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Crystal structure of a bacterial L-arabinonate dehydratase contains [2Fe-2S] cluster

DOI: 10.1021/acschembio.7b00304 DOI Help

Authors: Mohammad Mubinur Rahman (University of Eastern Finland) , Martina Blomster Andberg (VTT Technical Research Centre of Finland Ltd) , Senthil Kumar Thangaraj (University of Eastern Finland) , Tarja Parkkinen (University of Eastern Finland) , Merja Penttilä (VTT Technical Research Centre of Finland Ltd) , Janne Jänis (University of Eastern Finland) , Anu Koivula (VTT Technical Research Centre of Finland Ltd) , Juha Rouvinen (University of Eastern Finland) , Nina Hakulinen (University of Eastern Finland)
Co-authored by industrial partner: No

Type: Journal Paper
Journal: Acs Chemical Biology

State: Published (Approved)
Published: June 2017
Diamond Proposal Number(s): 10291

Abstract: We present a novel crystal structure of the IlvD/EDD family enzyme, L-arabinonate dehydratase from Rhizobium leguminosarum bv. trifolii (RlArDHT, EC 4.2.1.25), which catalyzes the conversion of L-arabinonate to 2-dehydro-3-deoxy-L-arabinonate. The enzyme is a tetramer consisting of a dimer of dimers, where each monomer is composed of two domains. The active site contains a catalytically important [2Fe-2S] cluster and Mg2+ ion, and is buried between two domains, and also at the dimer interface. The active site Lys129 was found to be carbamylated. Ser480 and Thr482 were shown to be essential residues for catalysis, and the S480A mutant structure showed an unexpected open conformation in which the active site was more accessible for the substrate. This structure showed the partial binding of L-arabinonate, which allowed us to suggest that the alkoxide ion form of the Ser480 side chain functions as a base and the [2Fe-2S] cluster functions as a Lewis acid in the elimination reaction.

Journal Keywords: L-arabinonate dehydratase; hydrolyase; iron-sulfur cluster; [2Fe-2S]; pentose sugar acid; IlvD/EDD family

Subject Areas: Chemistry, Biology and Bio-materials


Instruments: I04-Macromolecular Crystallography

Other Facilities: European Synchrotron Radiation Facility

Added On: 05/06/2017 08:55

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