Urich, Tim (2005)
The sulfur oxygenase reductase from Acidianus ambivalens.
Technische Universität Darmstadt
Dissertation, Erstveröffentlichung
Kurzbeschreibung (Abstract)
The microbial oxidation of reduced inorganic sulfur compounds and elemental sulfur to sulfate is one of the major reactions in the global sulfur cycle. Despite its importance, only limited information is available about molecular details of the enzymes involved. The present work was aimed to contribute to the understanding of the underlying molecular mechanisms by investigating the function and structure of the sulfur oxygenase reductase (SOR) from the thermoacidophilic crenarchaeote Acidianus ambivalens. The expression of the sor gene in Escherichia coli resulted in active, soluble SOR and in inclusion bodies from which active SOR could be refolded as long as ferrous ions were present in the refolding solution. The wild type and recombinant SOR preparations possessed indistinguishable properties when analyzed for activity and by gel permeation chromatography, CD spectroscopy and electron microscopy. The analysis of the quaternary structure showed a multi-subunit shell-like assembly with a central hollow core. The subunits formed homodimers as the building blocks of the holoenzyme, as shown by denaturation experiments. Conformational stability studies showed that the apparent unfolding free energy in water was ~5 kcal mol-1, at pH 7. Iron was found in the wild type enzyme at a stoichiometry of one iron per subunit. EPR spectroscopy of the colorless SOR resulted in a single isotropic signal at g = 4.3 characteristic of high-spin ferric iron. The signal disappeared upon reduction with dithionite or incubation with sulfur at elevated temperature. The iron center had a reduction potential of E0´ = -268 mV at pH 6.5. Protein database inspection identified five SOR protein homologues which allowed the prediction of amino acids putatively involved in catalysis. The recombinant SOR was crystallized by the sitting drop vapor diffusion method. The crystal structure was determined at 1.7 Å resolution. The homo-icosatetrameric holoenzyme was a highly symmetrical hollow protein particle with 432 point group symmetry and a molecular mass of 871 kDa. The subunits were αβ-proteins and comprised a central β-barrel surrounded by α-helices. Each monomer contained one mononuclear non-heme iron site with the ligands H85, H89, E113 and two water molecules in an octahedral arrangement. The protein ligands formed a 2-His-1-carboxylate facial triad for iron binding. The cysteines C30, C100 and C103 were in the vicinity of the iron site and located along the same cavity within the interior of the subunit, therefore defining the enzyme´s active site. C30 was persulfurated. The 24 active sites were spacially separated from each other, making an electronic interaction during catalysis unlikely. They were accessible solely via the inner compartment. Access of substrate to the inner compartment is most probably provided by six hydrophobic channels along the four-fold symmetry axes of the particle. Furthermore, the structure suggested that a linear polysufide species and not the cyclic α-S8 is the substrate of the SOR. Crystal structures of the SOR in complex with the inhibitors p-hydroxy-mercury-benzoic acid and iodoacetamide identified the cysteines as the inhibitor binding sites. The iron-binding residues H85, H89 and E113 and the three cysteines C30, C100 and C103 were altered by site-directed mutagenesis and the mutant proteins were analyzed for activity and iron content. Mutations of the iron ligands and C30 resulted in inactive enzyme, whereas mutations of C100 and C103 resulted in a reduced activity. All mutations affected the oxygenase and reductase partial reactions to a similar degree. These analyses allowed the first detailed insight into the mode of action of this self-compartmentalizing metalloenzyme. C30 is most probably the sulfur binding residue which aligns the substrate for the initial oxygenation catalyzed by the Fe site. The role of C100 and C103 is not clear, but they might act in the subsequent sulfur disproportionation reaction. The comparison of the SOR with SoxAX, the only other sulfur compound oxidizing enzyme from prokaryotes for which a high resolution structure is available, showed no structural similarity. SoxAX and other sulfur oxidizing enzymes contain different cofactors, demonstrating the diversity of mechanistic approaches utilized for sulfur compound oxidation. In contrast, a basic functional principle seems to be the central role of cysteine residues, acting as covalent binding sites for the substrate.
Typ des Eintrags: |
Dissertation
|
Erschienen: |
2005 |
Autor(en): |
Urich, Tim |
Art des Eintrags: |
Erstveröffentlichung |
Titel: |
The sulfur oxygenase reductase from Acidianus ambivalens |
Sprache: |
Englisch |
Referenten: |
Kletzin, PD Dr. Arnulf ; Pfeifer, Prof. Dr. Felicitas |
Berater: |
Kletzin, PD Dr. Arnulf |
Publikationsjahr: |
18 Oktober 2005 |
Ort: |
Darmstadt |
Verlag: |
Technische Universität |
Datum der mündlichen Prüfung: |
17 Juni 2005 |
URL / URN: |
urn:nbn:de:tuda-tuprints-6151 |
Kurzbeschreibung (Abstract): |
The microbial oxidation of reduced inorganic sulfur compounds and elemental sulfur to sulfate is one of the major reactions in the global sulfur cycle. Despite its importance, only limited information is available about molecular details of the enzymes involved. The present work was aimed to contribute to the understanding of the underlying molecular mechanisms by investigating the function and structure of the sulfur oxygenase reductase (SOR) from the thermoacidophilic crenarchaeote Acidianus ambivalens. The expression of the sor gene in Escherichia coli resulted in active, soluble SOR and in inclusion bodies from which active SOR could be refolded as long as ferrous ions were present in the refolding solution. The wild type and recombinant SOR preparations possessed indistinguishable properties when analyzed for activity and by gel permeation chromatography, CD spectroscopy and electron microscopy. The analysis of the quaternary structure showed a multi-subunit shell-like assembly with a central hollow core. The subunits formed homodimers as the building blocks of the holoenzyme, as shown by denaturation experiments. Conformational stability studies showed that the apparent unfolding free energy in water was ~5 kcal mol-1, at pH 7. Iron was found in the wild type enzyme at a stoichiometry of one iron per subunit. EPR spectroscopy of the colorless SOR resulted in a single isotropic signal at g = 4.3 characteristic of high-spin ferric iron. The signal disappeared upon reduction with dithionite or incubation with sulfur at elevated temperature. The iron center had a reduction potential of E0´ = -268 mV at pH 6.5. Protein database inspection identified five SOR protein homologues which allowed the prediction of amino acids putatively involved in catalysis. The recombinant SOR was crystallized by the sitting drop vapor diffusion method. The crystal structure was determined at 1.7 Å resolution. The homo-icosatetrameric holoenzyme was a highly symmetrical hollow protein particle with 432 point group symmetry and a molecular mass of 871 kDa. The subunits were αβ-proteins and comprised a central β-barrel surrounded by α-helices. Each monomer contained one mononuclear non-heme iron site with the ligands H85, H89, E113 and two water molecules in an octahedral arrangement. The protein ligands formed a 2-His-1-carboxylate facial triad for iron binding. The cysteines C30, C100 and C103 were in the vicinity of the iron site and located along the same cavity within the interior of the subunit, therefore defining the enzyme´s active site. C30 was persulfurated. The 24 active sites were spacially separated from each other, making an electronic interaction during catalysis unlikely. They were accessible solely via the inner compartment. Access of substrate to the inner compartment is most probably provided by six hydrophobic channels along the four-fold symmetry axes of the particle. Furthermore, the structure suggested that a linear polysufide species and not the cyclic α-S8 is the substrate of the SOR. Crystal structures of the SOR in complex with the inhibitors p-hydroxy-mercury-benzoic acid and iodoacetamide identified the cysteines as the inhibitor binding sites. The iron-binding residues H85, H89 and E113 and the three cysteines C30, C100 and C103 were altered by site-directed mutagenesis and the mutant proteins were analyzed for activity and iron content. Mutations of the iron ligands and C30 resulted in inactive enzyme, whereas mutations of C100 and C103 resulted in a reduced activity. All mutations affected the oxygenase and reductase partial reactions to a similar degree. These analyses allowed the first detailed insight into the mode of action of this self-compartmentalizing metalloenzyme. C30 is most probably the sulfur binding residue which aligns the substrate for the initial oxygenation catalyzed by the Fe site. The role of C100 and C103 is not clear, but they might act in the subsequent sulfur disproportionation reaction. The comparison of the SOR with SoxAX, the only other sulfur compound oxidizing enzyme from prokaryotes for which a high resolution structure is available, showed no structural similarity. SoxAX and other sulfur oxidizing enzymes contain different cofactors, demonstrating the diversity of mechanistic approaches utilized for sulfur compound oxidation. In contrast, a basic functional principle seems to be the central role of cysteine residues, acting as covalent binding sites for the substrate. |
Alternatives oder übersetztes Abstract: |
Alternatives Abstract | Sprache |
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Die mikrobielle Oxidation von reduzierten anorganischen Schwefelverbindungen und elementarem Schwefel zu Sulfat ist eine der wichtigsten Reaktionen im globalen Schwefelzyklus. Allerdings sind nur wenige detaillierte Informationen über die daran beteiligten Enzyme vorhanden. Diese Arbeit sollte zum Verständnis der zugrundeliegenden molekularen Mechanismen der Oxidation von anorganischen Schwefelverbindungen beitragen. Hierzu wurden die Funktion und Struktur der Schwefel-Oxygenase/-Reduktase (SOR) aus dem thermophilen und acidophilen Crenarchaeon Acidianus ambivalens näher untersucht. Die Expression des sor Gens in Escherichia coli resultierte in aktiver, löslicher SOR und in Einschlusskörperchen, aus welchen aktive SOR rückgefaltet werden konnte, solange FeII im Rückfaltungspuffer vorhanden waren. Wildtyp und rekombinante SOR Präparationen wurden mit Gelfiltrationschromatographie, CD Spektroskopie und Elektronenmikroskopie untersucht und besassen vergleichbare Eigenschaften. Auch deren spezifische Aktivitäten waren ähnlich. Die Analyse der Quartärstruktur zeigte einen homo-oligomeren, kugelartigen Komplex mit einem zentralen Hohlraum. Denaturierungsexperimente zeigten, dass die Untereinheiten Homodimere als strukturelle Bausteine des Holoenzyms bilden. Die apparente freie Entfaltungenergie betrug ~5 kcal mol-1, bei pH 7. Eisen war im Wildtyp in einer Stöchiometrie von 1 pro Monomer enthalten. EPR-spektroskopische Untersuchungen der farblosen SOR zeigten ein isotropes Signal bei g = 4.3, welches typisch für mononukleare "high-spin" Eisenzentren ist. Das Signal verschwand bei Reduktion durch Dithionit oder bei Inkubation mit elementarem Schwefel. Das Redoxpotenzial des Zentrums betrug E0´ = -268 mV bei pH 6.5. Datenbankanalysen führten zur Identifikation von fünf SOR Homologen, was die Vorhersage von möglicherweise an der Katalyse beteiligten Aminosäuren ermöglichte. Die rekombinante SOR wurde durch "sitting drop" Dampfdiffusion kristallisiert. Anschliessend wurde die Kristallstruktur mit einer Auflösung von 1.7 Å bestimmt. Das homo-ikosatetramere Holoenzym ist ein hochsymmetrisches, hohles Partikel mit einer 432 Puktgruppensymmetrie. Die Monomere bestehen aus einer zentralen β-Fass-Struktur, welche von α-Helices umgeben ist. Jedes Monomer enthält ein mononukleares Nicht-Häm Eisenzentrum mit einer oktaedrischen Geometrie und mit H85, H89, E113 und zwei H2O Molekülen als Liganden. Die Proteinliganden bilden eine sogenannte "2-His-1-Carboxylat Gesichtstriade" zur Eisenbindung. Die Cysteine C30, C100 und C103 sind in räumlicher Nähe zum Eisenzentrum und entlang der gleichen Kavität im Innern des Monomers angeordnet. Dieses Areal stellt somit das aktive Zentrum dar. C30 ist persulfuriert. Die 24 aktiven Zentren sind räumlich getrennt voneinander, was eine elektronische Interaktion während der Katalyse unwahrscheinlich erscheinen lässt. Sie sind ausschliesslich durch das innere Kompartiment zugänglich. Das Substrat gelangt wahrscheinlich durch sechs hydrophobe Poren an den vierfach Symmetrieachsen des Holoenzyms in das innere Kompartiment. Darüberhinaus weist die Struktur auf lineares Polysulfid und nicht auf den zyklischen α-S8 Schwefel als Substrat der SOR hin. Kristallstrukturen der SOR mit den Inhibitoren p-Hydroxy-Quecksilbersäure und Iodacetamid identifizierten die Cysteine als die Inhibitorbindestellen. Die eisenbindenden Aminosäuren H85, H89 und E113 und die Cysteine C30, C100 and C103 wurden mittels Orts-spezifischer Mutagenese ausgetauscht und die mutierten Proteine wurden auf Aktivität und Eisengehalt untersucht. Mutationen der Eisenliganden und C30 resultierten in inaktivem Enzym, während Mutationen von C100 und C103 zu einer reduzierten Aktivität führten. Alle Mutationen beeinflussten die Oxygenase- und Reduktase-Teilreaktionen zu einem ähnlichen Grad. Diese Analysen erlauben erste detaillierte Einblicke in die Struktur-Funktionsbeziehung dieses kompartimentbildenden Enzyms. C30 ist höchstwahrscheinlich der Ort der Schwefelbindung, was zu einer Ausrichtung des Substrates am Eisenzentrum und dessen anschliessender Oxygenierung führt. Die Funktion von C100 und C103 ist unklar, sie könnten eine Rolle in der anschliessenden Schwefeldisproportionierung spielen. Der Vergleich der SOR mit SoxAX, dem einzigen weiteren schwefeloxidierenden Enzym aus Prokaryonten für das hochauflösende Strukturinformationen verfügbar sind, zeigte keinerlei strukturelle Ähnlichkeit. SoxAX und andere schwefeloxidierende Enzyme besitzen unterschiedliche Kofaktoren, was die Diversität der enzymatischen Mechanismen demonstriert. Die Verwendung von Cysteinen als kovalente Substratbindestellen scheint dagegen ein grundlegendes funktionales Prinzip der schwefeloxidierenden Enzyme zu sein. | Deutsch |
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Sachgruppe der Dewey Dezimalklassifikatin (DDC): |
500 Naturwissenschaften und Mathematik > 570 Biowissenschaften, Biologie |
Fachbereich(e)/-gebiet(e): |
10 Fachbereich Biologie |
Hinterlegungsdatum: |
17 Okt 2008 09:22 |
Letzte Änderung: |
05 Mär 2013 09:26 |
PPN: |
|
Referenten: |
Kletzin, PD Dr. Arnulf ; Pfeifer, Prof. Dr. Felicitas |
Datum der mündlichen Prüfung / Verteidigung / mdl. Prüfung: |
17 Juni 2005 |
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