Publikationsserver der Universitätsbibliothek Marburg

Titel: Charakterisierung der an der Biosynthese des Cofaktors der [Fe]-Hydrogenase Hmd beteiligten Hcg-Proteine
Autor: Bai, Liping
Weitere Beteiligte: Shima, Seigo (Dr.)
Veröffentlicht: 2017
URI: https://archiv.ub.uni-marburg.de/diss/z2017/0665
URN: urn:nbn:de:hebis:04-z2017-06654
DOI: https://doi.org/10.17192/z2017.0665
DDC: Biowissenschaften, Biologie
Titel(trans.): Characterization of the Hcg proteins involved in [Fe]-hydropgenase cofactor biosynthesis
Publikationsdatum: 2017-10-04
Lizenz: https://rightsstatements.org/vocab/InC-NC/1.0/

Dokument

Schlagwörter:
Cofacor, Biosynthese, Hydrogenase

Summary:
[Fe]-hydrogenase (Hmd) catalyzes the reduction of methenyl-H4MPT+ to methylene-H4MPT using H2 as electron donor in the hydrogenotrophic methanogenic pathway. The production of Hmd was upregulated when the cell was grown under Ni-limiting environment. Hmd is composed of homodimer; the active sites are located at the cleft formed by the N-terminal domain and central domain. The N-terminal domain binds an iron-guanylylpyridinol (FeGP) cofactor, which is prosthetic group of this enzyme. The FeGP cofactor is composed of a low spin FeII ligated with two CO, an acyl-C and pyridinol-N; in addition, Cys-S and a solvent are bound to the iron site in the enzyme. The pyridinol ring is substituted with GMP moiety and two methyl groups. Genome analysis indicated that there are seven conserved genes which is named hcg gene cluster containing hcgAG and hmd genes. Therefore, it was predicted that the hcg cluster is responsible for biosynthesis of the FeGP cofactor. From the hcg genes sequences, we could not deduce the function of the proteins. However, using the “structure to function” strategy and biochemical assays, we could identify the function of some Hcg proteins. In this thesis, I describe the function of HcgC based on crystal structure and biochemical analyses. The isotope-labeling experiment indicated that the C3 methyl group comes from methionine, probably via S-adenosylmethionine (SAM). Structure comparisons of HcgC with other proteins suggested similarity of HcgC to SAM-dependent methyltransferases. Co-crystallization of HcgC and SAM revealed that SAM binds to the active site of HcgC. Docking simulation with a possible methyl-acceptor pyridinol suggested that the binding site of the pyridinol. The predicted substrate pyridinol was chemically synthesized and the enzyme activity was determined. The structure of the HcgC-reaction product was determined by NMR, which confirmed that HcgC transfer the methyl group from SAM to C3 of pyridinol. In order to analyze the catalytic mechanism of HcgC, co-crystallizaiton of HcgC, pyridinol, SAM or SAH was performed. The substrate binding site structure showed that seven water molecules connected pyridinol to protein. The only interaction of pyridinol with amino acid side chain was Thr179-OH. The C3 of pyridinol was close to the sulfur of SAH. In the crystal structure, there was no amino acid, which functions as general base of the typical methyl-transfer reaction. We proposed that the water molecules stabilize the deprotonated form of pyridinol by resonance effect, which increases the nucleophilicity of C3. Mutation analysis supported the essential contribution of the water molecules.

Zusammenfassung:
Die [Fe]-Hydrogenase Hmd katalysiert die Reduktion von Methenyl-H4MPT+ zu Methylen-H4MPT unter Nutzung von H2 als Elektrondonor in der hydrogenotrophen Methanogenese. Die Produktion der Hmd war erhöht, wenn die Zellen unter Ni-limitierten Bedingungen kultiviert wurden. Hmd ist ein homodimeres Enzym, in dem die aktiven Zentren in einer Spalte zwischen den N-terminalen Domänen und den zentralen Domänen lokalisiert sind. Die N-terminale Domäne bindet einen Eisen-Guanylylpyridinol- (FeGP-) Cofaktor als prosthetische Gruppe. Der FeGP-Cofaktor besteht aus einem low-spin FeII, ligandiert durch zwei CO, einem Acyl-C und eine Pyridinol-N. Zusätzlich ist das Eisenzentrum durch ein Cys-S und ein Wassermolekül im Enzym koordiniert. Der Pyridinol-Ring ist mit einem GMP-Rest und zwei Methylgruppen substituiert. Genom-Analysen deuteten auf einen Cluster aus sieben konservierten Genen hin, der sowohl die hcgAG Gene als auch das hmd-Gen umfasst. Aufgrund dessen wurde angenommen, dass die hcg-Gene für die Biosynthese des FeGP-Cofaktors verantwortlich sind. Von den Gensequenzen selbst konnten jedoch keine Funktionen für die entsprechenden Proteine abgeleitet werden. Sowohl eine „Struktur-zu-Funktion“-Strategie, als auch biochemische Charakterisierungen wurden genutzt, um die Funktionen einiger Hcg-Proteine aufzuklären. In der vorliegenden Studie wird die Funktion von HcgC, anhand seiner Kristallstruktur und biochemischer Analysen beschrieben. Isotopenmarkierungen wiesen darauf hin, dass die C3-Methylgruppe des Pyridinol-Rings aus Methionin stammt und wahrscheinlich in einer S-Adenosylmethionin- (SAM-) abhängigen Reaktion übertragen wird. Strukturvergleiche zwischen HcgC und anderen verwandten Proteinen deuteten auf Ähnlichkeiten zu SAM-abhängigen Methyltransferasen hin. Co-Kristallisation von HcgC und SAM zeigte, dass SAM tatsächlich im aktiven Zentrum von HcgC bindet. Docking-Simulationen mit einem möglichen Methylakzeptor-Pyridinol zeigten eine wahrscheinliche Bindestelle für das Pyridinol auf. Das vorhergesagte Substrat-Pyridinolderivat wurde chemisch synthetisiert und die Enzymaktivität der HcgC wurde bestimmt. Die Struktur des Reaktionsproduktes der HcgC wurde mit NMR aufgeklärt und es wurde bestätigt, dass die Methylgruppe tatsächlich von SAM auf das C3 des Pyridinols übertragen wurde. Um den Katalysemechanismus näher zu untersuchen, wurde HcgC mit Pyridinol und SAM oder S-Adenosylhomocystein (SAH) co-kristallisiert. Es zeigte sich, dass sieben Wassermoleküle an der Bindung des Pyridinols im aktiven Zentrum beteiligt waren. Die einzige direkte Interaktion des Pyridinols und einer Aminosäureseitenkette war mit der Hydroxylgruppe von Thr179. Das C3 des Pyridinols lag in Nähe zum SAH-Schwefelatom. Die Kristallstruktur wies auf keine Aminosäure hin, die als generelle Base in der Reaktion hätte dienen können. Es wird vorgeschlagen, dass die koordinierenden Wassermoleküle die deprotonierte Form des Pyridinols über einen Resonanzeffekt stabilisieren, welcher die Nucleophilie des C3 erhöht. Mutationsstudien konnten die essentielle Rolle der Wassermoleküle in der Reaktion untermauern.

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