ↗

  Förderer: DFG Sachbeihilfe Internationale Kooperation Zeitraum: 03/2026 - 02/2029 Projektleitung: Prof. Dr. rer. nat. Holger Dobbek

• EXC 2008: Unifying Systems in Catalysis (UniSysCat)

  Quelle ↗

  Förderer: DFG Exzellenzstrategie Cluster Zeitraum: 01/2019 - 12/2025 Projektleitung: Prof. Dr. Arne Thomas

• EXC 314/1: Die Aufklärung des photo-induzierten Assemblierungsmechanismus, ausgehend von nativen und modifizierten Wasseroxidations-Katalysatoren des Photosystem II (AG Zouni) Biokatalytische Kopplung von Photosystem I mit FDH und CO-DH Superkomplexen

  Quelle ↗

  Förderer: DFG Exzellenzstrategie Cluster Zeitraum: 01/2019 - 12/2022 Projektleitung: Prof. Dr. Athina Zouni

• Fe/S-Doppel-Kuban-Cluster: ein neuer Kofaktor in der Biologie

  Quelle ↗

  Förderer: DFG Sachbeihilfe Zeitraum: 05/2020 - 03/2025 Projektleitung: Prof. Dr. rer. nat. Holger Dobbek

• Mechanismus und Assemblierung Ni, Fe-haltiger Kohlenmonoxid-Dehydrogenasen

  Quelle ↗

  Förderer: DFG Sachbeihilfe Zeitraum: 07/2019 - 06/2024 Projektleitung: Prof. Dr. rer. nat. Holger Dobbek

• Mechanismus und Assemblierung Ni, Fe-haltiger Kohlenmonoxid-Dehydrogenasen

  Quelle ↗

  Förderer: DFG Sachbeihilfe Zeitraum: 10/2011 - 06/2016 Projektleitung: Prof. Dr. rer. nat. Holger Dobbek

• Methyltransfer-Reaktionen im reduktiven Acetyl-Coenzym A Weg

  Quelle ↗

  Förderer: DFG Sachbeihilfe Zeitraum: 11/2010 - 08/2015 Projektleitung: Prof. Dr. rer. nat. Holger Dobbek

• Methyltransfer-Reaktionen im reduktiven Acetyl-Coenzym-A-Weg

  Quelle ↗

  Förderer: DFG Sachbeihilfe Zeitraum: 11/2015 - 12/2022 Projektleitung: Prof. Dr. rer. nat. Holger Dobbek

• Radikal-abhängige Katalyse in Fe/S-abhängigen Dehydratasen

  Quelle ↗

  Förderer: DFG Sachbeihilfe Zeitraum: 04/2010 - 09/2012 Projektleitung: Prof. Dr. rer. nat. Holger Dobbek

• SFB 1078/1: Strukturelle Grundlagen der Protonenabgabe in der Wasser-Oxidation durch das Photosystem-II: Kristallisation, Röntgen- und Neutronenbeugungsanalyse von Chlorid-modifizierten und ortsgerichteten Varianten (TP A05)

  Quelle ↗

  Förderer: DFG Sonderforschungsbereich Zeitraum: 01/2013 - 12/2020 Projektleitung: Prof. Dr. rer. nat. Holger Dobbek, Prof. Dr. Athina Zouni

• SFB 1078/1: Strukturelle Grundlagen der Protonenabgabe in der Wasser-Oxidation durch das Photosystem II (TP A05)

  Quelle ↗

  Förderer: DFG Sonderforschungsbereich Zeitraum: 01/2013 - 03/2021 Projektleitung: Prof. Dr. Athina Zouni, Prof. Dr. rer. nat. Holger Dobbek, Prof. i. R. Nikolaus Ernsting Ph. D., Prof. Dr. Dr. h. c. Peter Hegemann

• Strukturelle Enzymology der Hydroxylierungsreaktionen an aromatischen Verbindungen

  Quelle ↗

  Förderer: DFG Sachbeihilfe Zeitraum: 04/2010 - 04/2011 Projektleitung: Prof. Dr. rer. nat. Holger Dobbek

• Struktur und Funktion von Metalloproteinen des anaeroben CO-Metabolismus

  Quelle ↗

  Förderer: DFG Sachbeihilfe Zeitraum: 04/2010 - 12/2014 Projektleitung: Prof. Dr. rer. nat. Holger Dobbek

• novozymess

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  75 Treffer59.9%
  • Engineering of New-Generation Protein Secretion Systems
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    59.9%

• UCB Celltech

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  76 Treffer59.9%
  • Engineering of New-Generation Protein Secretion Systems
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    59.9%

• DSM Food Specialities BV

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  76 Treffer59.9%
  • Engineering of New-Generation Protein Secretion Systems
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    59.9%

• Isogen GmbH & Co KG

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  24 Treffer56.7%
  • Bewertung der physiologischen Plastizität und genetischen Variabilität der Kiefer (Pinus sylvestris L.) an ihrer westlichen Verbreitungsgrenze unter den Bedingungen des Klimawandels
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    56.7%

• TechOnYou Srl

  PT

  59 Treffer56.5%
  • EU: Hybrid Organic/Inorganic Memory Elements for Integration of Electronic and Photonic Circuitry (HYMEC)
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    56.5%

• Science & Startups Berlin

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  18 Treffer56.4%
  • Zuwendung im Rahmen des Programms „exist – Existenzgründungen aus der Wissenschaft“ aus dem Bundeshaushalt, Einzelplan 09, Kapitel 02, Titel 68607, Haushaltsjahr 2026, sowie aus Mitteln des Europäischen Strukturfonds (hier Euro-päischer Sozialfonds Plus – ESF Plus) Förderperiode 2021-2027 – Kofinanzierung für das Vorhaben: „exist Women“
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    56.4%

• InnovationLab GmbH

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  47 Treffer55.5%
  • Interfaces in opto-electronic thin film multilayer devices
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    55.5%

• ROBOSOFT Services Robots

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  13 Treffer55.0%
  • INTeractive RObotics Research Network
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    55.0%

• space application services

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  13 Treffer55.0%
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    55.0%

• Asociación Centro de Investigación Cooperativa en Nanociencia – CIC nanoGUNE

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  103 Treffer54.0%
  • DYnamic control in hybrid plasmonic NAnopores: road to next generation multiplexed single MOlecule detection
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    54.0%

• Frontiers, Opportunities, and Challenges in Biochemical and Chemical Catalysis of CO₂ Fixation

  2013

  Chemical Reviews · 2111 Zitationen · DOI

  Two major energy-related problems confront the world in the
\nnext 50 years. First, increased worldwide competition for
\ngradually depleting fossil fuel reserves (derived from past
\nphotosynthesis) will lead to higher costs, both monetarily and politically. Second, atmospheric CO_2 levels are at their highest recorded level since records began. Further increases are predicted to produce large and uncontrollable impacts on the world climate. These projected impacts extend beyond climate to ocean acidification, because the ocean is a major sink for atmospheric CO2.1 Providing a future energy supply that is secure and CO_2-neutral will require switching to nonfossil energy sources such as wind, solar, nuclear, and geothermal energy and developing methods for transforming the energy produced by these new sources into forms that can be stored, transported, and used upon demand.

• Carbon Dioxide Activation at the Ni,Fe-Cluster of Anaerobic Carbon Monoxide Dehydrogenase

  2007

  Science · 593 Zitationen · DOI

  Anaerobic CO dehydrogenases catalyze the reversible oxidation of CO to CO2 at a complex Ni-, Fe-, and S-containing metal center called cluster C. We report crystal structures of CO dehydrogenase II from Carboxydothermus hydrogenoformans in three different states. In a reduced state, exogenous CO2 supplied in solution is bound and reductively activated by cluster C. In the intermediate structure, CO2 acts as a bridging ligand between Ni and the asymmetrically coordinated Fe, where it completes the square-planar coordination of the Ni ion. It replaces a water/hydroxo ligand bound to the Fe ion in the other two states. The structures define the mechanism of CO oxidation and CO2 reduction at the Ni-Fe site of cluster C.

• Crystal Structure of a Carbon Monoxide Dehydrogenase Reveals a [Ni-4Fe-5S] Cluster

  2001

  Science · 550 Zitationen · DOI

  The homodimeric nickel-containing CO dehydrogenase from the anaerobic bacterium Carboxydothermus hydrogenoformans catalyzes the oxidation of CO to CO2. A crystal structure of the reduced enzyme has been solved at 1.6 angstrom resolution. This structure represents the prototype for Ni-containing CO dehydrogenases from anaerobic bacteria and archaea. It contains five metal clusters of which clusters B, B', and a subunit-bridging, surface-exposed cluster D are cubane-type [4Fe-4S] clusters. The active-site clusters C and C' are novel, asymmetric [Ni-4Fe-5S] clusters. Their integral Ni ion, which is the likely site of CO oxidation, is coordinated by four sulfur ligands with square planar geometry.

• Catalysis at a dinuclear [CuSMo(O)OH] cluster in a CO dehydrogenase resolved at 1.1-Å resolution

  2002

  Proceedings of the National Academy of Sciences · 376 Zitationen · DOI

  The CO dehydrogenase of the eubacterium Oligotropha carboxidovorans is a 277-kDa Mo- and Cu-containing iron-sulfur flavoprotein. Here, the enzyme's active site in the oxidized or reduced state, after inactivation with potassium cyanide or with n-butylisocyanide bound to the active site, has been reinvestigated by multiple wavelength anomalous dispersion measurements at atomic resolution, electron spin resonance spectroscopy, and chemical analyses. We present evidence for a dinuclear heterometal [CuSMoO)OH] cluster in the active site of the oxidized or reduced enzyme, which is prone to cyanolysis. The cluster is coordinated through interactions of the Mo with the dithiolate pyran ring of molybdopterin cytosine dinucleotide and of the Cu with the Sgamma of Cys-388, which is part of the active-site loop VAYRC(388)SFR. The previously reported active-site structure [Dobbek, H., Gremer, L., Meyer, O. & Huber, R. (1999) Proc. Natl. Acad. Sci. USA 96, 8884-8889] of an Mo with three oxygen ligands and an SeH-group bound to the Sgamma atom of Cys-388 could not be confirmed. The structure of CO dehydrogenase with the inhibitor n-butylisocyanide bound has led to a model for the catalytic mechanism of CO oxidation which involves a thiocarbonate-like intermediate state. The dinuclear [CuSMo(O)OH] cluster of CO dehydrogenase establishes a previously uncharacterized class of dinuclear molybdoenzymes containing the pterin cofactor.

• Structural basis for organohalide respiration

  2014

  Science · 269 Zitationen · DOI

  Organohalide-respiring microorganisms can use a variety of persistent pollutants, including trichloroethene (TCE), as terminal electron acceptors. The final two-electron transfer step in organohalide respiration is catalyzed by reductive dehalogenases. Here we report the x-ray crystal structure of PceA, an archetypal dehalogenase from Sulfurospirillum multivorans, as well as structures of PceA in complex with TCE and product analogs. The active site harbors a deeply buried norpseudo-B12 cofactor within a nitroreductase fold, also found in a mammalian B12 chaperone. The structures of PceA reveal how a cobalamin supports a reductive haloelimination exploiting a conserved B12-binding scaffold capped by a highly variable substrate-capturing region.

• A functional Ni-Ni-[4Fe-4S] cluster in the monomeric acetyl-CoA synthase from <i>Carboxydothermus hydrogenoformans</i>

  2003

  Proceedings of the National Academy of Sciences · 258 Zitationen · DOI

  In anaerobic microorganisms employing the acetyl-CoA pathway, acetyl-CoA synthase (ACS) and CO dehydrogenase (CODH) form a complex (ACS/CODH) that catalyzes the synthesis of acetyl-CoA from CO, a methyl group, and CoA. Previously, a [4Fe-4S] cubane bridged to a copper-nickel binuclear site (active site cluster A of the ACS component) was identified in the ACS(Mt)/CODH(Mt) from Moorella thermoacetica whereas another study revealed a nickel-nickel site in the open form of ACS(Mt), and a zink-nickel site in the closed form. The ACS(Ch) of the hydrogenogenic bacterium Carboxydothermus hydrogenoformans was found to exist as an 82.2-kDa monomer as well as in a 1:1 molar complex with the 73.3-kDa CODHIII(Ch). Homogeneous ACS(Ch) and ACS(Ch)/CODHIII(Ch) catalyzed the exchange between [1-(14)C]acetyl-CoA and (12)CO with specific activities of 2.4 or 5.9 micromol of CO per min per mg, respectively, at 70 degrees C and pH 6.0. They also catalyzed the synthesis of acetyl-CoA from CO, methylcobalamin, corrinoid iron-sulfur protein, and CoA with specific activities of 0.14 or 0.91 micromol of acetyl-CoA formed per min per mg, respectively, at 70 degrees C and pH 7.3. The functional cluster A of ACS(Ch) contains a Ni-Ni-[4Fe-4S] site, in which the positions proximal and distal to the cubane are occupied by Ni ions. This result is apparent from a positive correlation of the Ni contents and negative correlations of the Cu or Zn contents with the acetyl-CoA/CO exchange activities of different preparations of monomeric ACS(Ch), a 2.2-A crystal structure of the dithionite-reduced monomer in an open conformation, and x-ray absorption spectroscopy.

• Crystal structure and mechanism of CO dehydrogenase, a molybdo iron-sulfur flavoprotein containing <i>S</i> -selanylcysteine

  1999

  Proceedings of the National Academy of Sciences · 253 Zitationen · DOI

  CO dehydrogenase from the aerobic bacterium Oligotropha carboxidovorans catalyzes the oxidation of CO with H(2)O, yielding CO(2), two electrons, and two H(+). Its crystal structure in the air-oxidized form has been determined to 2.2 A. The active site of the enzyme, which contains molybdenum with three oxygen ligands, molybdopterin-cytosine dinucleotide and S-selanylcysteine, delivers the electrons to an intramolecular electron transport chain composed of two types of [2Fe-2S] clusters and flavin-adenine dinucleotide. CO dehydrogenase is composed of an 88.7-kDa molybdoprotein (L), a 30. 2-kDa flavoprotein (M), and a 17.8-kDa iron-sulfur protein (S). It is organized as a dimer of LMS heterotrimers and resembles xanthine dehydrogenase/oxidase in many, but not all, aspects. A mechanism based on a structure with the bound suicide-substrate cyanide is suggested and displays the necessity of S-selanylcysteine for the catalyzed reaction.

• How the [NiFe₄S₄] Cluster of CO Dehydrogenase Activates CO₂ and NCO⁻

  2015

  Angewandte Chemie International Edition · 132 Zitationen · DOI

  Ni,Fe-containing CO dehydrogenases (CODHs) use a [NiFe4S4] cluster, termed cluster C, to reversibly reduce CO2 to CO with high turnover number. Binding to Ni and Fe activates CO2, but current crystal structures have insufficient resolution to analyze the geometry of bound CO2 and reveal the extent and nature of its activation. The crystal structures of CODH in complex with CO2 and the isoelectronic inhibitor NCO(-) are reported at true atomic resolution (dmin ≤1.1 Å). Like CO2, NCO(-) is a μ2,η(2) ligand of the cluster and acts as a mechanism-based inhibitor. While bound CO2 has the geometry of a carboxylate group, NCO(-) is transformed into a carbamoyl group, thus indicating that both molecules undergo a formal two-electron reduction after binding and are stabilized by substantial π backbonding. The structures reveal the combination of stable μ2,η(2) coordination by Ni and Fe2 with reductive activation as the basis for both the turnover of CO2 and inhibition by NCO(-).

• Structural insights into methyltransfer reactions of a corrinoid iron–sulfur protein involved in acetyl-CoA synthesis

  2006

  Proceedings of the National Academy of Sciences · 130 Zitationen · DOI

  The cobalt- and iron-containing corrinoid iron-sulfur protein (CoFeSP) is functional in the acetyl-CoA (Ljungdahl-Wood) pathway of autotrophic carbon fixation in various bacteria and archaea, where it is essential for the biosynthesis of acetyl-CoA. CoFeSP acts in two methylation reactions: the transfer of a methyl group from methyltransferase (MeTr)-bound methyltetrahydrofolate to the cob(I)amide of CoFeSP and the transfer of the methyl group of methyl-cob(III)amide to the reduced Ni-Ni-[4Fe-4S] active site cluster A of acetyl-CoA synthase (ACS). We have solved the crystal structure of as-isolated CoFeSP(Ch) from the CO-oxidizing hydrogenogenic bacterium Carboxydothermus hydrogenoformans at 1.9-A resolution. The heterodimeric protein consists of two tightly interacting subunits with pseudo-twofold symmetry. The large CfsA subunit comprises three domains, of which the N-terminal domain binds the [4Fe-4S] cluster, the middle domain is a (betaalpha)(8)-barrel, and the C-terminal domain shows an open fold and binds Cobeta-aqua-(5,6-dimethylbenzimidazolylcobamide) in a "base-off" state without a protein ligand at the cobalt ion. The small CfsB subunit also displays a (betaalpha)(8)-barrel fold and interacts with the upper side of the corrin macrocycle. Structure-based alignments show that both (betaalpha)(8)-barrel domains are related to the MeTr in the acetyl-CoA pathway and to the folate domain of methionine synthase. We suggest that the C-terminal domain of the large subunit is the mobile element that allows the necessary interaction of CoFeSP(Ch) with the active site of ACS(Ch) and the methyltetrahydrofolate carrying MeTr. The conformation in the crystal structure shields the two open coordinations of cobalt and likely represents a resting state.

• A novel free-mounting system for protein crystals: transformation and improvement of diffraction power by accurately controlled humidity changes

  2000

  Journal of Applied Crystallography · 121 Zitationen · DOI

  A novel device for capillary-free mounting of protein crystals is described. A controlled stream of air allows an accurate adjustment of the humidity at the crystal. The crystal is held on the tip of a micropipette. With a video system (CCD camera), the two-dimensional shadow projections of crystals can be recorded for optical analysis. Instead of the micropipette, a standard loop can also be used. Experiments and results for different crystal systems demonstrate the use of this method, also in combination with shock-freezing, to improve crystal order. Working with oxygen-free gases offers the possibility of crystal measurements under anaerobic conditions. Furthermore, the controlled application of arbitrary volatile substances with the gas stream is practicable.

• Carbon Monoxide Induced Decomposition of the Active Site [Ni−4Fe−5S] Cluster of CO Dehydrogenase

  2004

  Journal of the American Chemical Society · 109 Zitationen · DOI

  During the past two years, crystal structures of Cu- and Mo-containing carbon monoxide dehydrogenases (CODHs) and Ni- and Fe-containing CODHs have been reported. The active site of CODHs from anaerobic bacteria (cluster C) is composed of Ni, Fe, and S for which crystallographic studies of the enzymes from Carboxydothermus hydrogenoformans, Rhodospirillum rubrum, and Moorella thermoaceticarevealed structural similarities in the overall protein fold but showed substantial differences in the essential Ni coordination environment. The [Ni-4Fe-5S] cluster C in the fully catalytically competent dithionite-reduced CODH II from C. hydrogenoformans (CODHII(Ch)) at 1.6 A resolution contains a characteristic mu(2)-sulfido ligand between Ni and Fe1, resulting in a square-planar ligand arrangement with four S-ligands at the Ni ion. In contrast, the [Ni-4Fe-4S] clusters C in CO-treated CODH from R. rubrum resolved at 2.8 A and in CO-treated acetyl-CoA synthase/CODH complex from M. thermoacetica at 2.2 and 1.9 A resolution, respectively, do not contain the mu(2)-sulfido ligand between Ni and Fe1 and display dissimilar geometries at the Ni ion. The [Ni-4Fe-4S] cluster is composed of a cubane [Ni-3Fe-4S] cluster linked to a mononuclear Fe site. The described coordination geometries of the Ni ion in the [Ni-4Fe-4S] cluster of R. rubrum and M. thermoacetica deviate from the square-planar ligand geometry in the [Ni-4Fe-5S] cluster C of CODHII(Ch). In addition, the latter was converted into a [Ni-4Fe-4S] cluster under specific conditions. The objective of this study was to elucidate the relationship between the structure of cluster C in CODHII(Ch) and the functionality of the protein. We have determined the CO oxidation activity of CODHII(Ch) under different conditions of crystallization, prepared crystals of the enzyme in the presence of dithiothreitol or dithionite as reducing agents under an atmosphere of N(2) or CO, and solved the corresponding structures at 1.1 to 1.6 A resolutions. Fully active CODHII(Ch) obtained after incubation of the enzyme with dithionite under N(2) revealed the [Ni-4Fe-5S] cluster. Short treatment of the enzyme with CO in the presence of dithiothreitol resulted in a catalytically competent CODHII(Ch) with a CO-reduced [Ni-4Fe-5S] cluster, but a prolonged treatment with CO caused the loss of CO-oxidizing activity and revealed a [Ni-4Fe-4S] cluster, which did not contain a mu(2)-S. These data suggest that the [Ni-4Fe-4S] cluster of CODHII(Ch) is an inactivated decomposition product originating from the [Ni-4Fe-5S] cluster.

• Cobamide-mediated enzymatic reductive dehalogenation via long-range electron transfer

  2017

  Nature Communications · 101 Zitationen · DOI

  The capacity of metal-containing porphyrinoids to mediate reductive dehalogenation is implemented in cobamide-containing reductive dehalogenases (RDases), which serve as terminal reductases in organohalide-respiring microbes. RDases allow for the exploitation of halogenated compounds as electron acceptors. Their reaction mechanism is under debate. Here we report on substrate-enzyme interactions in a tetrachloroethene RDase (PceA) that also converts aryl halides. The shape of PceA's highly apolar active site directs binding of bromophenols at some distance from the cobalt and with the hydroxyl substituent towards the metal. A close cobalt-substrate interaction is not observed by electron paramagnetic resonance spectroscopy. Nonetheless, a halogen substituent para to the hydroxyl group is reductively eliminated and the path of the leaving halide is traced in the structure. Based on these findings, an enzymatic mechanism relying on a long-range electron transfer is concluded, which is without parallel in vitamin B₁₂-dependent biochemistry and represents an effective mode of RDase catalysis.

• Photoactivatable Mussel‐Based Underwater Adhesive Proteins by an Expanded Genetic Code

  2017

  ChemBioChem · 96 Zitationen · DOI

  Marine mussels exhibit potent underwater adhesion abilities under hostile conditions by employing 3,4-dihydroxyphenylalanine (DOPA)-rich mussel adhesive proteins (MAPs). However, their recombinant production is a major biotechnological challenge. Herein, a novel strategy based on genetic code expansion has been developed by engineering efficient aminoacyl-transfer RNA synthetases (aaRSs) for the photocaged noncanonical amino acid ortho-nitrobenzyl DOPA (ONB-DOPA). The engineered ONB-DOPARS enables in vivo production of MAP type 5 site-specifically equipped with multiple instances of ONB-DOPA to yield photocaged, spatiotemporally controlled underwater adhesives. Upon exposure to UV light, these proteins feature elevated wet adhesion properties. This concept offers new perspectives for the production of recombinant bioadhesives.

• 2-Oxoquinoline 8-Monooxygenase Oxygenase Component: Active Site Modulation by Rieske-[2Fe-2S] Center Oxidation/Reduction

  2005

  Structure · 96 Zitationen · DOI

• Increased Folding Stability of TEM-1 β-Lactamase by In Vitro Selection

  2008

  Journal of Molecular Biology · 86 Zitationen · DOI

• The effect of intracellular molybdenum in Hydrogenophaga pseudoflava on the crystallographic structure of the seleno-molybdo-iron-sulfur flavoenzyme carbon monoxide dehydrogenase

  2000

  Journal of Molecular Biology · 85 Zitationen · DOI

• Quercetin 2,4‐Dioxygenase Activates Dioxygen in a Side‐On O₂–Ni Complex

  2016

  Angewandte Chemie International Edition · 78 Zitationen · DOI

  Quercetin 2,4-dioxygenase (quercetinase) from Streptomyces uses nickel as the active-site cofactor to catalyze oxidative cleavage of the flavonol quercetin. How this unusual active-site metal supports catalysis and O2 activation is under debate. We present crystal structures of Ni-quercetinase in three different states, thus providing direct insight into how quercetin and O2 are activated at the Ni(2+) ion. The Ni(2+) ion is coordinated by three histidine residues and a glutamate residue (E(76)) in all three states. Upon binding, quercetin replaces one water ligand at Ni and is stabilized by a short hydrogen bond through E(76) , the carboxylate group of which rotates by 90°. This conformational change weakens the interaction between Ni and the remaining water ligand, thereby preparing a coordination site at Ni to bind O2. O2 binds side-on to the Ni(2+) ion and is perpendicular to the C2-C3 and C3-C4 bonds of quercetin, which are cleaved in the following reaction steps.

• CODH‐IV: A High‐Efficiency CO‐Scavenging CO Dehydrogenase with Resistance to O₂

  2017

  Angewandte Chemie International Edition · 75 Zitationen · DOI

  CO dehydrogenases (CODHs) catalyse the reversible conversion between CO and CO₂ . Genomic analysis indicated that the metabolic functions of CODHs vary. The genome of Carboxydothermus hydrogenoformans encodes five CODHs (CODH-I-V), of which CODH-IV is found in a gene cluster near a peroxide-reducing enzyme. Our kinetic and crystallographic experiments reveal that CODH-IV differs from other CODHs in several characteristic properties: it has a very high affinity for CO, oxidizes CO at diffusion-limited rate over a wide range of temperatures, and is more tolerant to oxygen than CODH-II. Thus, our observations support the idea that CODH-IV is a CO scavenger in defence against oxidative stress and highlight that CODHs are more diverse in terms of reactivity than expected.

• Active Site Geometry and Substrate Recognition of the Molybdenum Hydroxylase Quinoline 2-Oxidoreductase

  2004

  Structure · 75 Zitationen · DOI

• Crystal structure of 4-hydroxybutyryl-CoA dehydratase: Radical catalysis involving a [4Fe–4S] cluster and flavin

  2004

  Proceedings of the National Academy of Sciences · 75 Zitationen · DOI

  Dehydratases catalyze the breakage of a carbon-oxygen bond leading to unsaturated products via the elimination of water. The 1.6-A resolution crystal structure of 4-hydroxybutyryl-CoA dehydratase from the gamma-aminobutyrate-fermenting Clostridium aminobutyricum represents a new class of dehydratases with an unprecedented active site architecture. A [4Fe-4S](2+) cluster, coordinated by three cysteine and one histidine residues, is located 7 A from the Re-side of a flavin adenine dinucleotide (FAD) moiety. The structure provides insight into the function of these ubiquitous prosthetic groups in the chemically nonfacile, radical-mediated dehydration of 4-hydroxybutyryl-CoA. The substrate can be bound between the [4Fe-4S](2+) cluster and the FAD with both cofactors contributing to its radical activation and catalytic conversion. Our results raise interesting questions regarding the mechanism of acyl-CoA dehydrogenases, which are involved in fatty acid oxidation, and address the divergent evolution of the ancestral common gene.

• Site‐Resolved Observation of Vibrational Energy Transfer Using a Genetically Encoded Ultrafast Heater

  2018

  Angewandte Chemie International Edition · 73 Zitationen · DOI

  Allosteric information transfer in proteins has been linked to distinct vibrational energy transfer (VET) pathways in a number of theoretical studies. Experimental evidence for such pathways, however, is sparse because site-selective injection of vibrational energy into a protein, that is, localized heating, is required for their investigation. Here, we solved this problem by the site-specific incorporation of the non-canonical amino acid β-(1-azulenyl)-l-alanine (AzAla) through genetic code expansion. As an exception to Kasha's rule, AzAla undergoes ultrafast internal conversion and heating after S₁ excitation while upon S₂ excitation, it serves as a fluorescent label. We equipped PDZ3, a protein interaction domain of postsynaptic density protein 95, with this ultrafast heater at two distinct positions. We indeed observed VET from the incorporation sites in the protein to a bound peptide ligand on the picosecond timescale by ultrafast IR spectroscopy. This approach based on genetically encoded AzAla paves the way for detailed studies of VET and its role in a wide range of proteins.

• The Role of Se, Mo and Fe in the Structure and Function of Carbon Monoxide Dehydrogenase

  2000

  Biological Chemistry · 71 Zitationen · DOI

  CO dehydrogenase (EC 1.2.99.2) catalyzes the oxidation of CO according to the following equation: CO + H2O-->CO2 + 2 e- + 2 H+. It is a selenium-containing molybdo-iron-sulfur-flavoenzyme, which has been crystallized and structurally characterized in its oxidized state from the aerobic CO utilizing bacteria Oligotropha carboxidovorans and Hydrogenophaga pseudoflava. Both CO dehydrogenase structures show only minor differences, and the enzymes are dimers of two heterotrimers. Each heterotrimer is composed of a molybdoprotein, a flavoprotein, and an iron-sulfur protein. CO oxidation takes place at the molybdoprotein which contains a 1:1 mononuclear complex of molybdopterin-cytosine dinucleotide and a Mo-ion, along with a catalytically essential S-selanylcysteine. The latter is appropriately positioned in the SeMo-active site by a unique VAYRCSFR active site loop. In H. pseudoflava the arginine preceeding the cysteine in the active site loop is modified to a Cgamma-hydroxy arginine residue which has no obvious function. The substituents in the first coordination sphere of the Mo-ion are the enedithiolate sulfur atoms of the molybdopterin-cytosine dinucleotide, two oxo- and a sulfido-group. Extended X-ray absorption fine structure spectroscopy (EXAFS), along with the crystal structure of CO dehydrogenase (23.2 U mg(-1)) at 1.85 A resolution, have identified a sulfur atom at 2.3 A from the Mo-ion. The sulfur reacts with cyanide yielding thiocyanate. The corresponding inactive desulfo-CO dehydrogenase shows a typical desulfo inhibited-type of Mo-electron paramagnetic resonance (EPR) spectrum. Structural changes at the SeMo-site during catalysis are suggested by the Mo to Se distance of 3.7 A and the Mo-S-Se angle of 113 degrees in the oxidized enzyme which increase to 4.1 A, and 121 degrees, respectively, in the reduced enzyme. The intramolecular electron transport chain in CO dehydrogenase involves the following prosthetic groups and minimal distances: CO-->[Mo of the molybdenum cofactor] - 14.6 A - [2Fe-2S]I - 12.4 A - [2Fe-2S]II - 8.7 A - [FAD].

• Structural aspects of mononuclear Mo/W-enzymes

  2010

  Coordination Chemistry Reviews · 67 Zitationen · DOI

• Visualizing the substrate-, superoxo-, alkylperoxo-, and product-bound states at the nonheme Fe(II) site of homogentisate dioxygenase

  2013

  Proceedings of the National Academy of Sciences · 65 Zitationen · DOI

  Homogentisate 1,2-dioxygenase (HGDO) uses a mononuclear nonheme Fe(2+) to catalyze the oxidative ring cleavage in the degradation of Tyr and Phe by producing maleylacetoacetate from homogentisate (2,5-dihydroxyphenylacetate). Here, we report three crystal structures of HGDO, revealing five different steps in its reaction cycle at 1.7-1.98 Å resolution. The resting state structure displays an octahedral coordination for Fe(2+) with two histidine residues (His331 and His367), a bidentate carboxylate ligand (Glu337), and two water molecules. Homogentisate binds as a monodentate ligand to Fe(2+), and its interaction with Tyr346 invokes the folding of a loop over the active site, effectively shielding it from solvent. Binding of homogentisate is driven by enthalpy and is entropically disfavored as shown by anoxic isothermal titration calorimetry. Three different reaction cycle intermediates have been trapped in different HGDO subunits of a single crystal showing the influence of crystal packing interactions on the course of enzymatic reactions. The observed superoxo:semiquinone-, alkylperoxo-, and product-bound intermediates have been resolved in a crystal grown anoxically with homogentisate, which was subsequently incubated with dioxygen. We demonstrate that, despite different folds, active site architectures, and Fe(2+) coordination, extradiol dioxygenases can proceed through the same principal reaction intermediates to catalyze the O2-dependent cleavage of aromatic rings. Thus, convergent evolution of nonhomologous enzymes using the 2-His-1-carboxylate facial triad motif developed different solutions to stabilize closely related intermediates in unlike environments.

• Xenobiotic Reductase A in the Degradation of Quinoline by Pseudomonas putida 86: Physiological Function, Structure and Mechanism of 8-Hydroxycoumarin Reduction

  2006

  Journal of Molecular Biology · 63 Zitationen · DOI

• Charité – Universitätsmedizin Berlin

  EXC 314/1: Die Aufklärung des photo-induzierten Assemblierungsmechanismus, ausgehend von nativen und modifizierten Wasseroxidations-Katalysatoren des Photosystem II (AG Zouni) Biokatalytische Kopplung von Photosystem I mit FDH und CO-DH Superkomplexen

  university

• EWHA Womans University in Seoul

  Dioxygenase-Reaktivität von Hämoproteinen, die mit Nicht-Hem-Eisenkatalysatoren in asummetrischen cis-Dihydroxylierungs- und Indol-Oxidationsreaktionen rekonstituiert wurden

  university

• Freie Universität Berlin

  EXC 2008: Unifying Systems in Catalysis (UniSysCat)

  university

• Fritz-Haber-Institut der Max-Planck-Gesellschaft

  EXC 314/1: Die Aufklärung des photo-induzierten Assemblierungsmechanismus, ausgehend von nativen und modifizierten Wasseroxidations-Katalysatoren des Photosystem II (AG Zouni) Biokatalytische Kopplung von Photosystem I mit FDH und CO-DH Superkomplexen

  other

• Helmholtz-Zentrum Berlin für Materialien und Energie

  EXC 314/1: Die Aufklärung des photo-induzierten Assemblierungsmechanismus, ausgehend von nativen und modifizierten Wasseroxidations-Katalysatoren des Photosystem II (AG Zouni) Biokatalytische Kopplung von Photosystem I mit FDH und CO-DH Superkomplexen

  other

• Justus-Liebig-Universität Gießen

  SFB 1078/1: Strukturelle Grundlagen der Protonenabgabe in der Wasser-Oxidation durch das Photosystem II (TP A05)

  university

• Leibniz-Forschungsinstitut für Molekulare Pharmakologie

  EXC 314/1: Die Aufklärung des photo-induzierten Assemblierungsmechanismus, ausgehend von nativen und modifizierten Wasseroxidations-Katalysatoren des Photosystem II (AG Zouni) Biokatalytische Kopplung von Photosystem I mit FDH und CO-DH Superkomplexen

  other

• Max-Planck-Institut für Kolloid- und Grenzflächenforschung

  EXC 314/1: Die Aufklärung des photo-induzierten Assemblierungsmechanismus, ausgehend von nativen und modifizierten Wasseroxidations-Katalysatoren des Photosystem II (AG Zouni) Biokatalytische Kopplung von Photosystem I mit FDH und CO-DH Superkomplexen

  other

• Technische Universität Berlin

  EXC 314/1: Die Aufklärung des photo-induzierten Assemblierungsmechanismus, ausgehend von nativen und modifizierten Wasseroxidations-Katalysatoren des Photosystem II (AG Zouni) Biokatalytische Kopplung von Photosystem I mit FDH und CO-DH Superkomplexen

  university

• Universität Potsdam

  EXC 314/1: Die Aufklärung des photo-induzierten Assemblierungsmechanismus, ausgehend von nativen und modifizierten Wasseroxidations-Katalysatoren des Photosystem II (AG Zouni) Biokatalytische Kopplung von Photosystem I mit FDH und CO-DH Superkomplexen

  university

Name

Prof. Dr. rer. nat. Holger Dobbek

Titel

Prof. Dr. rer. nat.

Fakultät

Lebenswissenschaftliche Fakultät

Institut

Institut für Biologie

Arbeitsgruppe

Strukturbiologie / Biochemie

Telefon

+49 30 2093-49842

HU-FIS-Profil

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26.4.2026, 01:03:58