A fundamental catalytic difference between zinc and manganese dependent enzymes revealed in a bacterial isatin hydrolase.

Theis Sommer, Kaare Bjerregaard-Andersen, Lalita Uribe, Michael Etzerodt, Gregor Diezemann, Jürgen Gauss, Michele Cascella, J Preben Morth

Journal: Scientific reports 2019;8(1):13104

PMID: 30166577

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Abstract

The catalytic mechanism of the cyclic amidohydrolase isatin hydrolase depends on a catalytically active manganese in the substrate-binding pocket. The Mn ion is bound by a motif also present in other metal dependent hydrolases like the bacterial kynurenine formamidase. The crystal structures of the isatin hydrolases from Labrenzia aggregata and Ralstonia solanacearum combined with activity assays allow for the identification of key determinants specific for the reaction mechanism. Active site residues central to the hydrolytic mechanism include a novel catalytic triad Asp-His-His supported by structural comparison and hybrid quantum mechanics/classical mechanics simulations. A hydrolytic mechanism for a Mn dependent amidohydrolases that disfavour Zn as the primary catalytically active site metal proposed here is supported by these likely cases of convergent evolution. The work illustrates a fundamental difference in the substrate-binding mode between Mn dependent isatin hydrolase like enzymes in comparison with the vast number of Zn dependent enzymes.

Address: Norwegian Center for Molecular Medicine, Nordic EMBL Partnership University of Oslo, Gaustadalléen 21, 0349, Oslo, Norway.; Department of Chemistry, University of Oslo, Sem Sælands vei 26, 0371, Oslo, Norway.; Institut für Physikalische Chemie, Johannes Gutenberg-Universität Mainz, Duesbergweg 10-14, 55128, Mainz, Germany.; Graduate School Materials Science in Mainz, Johannes Gutenberg-Universität Mainz, Staudinger Weg 9, 55128, Mainz, Germany.; Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds vej 10C, 8000, Aarhus, Denmark.; Department of Chemistry, University of Oslo, Sem Sælands vei 26, 0371, Oslo, Norway. [email protected].; Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, Sem Saelands vei 26, 0371, Oslo, Norway. [email protected].; Norwegian Center for Molecular Medicine, Nordic EMBL Partnership University of Oslo, Gaustadalléen 21, 0349, Oslo, Norway. [email protected].; Institute for Experimental Medical Research, Oslo University Hospital, 0424, Oslo, Norway. [email protected].; Enzyme and Protein Chemistry, Section for Protein Chemistry and Enzyme Technology, Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, 2800, Kgs. Lyngby, Denmark. [email protected].

DOI: 10.1038/s41598-018-31259-y

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MeSH Terms: Amidohydrolases, Amino Acid Sequence, Arylformamidase, Bacterial Proteins, Biocatalysis, Catalytic Domain, Conserved Sequence, Evolution, Molecular, Glutamine, Hydrolysis, Isatin, Kynurenine, Manganese, Models, Molecular, Protons, Quantum Theory, Rhodobacteraceae, Zinc