[N,N??-bis-(mercaptoethyl)-1,5-diazacyclooctanato]NiII, Ni-1, is known to undergo metallation reactions with numerous metals. [N,N??-bis-(mercaptoethyl)-1,5-diazacycloheptanato]NiII, (bme-dach)Ni or Ni-1??, differs from Ni-1 by one less carbon in its diazacycle backbone ring producing subtle differences in N2S2Ni geometry. Metallation of Ni-1?? with PdCl2, Pd(NO3)2, and NiBr2 produced three structural forms: Ni2Pd basket, Ni4Pd2 C4-paddlewheel, and Ni3 slant chair. In attempts to provide a rationale for the heterogeneity in the active site of Acetyl coA Synthase, metal ion capture studies of Ni-1 in methanol found a qualitative ranking of metal ion preference: Zn2+ < Ni2+ < Cu+. Formation constants for metal ion capture of Ni-1?? in water were determined for Pb2+, Ni2+, Zn2+, Cu+, and Ag+. A quantitative estimate places copper some 15 orders of magnitude above nickel or zinc in binding affinity. Sulfur dioxide uptake by Ni-1?? is characterized by significant color change, improved adduct solubility, and reversible binding of two equivalents of SO2. These combined properties establish Ni-1?? as a suitable model for gas uptake at nickel thiolate sites and as a possibly useful chemical sensor for this poisonous gas. Comparisons of molecular structures, ν(SO) stretching frequencies, and thermal gravimetric analyses are made to reported adducts including the diazacyclooctane derivative, Ni-1·2SO2. Visual SO2 detection limits of Ni-1 and Ni-1?? are established at 25 ppm and 100 ppm, respectively. Structural studies of products resulting from reaction at the nucleophilic S-sites of (bme-dach)Ni and [(bme-dach)Zn]2 included acetyl chloride and sodium iodoacetate as electrophiles are shown. The acetyl group is a natural electrophile important to the citric acid cycle. Acetylation of (bme-dach)Ni produces a five coordinate, paramagnetic species. Iodoacetate is a cysteine modification agent known to inhibit enzymatic activity. The reaction of (bme-dach)Ni and sodium iodoacetate yields a blue, six coordinate nickel complex in a N2S2O2 donor environment. The bismercaptodiazacycloheptane ligand binds lead(II) forming an unprecedented structural form of N2S2M dimers, in which Pb2+ is largely bound to sulfur in a highly distorted trigonal geometry. Its unusual structure is described in comparison to other derivatives of the bme-daco ligand. The synthesis and structural characterization of square pyramidal (bme-dach)GaCl are also given and compared to the analogous (bme-daco)GaCl.

[N,N??-bis-(mercaptoethyl)-1,5-diazacyclooctanato]NiII, Ni-1, is known to undergo metallation reactions with numerous metals. [N,N??-bis-(mercaptoethyl)-1,5-diazacycloheptanato]NiII, (bme-dach)Ni or Ni-1??, differs from Ni-1 by one less carbon in its diazacycle backbone ring producing subtle differences in N2S2Ni geometry. Metallation of Ni-1?? with PdCl2, Pd(NO3)2, and NiBr2 produced three structural forms: Ni2Pd basket, Ni4Pd2 C4-paddlewheel, and Ni3 slant chair. In attempts to provide a rationale for the heterogeneity in the active site of Acetyl coA Synthase, metal ion capture studies of Ni-1 in methanol found a qualitative ranking of metal ion preference: Zn2+ < Ni2+ < Cu+. Formation constants for metal ion capture of Ni-1?? in water were determined for Pb2+, Ni2+, Zn2+, Cu+, and Ag+. A quantitative estimate places copper some 15 orders of magnitude above nickel or zinc in binding affinity. Sulfur dioxide uptake by Ni-1?? is characterized by significant color change, improved adduct solubility, and reversible binding of two equivalents of SO2. These combined properties establish Ni-1?? as a suitable model for gas uptake at nickel thiolate sites and as a possibly useful chemical sensor for this poisonous gas. Comparisons of molecular structures,&#61472; &#957;(SO) stretching frequencies, and thermal gravimetric analyses are made to reported adducts including the diazacyclooctane derivative, Ni-1&#903;2SO2. Visual SO2 detection limits of Ni-1 and Ni-1?? are established at 25 ppm and 100 ppm, respectively. Structural studies of products resulting from reaction at the nucleophilic S-sites of (bme-dach)Ni and [(bme-dach)Zn]2 included acetyl chloride and sodium iodoacetate as electrophiles are shown. The acetyl group is a natural electrophile important to the citric acid cycle. Acetylation of (bme-dach)Ni produces a five coordinate, paramagnetic species. Iodoacetate is a cysteine modification agent known to inhibit enzymatic activity. The reaction of (bme-dach)Ni and sodium iodoacetate yields a blue, six coordinate nickel complex in a N2S2O2 donor environment. The bismercaptodiazacycloheptane ligand binds lead(II) forming an unprecedented structural form of N2S2M dimers, in which Pb2+ is largely bound to sulfur in a highly distorted trigonal geometry. Its unusual structure is described in comparison to other derivatives of the bme-daco ligand. The synthesis and structural characterization of square pyramidal (bme-dach)GaCl are also given and compared to the analogous (bme-daco)GaCl.

京都大学 / 0048 / 新制・課程博士 / 博士(農学) / 甲第18339号 / 農博第2064号 / 新制||農||1023(附属図書館) / 学位論文||H26||N4846(農学部図書室) / 31197 / 京都大学大学院農学研究科応用生物科学専攻 / (主査)教授 左子 芳彦, 教授 澤山 茂樹, 教授 菅原 達也 / 学位規則第4条第1項該当 / Doctor of Agricultural Science / Kyoto University / DFAM

Der Komplex aus Kohlenmonoxid-Dehydrogenase und Acetyl-CoA-Synthase (CODH/ACS Komplex) des thermophilen Bakteriums Carboxydothermus hydrogenoformans katalysiert die Fixierung von CO2 in Acetyl-CoA und ist damit ein potenzieller Katalysator für die Erzeugung erneuerbarer Kraftstoffe aus CO2. Die Katalyse erfolgt an zwei verschiedenen Stellen: CO2 wird am Cluster C in der CODH-Untereinheit zu CO reduziert, das dann durch einen Tunnel innerhalb des Proteins zum Cluster A in der ACS-Untereinheit wandert, wo es mit einer Methylgruppe und CoA zu Acetyl-CoA reagiert. Die Art und Weise, wie die beiden katalytischen Aktivitäten zusammenwirken, sind noch unklar. Um hier mehr Licht ins Dunkel zu bringen, verfolgte diese Arbeit drei Ziele: die Bestimmung der Struktur des CODH/ACS-Komplexes von C. hydrogenoformans, die Untersuchung der CO2-Reduktionsaktivität von CODHasen und die Analyse der Rolle des internen Tunnels im CODH/ACS-Komplex. Die Struktur des CODH/ACS-Komplexes von C. hydrogenoformans wurde durch Röntgenkristallographie mit einer Auflösung von 2,04 Å bestimmt. Die CO2-Reduktion am Cluster C wurde kinetisch untersucht. Es zeigte sich, dass die CO2-Reduktion durch einen Ping-Pong-Mechanismus mit zwei Reaktionsstellen erfolgen könnte, der in früheren Studien vorgeschlagen wurde, aber auch durch andere Mechanismen. Um eine Struktur-Funktionsbeziehung für CODHs zu ermitteln, wurde die CO2-Reduktionsaktivität für drei CODHasen von C. hydrogenoformans untersucht, deren Strukturen bekannt sind: CODH-II, CODH-IV, und der CODH/ACS-Komplex. Das Tunnelsystem im CODH/ACS-Komplex ist viel enger als in den anderen CODHs und könnte somit der Grund für die vergleichsweise geringe Aktivität des CODH/ACS-Komplexes sein. Dies wurde auch durch die Manipulation und Analyse des internen Tunnels des CODH/ACS-Komplexes unterstützt. Die Ergebnisse deuten darauf hin, dass der Hauptzweck des Tunnels im CODH/ACS-Komplex die Kompartimentierung von CO und nicht der schnelle Substrattransport ist. / The complex of carbon monoxide dehydrogenase and acetyl-CoA synthase (CODH/ACS complex) of the thermophilic bacterium Carboxydothermus hydrogenoformans catalyses the fixation of CO2 into acetyl-CoA and is thus a potential catalyst for the production of renewable fuels from CO2. Catalysis occurs at two different sites: CO2 is reduced to CO at cluster C in the CODH subunit, which then travels through a tunnel within the protein to cluster A in the ACS subunit, where it reacts with a methyl group and CoA to form acetyl-CoA. The way in which the two catalytic activities interact is still unclear. To shed more light on this, this work pursued three goals: to determine the structure of the CODH/ACS complex of C. hydrogenoformans, to investigate the CO2 reduction activity of CODHases and to analyse the role of the internal tunnel in the CODH/ACS complex. The structure of the CODH/ACS complex of C. hydrogenoformans was determined by X-ray crystallography at 2.04 Å resolution. The CO2 reduction at cluster C was investigated kinetically. It was found that CO2 reduction could occur by a two-site ping-pong mechanism proposed in previous studies, but also by other mechanisms. To establish a structure-function relationship for CODHs, CO2 reduction activity was investigated for three CODHases of C. hydrogenoformans whose structures are known: CODH-II, CODH-IV, and the CODH/ACS complex. The tunnel system in the CODH/ACS complex is much narrower than in the other CODHs and could thus be the reason for the comparatively low activity of the CODH/ACS complex. This was also supported by the manipulation and analysis of the internal tunnel of the CODH/ACS complex. The results suggest that the main purpose of the tunnel in the CODH/ACS complex is to compartmentalise CO and not to rapidly transport substrate.

The Ni-Fe-S C-cluster of carbon monoxide dehydrogenases (CODH), which catalyzes the reversible oxidation of CO to CO2, can be stabilized in four redox states: Cox, Cred1, Cint, and Cred2. The best-supported mechanism of catalysis involves a one-electron reductive activation of Cox to Cred1 and a catalytic cycle in which Cred1 binds and oxidizes CO, forming Cred2 and releasing CO2. Recently reported experiments appear to have disqualified this mechanism, as activation was concluded to require reduction to a C-cluster state more reduced than Cred1. The results presented in this dissertation suggest that the activation potential was milder than that required to reduce these clusters. The results support a mechanism in which Cred1 is the form of the cluster that reacts with CO. The structure of the active-site C-cluster in CO dehydrogenase from Carboxydothermus hydrogenoformans (CODHCh) includes a ??2-sulfide ion bridged to the Ni and unique Fe, while the same cluster in enzymes from Rhodospirillum rubrum (CODHRr) and Moorella thermoacetica (CODHMt) lack this ion. This difference was investigated by exploring effects of sulfide on activity and spectral properties. Sulfide partially inhibited CO oxidation activities of CODHRr and CODHMt. Adding sulfide to CODHMt in the Cred1 state caused the gav = 1.82 Electron Paramagnetic Resonance spectroscopy (EPR) signal to decline and new features to appear. Sulfide did not affect the gav = 1.86 signal from the Cred2 state. A model was developed in which sulfide binds reversibly to Cred1, inhibiting catalysis. The results also suggest that the substrate hydroxyl group bridges the Ni and unique Fe. A cysteine residue recently found to form a persulfide bond with the C-cluster was characterized. The Ser mutant of the persulfide-forming Cys316 was inactive and displayed no C-cluster EPR signals. Electronic absorption and metal analysis suggest that the C-cluster is absent in this mutant. The persulfide bond appears to be essential for either the assembly or stability of the C-cluster, and/or for eliciting the redox chemistry of the C-cluster required for catalytic activity.

The Ni-Fe-S C-cluster of carbon monoxide dehydrogenases (CODH), which catalyzes the reversible oxidation of CO to CO2, can be stabilized in four redox states: Cox, Cred1, Cint, and Cred2. The best-supported mechanism of catalysis involves a one-electron reductive activation of Cox to Cred1 and a catalytic cycle in which Cred1 binds and oxidizes CO, forming Cred2 and releasing CO2. Recently reported experiments appear to have disqualified this mechanism, as activation was concluded to require reduction to a C-cluster state more reduced than Cred1. The results presented in this dissertation suggest that the activation potential was milder than that required to reduce these clusters. The results support a mechanism in which Cred1 is the form of the cluster that reacts with CO. The structure of the active-site C-cluster in CO dehydrogenase from Carboxydothermus hydrogenoformans (CODHCh) includes a ??2-sulfide ion bridged to the Ni and unique Fe, while the same cluster in enzymes from Rhodospirillum rubrum (CODHRr) and Moorella thermoacetica (CODHMt) lack this ion. This difference was investigated by exploring effects of sulfide on activity and spectral properties. Sulfide partially inhibited CO oxidation activities of CODHRr and CODHMt. Adding sulfide to CODHMt in the Cred1 state caused the gav = 1.82 Electron Paramagnetic Resonance spectroscopy (EPR) signal to decline and new features to appear. Sulfide did not affect the gav = 1.86 signal from the Cred2 state. A model was developed in which sulfide binds reversibly to Cred1, inhibiting catalysis. The results also suggest that the substrate hydroxyl group bridges the Ni and unique Fe. A cysteine residue recently found to form a persulfide bond with the C-cluster was characterized. The Ser mutant of the persulfide-forming Cys316 was inactive and displayed no C-cluster EPR signals. Electronic absorption and metal analysis suggest that the C-cluster is absent in this mutant. The persulfide bond appears to be essential for either the assembly or stability of the C-cluster, and/or for eliciting the redox chemistry of the C-cluster required for catalytic activity.

La CO déshydrogénase (CODH) de Desulfovibrio vulgaris est une métalloenzyme qui catalyse la réduction réversible du CO2 en CO. C’est un homodimère composé de deux sites actifs Ni-4Fe-4S et de trois centres fer-soufre. Durant ma thèse, nous avons étudié la maturation de la CODH à nickel et les propriétés catalytiques de la CODH à nickel de D. vulgaris.Pour comprendre le mécanisme de maturation de la CODH à nickel, nous avons caractérisé deux formes de la CODH à nickel produites en présence ou en absence de CooC par des approches biochimiques, spectroscopiques, électrochimiques et cristallographiques. Notre caractérisation montre que la présence de CooC est nécessaire à l’obtention d’une CODH mature et activable. Nous avons également mis en évidence un processus d’activation en présence de nickel dans des conditions réductrices qui n’implique apparemment pas de changement structural du site actif.Notre étude de la CODH à nickel par électrochimie nous a permis de mettre en évidence plusieurs phénomènes d’activations/inactivations de l’enzyme dans des conditions aérobies et anaérobies, et l’existence d’une hétérogénéité fonctionnelle : plusieurs formes de l’enzyme qui montrent des propriétés catalytiques différentes peuvent être présentes simultanément. Cette observation pourrait éclairer d’une façon nouvelle l’hétérogénéité structurale observée par cristallographie et remettre en question les mécanismes proposés sur la base de ces structures. / The monoxide carbon dehydrogenase (CODH) from Desulfovibrio vulgaris is a metalloenzyme which catalyses the reversible reduction of CO2 into CO. It is a homodimer containing two active sites and three iron-sulfur clusters. During my thesis, we studied the maturation of CODH nickel and catalytic properties of Ni-CODH from D. vulgaris.In order to understand, the maturation mechanism of Ni-CODH, we have characterized two forms of Ni-CODH produced in the presence or absence of CooC by biochemical, spectroscopic, electrochemical and crystallographic approaches. Our characterisation shows that the presence of CooC is necessary to obtain a mature Ni-CODH which can be activated. We have also identified an activation process in the presence of nickel in reducing conditions that apparently involves no structural change in the active site.Our study of the Ni-CODH by electrochemistry has shown several phenomena of activation/inactivation of the enzyme under aerobic and anaerobic conditions, and the existence of a functional heterogeneity : several forms of the enzyme which show different catalytic properties may be present simultaneously. This observation could illuminate the structural heterogeneity observed by crystallography and question the proposed mechanisms on the basis of these structures.

Es konnte eine Grundsatzbestätigung des Reaktionsprinzips zur Bildung eines Ni–CO22–-Adduktes durch Deprotonierung eines Ni-Formiat-Komplexes erreicht und die Stöchiometrie dieser Reaktion aufgeklärt werden. Das gebildete Ni–CO22–-Addukt ist ein strukturelles und funktionelles Modell des Ni–CO22–-Adduktes der Ni,Fe-CODH. Durch Isotopenmarkierung und die Untersuchung der Umsetzung mit CO2 konnte außerdem die Beteiligung eines analogen Ni–CO22–-Intermediates in der Reduktion von CO2 an Ni0-Komplexen gezeigt und der Reaktionsmechanismus aufgeklärt werden. Im zweiten Teil wird die quantitative Bildung von CO aus dem Ni–CO22–-Addukt beschrieben. Außerdem konnten die verwandten Na+- und K+-Komplexe dargestellt und Struktur-Reaktivitäts-Beziehungen abgeleitet werden. Durch Einsatz substöchiometrischer Mengen des Gegenions K+ konnte kontrolliert Ni(I)- und CO2•–-Chemie ausgelöst werden. Es kam zur Bildung eines Ni(I)-Formiat- und eines Ni-Oxalat-Komplexes; bei hohen Konzentrationen entstand sogar ein gemischter Ni-Oxalat-Mesoxalat-Komplex. Die Bildung von Mesoxalat (C3O64-) aus einzelnen CO2-Bausteinen war bisher nur postuliert worden. Im dritten Teil wurde ein Ni(II)-Vorläuferkomplex jeweils mit Cobaltocen oder Decamethylcobaltocen reduziert. Es konnten die entsprechenden NiI-Verbindungen mit Cobaltocenium-Gegenionen als Feststoffe charakterisiert werden. Wurden jedoch Lösungen der entsprechenden Verbindungen untersucht, zeigte sich im Falle des Komplexes mit Cobaltoceneinheit, dass ein Redox-Gleichgewicht vorliegt, welches bei Raumtemperatur weit auf der Seite der Ausgangsverbindungen liegt und nicht den Nachweis der charakteristischen spektroskopischen Eigenschaften von Ni(I)-Verbindungen zulässt. Dennoch reagiert die Verbindung aus dem Gleichgewicht heraus mit CO2 und als Produkt wurde ein mononuklearer Ni-Carbonat-Komplex identifiziert. / A confirmation of the reaction principle for the formation of a Ni-CO22- adduct by deprotonation of a Ni formate complex was achieved and the stoichiometry of this reaction was elucidated. The Ni-CO22- adduct formed is a structural and functional model of the Ni-CO22- adduct of Ni,Fe-CODH. Isotopic labelling and investigation of the reaction with CO2 also revealed the involvement of an analogous Ni-CO22- intermediate in the reduction of CO2 on Ni0 complexes and elucidated the reaction mechanism. In the second part, the quantitative formation of CO from the Ni-CO22- adduct is described. Furthermore, the related Na+- and K+-complexes could be obtained and structure-reactivity relationships could be derived. By using sub-stoichiometric amounts of the counterion K+, Ni(I) and CO2-- chemistry could be triggered in a controlled manner. A Ni(I)-formate and a Ni--oxalate complex were formed; at high concentrations even a mixed Ni--oxalate-mesoxalate complex was formed. The formation of mesoxalate (C3O64-) from individual CO2 building blocks had previously only been postulated. In the third part, a Ni(II) precursor complex was reduced with cobaltocene or decamethylcobaltocene, respectively. It was possible to characterise the corresponding NiI compounds with cobaltocenium counterions as solids. When solutions of the corresponding compounds were examined, it was shown in the case of the complex with cobaltocenium unit that a redox equilibrium exists which is far on the side of the parent compounds at room temperature and does not allow the detection of the characteristic spectroscopic properties of Ni(I) compounds. Nevertheless, the compound reacts out of equilibrium with CO2 and a mononuclear Ni-carbonate complex was identified as the product.