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Structure and Catalytic Mechanism of N5,N10-Methenyltetrahydromethanopterin Cyclohydrolase

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Upadhyay,  Vikrant
Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Max Planck Society;

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Demmer,  Ulrike
Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Max Planck Society;

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Warkentin,  Eberhard
Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Max Planck Society;

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Ermler,  Ulrich
Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Max Planck Society;

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Citation

Upadhyay, V., Demmer, U., Warkentin, E., Moll, J., Shima, S., & Ermler, U. (2012). Structure and Catalytic Mechanism of N5,N10-Methenyltetrahydromethanopterin Cyclohydrolase. Biochemistry, 51(42), 8435-8443. doi:10.1021/bi300777k.


Cite as: http://hdl.handle.net/11858/00-001M-0000-0024-D544-0
Abstract
Methenyltetrahydromethanopterin (methenyl-H4MPT+) cyclohydrolase (Mch) catalyzes the interconversion of methenyl-H4MPT+ and formyl-H4MPT in the one-carbon energy metabolism of methanogenic, methanotrophic, and sulfate-reducing archaea and of methylotrophic bacteria. To understand the catalytic mechanism of this reaction, we kinetically characterized site-specific variants of Mch from Archaeoglobus f ulgidus (aMch) and determined the X-ray structures of the substrate-free aMch(E186Q), the aMch:H4MPT complex, and the aMch(E186Q):formyl-H4MPT complex. (Formyl-)H4MPT is embedded inside a largely preformed, interdomain pocket of the homotrimeric enzyme with the pterin and benzyl rings being oriented nearly perpendicular to each other. The active site is primarily built up by the segment 93:95, Arg183 and Glu186 that either interact with the catalytic water attacking methenyl-H4MPT+ or with the formyl oxygen of formyl-H4MPT. The catalytic function of the strictly conserved Arg183 and Glu186 was substantiated by the low enzymatic activities of the E186A, E186D, E186N, E186Q, R183A, R183Q, R183E, R183K, and R183E-E186Q variants. Glu186 most likely acts as a general base. Arg183 decisively influences the pKa value of Glu186 and the proposed catalytic water mainly by its positive charge. In addition, Glu186 appears to be also responsible for product specificity by donating a proton to the directly neighbored N10 tertiary amine of H4MPT. Thus, N10 becomes a better leaving group than N5 which implies the generation of N5-formyl-H4MPT. For comparison, methenyltetrahydrofolate (H4F) cyclohydrolase produces N10-formyl-H4F in an analogous reaction. An enzymatic mechanism of Mch is postulated and compared with that of other cyclohydrolases.